IL324392A - Antibodies directed against the cathepsin g peptide complex of human leukocyte antigen - Google Patents

Antibodies directed against the cathepsin g peptide complex of human leukocyte antigen

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Publication number
IL324392A
IL324392A IL324392A IL32439225A IL324392A IL 324392 A IL324392 A IL 324392A IL 324392 A IL324392 A IL 324392A IL 32439225 A IL32439225 A IL 32439225A IL 324392 A IL324392 A IL 324392A
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Israel
Prior art keywords
antibody
antigen binding
seq
fragment
hla
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IL324392A
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Hebrew (he)
Inventor
Jeffrey J Molldrem
Dongxing Zha
Melinda G Smith
Gheath Al-Atrash
Jason K Allen
Chunhua Shi
Ze Tian
Timothy E Lofton
Jun Yan
Jasbir Kaur
Bhupal Ban
Alona Kulesha
Nga Sze Amanda Mak
Melissa Jennifer Bikowitz
Original Assignee
Univ Texas
Jeffrey J Molldrem
Dongxing Zha
Melinda G Smith
Al Atrash Gheath
Jason K Allen
Chunhua Shi
Ze Tian
Timothy E Lofton
Jun Yan
Jasbir Kaur
Bhupal Ban
Alona Kulesha
Nga Sze Amanda Mak
Melissa Jennifer Bikowitz
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Application filed by Univ Texas, Jeffrey J Molldrem, Dongxing Zha, Melinda G Smith, Al Atrash Gheath, Jason K Allen, Chunhua Shi, Ze Tian, Timothy E Lofton, Jun Yan, Jasbir Kaur, Bhupal Ban, Alona Kulesha, Nga Sze Amanda Mak, Melissa Jennifer Bikowitz filed Critical Univ Texas
Publication of IL324392A publication Critical patent/IL324392A/en

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    • C07KPEPTIDES
    • C07K16/00Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
    • C07K16/18Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2803Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
    • C07K16/2809Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily against the T-cell receptor (TcR)-CD3 complex
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00Cellular immunotherapy
    • A61K40/10Cellular immunotherapy characterised by the cell type used
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    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00Cellular immunotherapy
    • A61K40/30Cellular immunotherapy characterised by the recombinant expression of specific molecules in the cells of the immune system
    • A61K40/31Chimeric antigen receptors [CAR]
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    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00Cellular immunotherapy
    • A61K40/40Cellular immunotherapy characterised by antigens that are targeted or presented by cells of the immune system
    • A61K40/41Vertebrate antigens
    • A61K40/42Cancer antigens
    • A61K40/4244Enzymes
    • A61K40/4247Proteinases
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61PSPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00Antineoplastic agents
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61PSPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00Antineoplastic agents
    • A61P35/02Antineoplastic agents specific for leukemia
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    • C07KPEPTIDES
    • C07K14/00Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70503Immunoglobulin superfamily
    • C07K14/7051T-cell receptor (TcR)-CD3 complex
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K16/00Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
    • C07K16/40Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against enzymes
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/575Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/5758Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumours, cancers or neoplasias, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides or metabolites
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00Medicinal preparations containing antigens or antibodies
    • A61K2039/505Medicinal preparations containing antigens or antibodies comprising antibodies
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00Indexing codes associated with cellular immunotherapy of group A61K40/00
    • A61K2239/46Indexing codes associated with cellular immunotherapy of group A61K40/00 characterised by the cancer treated
    • A61K2239/48Blood cells, e.g. leukemia or lymphoma
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    • C07ORGANIC CHEMISTRY
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    • C07K2317/00Immunoglobulins specific features
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    • C07K2317/31Immunoglobulins specific features characterized by aspects of specificity or valency multispecific
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    • C07K2317/60Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
    • C07K2317/62Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising only variable region components
    • C07K2317/622Single chain antibody (scFv)
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    • C07ORGANIC CHEMISTRY
    • C07KPEPTIDES
    • C07K2319/00Fusion polypeptide
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    • C07K2319/01Fusion polypeptide containing a localisation/targetting motif
    • C07K2319/03Fusion polypeptide containing a localisation/targetting motif containing a transmembrane segment

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Description

Attorney Docket No. 090723-1438905(MDA21-122PCT) ANTIBODIES TARGETING HUMAN LEUKOCYTE ANTIGEN CATHEPSIN G PEPTIDE COMPLEX CROSS-REFERENCE TO RELATED APPLICATIONS [0001]This application claims priority to and the benefit of U.S. Provisional Application No. 63/499,881, filed May 3, 2024, and U.S. Provisional Application No. 63/640,098, filed April 30, 2023, the contents of each of which are incorporated herein by this reference as if fully set forth herein.
REFERENCE TO A SEQUENCE LISTING SUBMITTED AS AN XML FILE id="p-2"
[0002]The official copy of the sequence listing is submitted electronically as an .xml formatted sequence listing with a file named , created on , and having a size of . The sequence listing contained in this .xml formatted document is part of the specification and is herein incorporated by reference in its entirety.
BACKGROUND [0003]Treatment for myeloid malignancies, for example in leukemia, have made progress in recent years. Stem cell transplant and other therapies (for example, chimeric antigen receptors) could benefit some patients. However, for acute myeloid leukemia (AML) patients, there exists a large patient group that will be refractory and relapsed from the standard of care. There is urgent need for novel therapy, the present disclosure could provide a new therapeutic avenue for many patients suffering from the effects of myeloid malignancies.
BRIEF SUMMARY [0004]The Summary is provided to introduce a selection of concepts that are further described below in the Detailed Description. This Summary is not intended to identify key or essential features of the claimed subj ect matter, nor is it intended to be used as an aid in limiting the scope of the claimed subject matter. id="p-5"
[0005]Described herein are antibodies that are capable of specifically binding to CG1//HLA- A2. Such antibodies can be monoclonal, synthetic/recombinant, or other type of antibody. id="p-6"
[0006]Also described herein are bispecific recombinant antibodies that are capable of specifically binding both CG1//HLA-A2 and CD3. 1US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-7"
[0007]Further described herein are chimeric antigen receptors (CARs). According to embodiments of the present disclosure, CARs as described herein can comprise an extracellular domain capable of specifically binding to CG1//HLA-A2 or CD3, and/or can be bispecific for specific binding to both CGI and CD3 both. id="p-8"
[0008]In certain aspects, described herein are isolated antibodies or antigen binding portion. Isolated antibodies or antigen binding portions thereof according to the present disclosure can comprise a heavy chain (HC) variable region sequence, wherein the HC variable region comprises a CDR1 sequence comprising one of SEQ ID NOs: 67-78; and a light chain (LC) variable region sequence, wherein the LC variable region comprises a CDR1 sequence comprising one of SEQ ID NOs: 96-105. Isolated antibodies or antigen binding portions thereof according to the present disclosure can further comprise, in the HC variable region, a CDR2 sequence comprising one of SEQ ID NOs: 79-87, or 129-131 and/or a CDR3 sequence comprising one of SEQ ID NOs: 88-95. Isolated antibodies or antigen binding portions thereof according to the present disclosure can further comprise, in the LC variable region, a CDRsequence comprising one of SEQ ID NOs: 106-117 and/or a CDR3 sequence comprising one of SEQ ID NOs: 118-123. id="p-9"
[0009]In other aspects, also described herein are variants of the provided isolated antibodies or antigen binding portion variants thereof comprising one or more amino acid substitutions in one or more CDR sequences as described herein that can alter the hydrophobicity of an amino acid (or antigen binding fragment thereof), thereby reducing the potential for aggregation of the antibodies and antigen-binding fragments thereof that are described herein. id="p-10"
[0010]Isolated antibodies or antibody fragments as described herein can be a human antibody or human antibody fragment. id="p-11"
[0011]In certain aspects, described herein are isolated antibodies or antigen binding portions thereof comprising a heavy chain variable region (VH) having at least 90% identity to any one of SEQ ID NOs: 7, 8, 9, 15, 16, 55, 133, or 134; and/or (b) a light chain variable region (VL) having at least 90% identity to any one of SEQ ID NOs: 24, 35, 36, 42, 43, 56, or 132. id="p-12"
[0012]In certain aspects, the antibody fragment can be a monovalent scFv (single chain fragment variable) antibody, divalent scFv, Fab fragment, F(ab ’)2 fragment, F(ab ’)3 fragment, Fv fragment, or single chain antibody. 2US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-13"
[0013]In certain aspects, the antibody can be a chimeric antibody, bispecific antibody, trispecific or other multi-specific antibody, or BiTE. In certain aspects, the antibody can be a IgG antibody or a recombinant IgG antibody or antibody fragment. id="p-14"
[0014]In certain aspects, antibodies or antibody fragments thereof can exhibit increased binding affinity for CGI presented by HLA-A*0201 compared to sample from a wild-type subject or subject not having a cancer. id="p-15"
[0015]In certain aspects, antibodies as described herein can be conjugated or fused to an imaging agent, a cytotoxic agent, a metal, or a radioactive moiety. In certain aspects, the imaging agent can be a fluorophore. In certain aspects, the radioactive moiety can comprise at least one 0fZr-89, Cu-64, F-18, Y-90, Lu-177, At-211, Ac-225, orPb-212. In certain aspects, the antibody can be an immune conjugate or a radio-immune conjugate. In certain aspects, the antibody is an antibody-drug conjugate. id="p-16"
[0016]In certain aspects, the isolated antibody or antibody fragment can further comprise an amino acid having at least 90% identity with SEQ ID NO:57. In certain aspects, the isolated antibody or antibody fragment thereof can comprise amino acid sequences having at least 90% similarity with any one of SEQ ID NOs: 55, 56, and 57. In certain aspects, the antibody or antibody fragment thereof can comprise any one of SEQ ID NOs: 55-57. In certain aspects, the antibody or antibody fragment thereof can consist essentially of any one of SEQ ID NOs. 55-57. In certain aspects, the antibody or antibody thereof can consist essentially of (a) a heavy chain variable region (VH) having at least 90% identity to any one of SEQ ID NOs: 7, 8, 9, 15, 16, 55, 133, or 134; and (b) a light chain variable region (VL) having at least 90% identity to any one of SEQ ID NOs: 34, 35, 36, 42, 43, 56, or 132. In certain aspects, the antibody or antibody fragment thereof can consist essentially of: (a) any one of SEQ ID NOs: 7, 8, 9, 15, 16, 55, 133, or 134; and (b) any one of SEQ ID NOs: 34, 35, 36, 42, 43, 56, or 132. In certain aspects, described herein is an isolated nucleic acid encoding the antibody heavy and/or light chain variable region of the antibody or antibody fragment or other amino acid of any aspect as described herein. Described herein are also expression vectors comprising a nucleic acid encoding any amino acid sequence as described herein. id="p-17"
[0017]In certain aspects, described herein are hybridoma or engineered cells comprising a nucleic acid encoding any of the antibodies or antibody fragments thereof or CARs provided in this disclosure. In certain aspects, described herein is a hybridoma or engineered cell 3US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) comprising a nucleic acid encoding any amino acid sequence, antibody or antibody fragment thereof, or CAR as described herein. id="p-18"
[0018]In certain aspects, also described herein are pharmaceutical preparations. In some embodiments, pharmaceutical preparations according to the present disclosure can comprise (a) a pharmaceutically acceptable carrier; and (b) an isolated antibody or antigen binding portion thereof of any embodiment as described herein. In some embodiments, pharmaceutical preparations according to the present disclosure can comprise (a) a pharmaceutically acceptable carrier; and (b) a cell expressing a CAR of any embodiment as described herein. id="p-19"
[0019]In certain aspects, also described herein are diagnostic preparations. As described herein, diagnostic compositions according to the present disclosure can comprise (a) a pharmaceutically acceptable carrier; and (b) an isolated antibody or antigen binding portion thereof of embodiment as described herein. id="p-20"
[0020]In certain aspects, also described herein are methods for treating a subject having cancer. Methods according to the present disclosure can comprise administering to a subject in need thereof a therapeutically effective amount of any pharmaceutical preparation or any antibody or any antibody fragment as described herein. In certain embodiments, the cancer can be a myeloid malignancy, for example, acute myeloid leukemia (AML), chronic myeloid leukemia (CML) or myelodysplastic syndrome (MDS). In certain embodiments, the cancer can be a non-myeloid leukemia, for example acute lymphoblastic leukemia (ALL) or chronic lymphocytic leukemia (CLL). In certain embodiments, the cancer can be a solid tumor malignancy, for example, lung cancer. id="p-21"
[0021]In certain aspects, described herein are methods for diagnosing a cancer. Diagnostic methods for cancer as described herein can comprise (a) administering to a subject in need thereof an effective amount of any diagnostic preparation as described herein, and (b) detecting binding of the isolated antibody or antigen binding portion thereof as a determination of the presence of the cancer. In certain embodiments, the cancer of which diagnosis is sought in the subject can be a myeloid malignancy, for example, AML, CML, or MDS. In certain embodiments, the cancer of which diagnosis is sought in the subject can be a non-myeloid leukemia, for example acute lymphoblastic leukemia (ALL) or chronic lymphocytic leukemia (CLL). In certain embodiments, the cancer of which diagnosis is sought in the subject can be a solid tumor malignancy, for example, lung cancer. 4US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-22"
[0022]In certain aspects, described herein are methods of detecting the presence of a cancer or malignant cell in a biological sample. Such methods can comprise (a) contacting said sample with any diagnostic preparation as described herein, and (b) detecting an amount of binding of the isolated antibody or antigen binding portion thereof as a determination of the presence of said cancer or malignant cell. In certain embodiments, the cancer or malignant cell of which detection is sought in the sample can be a myeloid malignancy, for example, AML, CML, or MDS. In certain embodiments, the cancer of which detection is sought in the sample can be a non-myeloid leukemia, for example acute lymphoblastic leukemia (ALL) or chronic lymphocytic leukemia (CLL). In certain embodiments, the cancer of which detection is sought in the sample can be a solid tumor malignancy, for example, lung cancer. id="p-23"
[0023]Also described herein are methods of making isolated antibodies or antibody fragments thereof. Methods as described herein can comprise, for example, culturing a hybridoma or engineered cell as described herein under conditions that allow expression of the antibody and, optionally, isolating the antibody from the culture.
BRIEF DESCRIPTION OF THE DRAWINGS [0024]The present application includes the following figures. The figures are intended to illustrate certain embodiments and/or features of the compositions and methods, and to supplement any description(s) of the compositions and methods. The figures do not limit the scope of the compositions and methods, unless the written description expressly indicates that such is the case. id="p-25"
[0025] FIG. 1is an overview of neutrophil granule proteases. Cathepsin G (CG), for example, is a myeloid azurophil granule serine protease that is involved in host immunity, cleavage of inflammatory mediators and receptors, degradation of extracellular matrix components and leukemogenesis. id="p-26"
[0026] FIG. 2depicts an overview of aspects of an amino acid sequence of an antigen target according to certain aspects of the present disclosure. CGI is a 9-mer peptide derived from cathepsin G (CG) protein leader sequence, presented by human leukocyte antigen (HLA) class I, specifically HLA-A*0201. id="p-27"
[0027] FIG. 3depicts a visual overview of aspects of CG1/HLA-A2 complex presentation according to certain aspects of the present disclosure. id="p-28"
[0028] FIGs.4shows the germline distributions of the 27 antibodies. 5US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-29"
[0029] FIGs. 5A-5Fare graphs illustrating the top leads in Specificities Assay in T2 cell surface binding according to certain aspects of the present disclosure. FIG. 5A:lead Antibodies only bound to CGI spiked T2 cells, but not the control peptides. Clone 46 from Group #1 is applied as the control. As can be seen in FIGs. 5A-5F.,lead compounds CGI-16 (FIG. 5A), CGI-23 (FIG. 5B),CGI-27 (FIG. 5C),CGI-46 FIG. 5D),CGI-60 (FIG. 5E),and CGI- (FIG. 5F)show specificity to HLA-A2/CG1 id="p-30"
[0030] FIGs. 5G-5Nare plots showing lead Anti-HLA-A2/CG1 compounds recognize their target on leukemia cell lines: U937-A2 (FIG. 5G),MV4-11-A2 (FIG. 5H),THP-1 (FIG. 51), MOLM-13-A2 (FIG. 5 J),OCI-AML3 (FIG. 5K),EM2 (FIG. 5L),SKM-1 (FIG. 5M),and ML-2 (FIG. 5N). Clone 46 has higher MFI for different HLA-A02+ leukemia cell lines for its non-specific binding. id="p-31"
[0031] FIGs. 6A-6B:Hydrogen Deuterium Exchange (HDX) mass spectrometry in amino acids resolution indicates CGI-16 binding epitope covers most of CGI peptide. id="p-32"
[0032] FIG. 7.Cartoon structure of a CGl-16xCD3e bispecific antibody according to aspects of this disclosure. id="p-33"
[0033] FIGs. 8A-8Eshow CGl-16xCD3e bispecific antibody characterization according to certain aspects of the present disclosure. FIG. 8A-8B.Biolayer interferometry (BLI) assay plots of the bispecific antibody binding to CGI monomer and CD3e-Fc , respectively. The data lines denoted with the dashed arrow is the real sensogram signal with 100 nM (top) and 20 nM (bottom) CD3e-Fc recombinant protein in lOxKinetics Buffer. The data lines denoted with solid arrows are the theory fitted lines based on the real sensogram signal). FIGs. 8C-8D.Cell surface binding of bispecific antibody to EM2 and Jurkat T-cells, respectively, measured using flow cytometry. EM2 HLA-A2+ CML cells express CGI on cell surface and therefore demonstrate high avidity binding of CGl-bispecific for CG1/HLA-A2. Staining of Jurkat T cells shows high avidity binding of CGl-bispecific Ab to CD3; Jurkat cells express CD3 and lack HLA-A2, CG and CGI. Human IgG (denoted as *3207) and Vel08/CD138-CD3e bispecific antibody were used as control antibodies. CGI-16 refers to the CG1/GHLA-Abinding Fab. FIG. 8E.Ultra-high Performance Liquid Chromatography-Size Exclusion Chromatography (UHPLC-SEC) data indicates the purity of monomer bispecific antibody. FIG. 8F.Stability assay of CGlxCD3e bispecific antibody at 4° and 37° degree in the concentration of 1 mg/ml with 20 mM arginine in PBS solution. 6US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-34"
[0034] FIGs. 9A-9Oshow that the CGl-bispecific antibody activates T cells and lyses CGl/HLA-A2-expressing myeloid leukemia cells in vitro according to various aspects of this disclosure. U937-A2 AML cells (FIGs. 9A, 9D-9G),ML2 AML cells (FIGs. 9B, 9H-9K)and EM2 CML cells (FIGs. 9C, 9L-9O)were co-cultured with PBMC and CGl-bispecific antibody for 24 hours. Addition of CGl-bispecific antibody led to T cell activation as measured using flow cytometry staining for early activation marker CD69 (FIGs. 9D, 9H, 9L),and increased cytokine section (IFNg, IL-2 and TNF-a) by T cells (FIGs. 9E-9G, 9I-9K, 9M-9O), in comparison with control bispecific antibody (with CD3e arm but without CG1-16 arm) (FIGs. 9A-9C).U937 parental cell line lacking HLA-A02 expression was used as the negative cell line. CGl-bispecific Ab increased killing target myeloid leukemia calls in comparison with control bispecific antibody. id="p-35"
[0035] FIGs. 10A-10Cshow the efficacy of CG1XCD3 bispecific antibody in MLxenograft model according to certain aspects of the present disclosure. FIG. 10A:Female NSG mice at 6-10 weeks old were engrafted via tail vein injection with 1 x 10A5 luciferase- transduced ML2 human AML cells per mouse. 11-18 days after tumor inoculation, I x 10APBMC/mouse were IV injected for humanization. Four days after PBMC injection mice were randomized into control and treatment groups. Mice were either treated with vehicle control or CGl-16xCD3 at different doses. FIG. 10B:The radiance plot bioluminescence imaging of control or CGl-16xCD3 treatment at 0.1, 0.05 or 0.01 mg/kg of the humanized mice. FIG. 10C:Percentage of CD3+ T cells in blood in the humanized mice. Data is shown as mean +/- SD. Immunohistological analysis shows lower MPO staining (FIG. 10D),lower numbers of tumor cells by H&E staining (FIG. 10E),and higher bone marrow restoration of normal hematopoiesis (FIG. 10F)in the CGlxCD3 bispecific antibody-treated group in contrast with the PBS-treated groups. id="p-36"
[0036] FIGs. 10G-10Hshow that the CG1XCD3 bispecific antibody eliminated primary AML in vivo according to certain aspects of the present disclosure. Patient primary AML was engrafted into NSG mice using tail vein injection. After confirming engraftment using flow cytometry staining of mouse blood for hCD45, lxlO A7 normal donor PBMC were infused intravenously to mice via tail vein. Mice were treated weekly for 3 weeks with increasing doses of CGl-bispecific Ab (1, 0.1 and 0.01 mg/Kg) or PBS. FIG. 10G:Leukemia burden in the blood was identified by flow cytometry staining for hCD45+/hCD3- cells. FIG. 10H: Kaplan-Meir curve showing increased survival on CGl-bispecific antibody treated mice, in comparison with PBS. 7US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-37"
[0037] FIGs. 11A-11Eshow the efficacy of CG1XCD3 bispecific antibody in U937-Axenograft model according to certain aspects of the present disclosure. FIG. 11 A:The radiance plot after control or CGl-16xCD3 treatment at I mg/kg IP from donor 6403 humanized mice. FIGs. 11B-11D:Percentage of CD3+ T cells in blood (FIG. 11B),BM (FIG. 11C)and spleen (FIG. 11D)in donor 6403 humanized mice. Data is shown as mean +/- SD. FIG. HE: Activated CD69+ T-cells in the control and bispecific treatment group in blood. id="p-38"
[0038] FIGs. 12A-12Bshow anti-tumor activity of CGl-16xCD3 BsAb in an AML patient derived xenograft model according to certain aspects of the present disclosure. Female NSG mice at 6-10 weeks old received tail vein injection with 5 x 10A6 of primary AML cells per mouse. When blood AML reached -2% after tumor inoculation, 1 x 10A7 PBMC/mouse were IV injected for humanization. Four days after PBMC injection mice were randomized into control and treatment groups. Mice were either treated with vehicle control or CGl-16xCD3 at 1, 0.1 or 0.01 mg/kg IV. FIG. 12A:The radiance plot after control or CGl-16xCD3 treatment at 1, 0.1, or 0.01 mg/kg IV. FIG. 12B:Survival curves of different treatment groups. id="p-39"
[0039] FIG. 13shows the pharmacokinetics of 1B7/CD3 BsAb according to certain aspects of the present disclosure. Single dose CGl-16xCD3 PK in human CGI & HLA-A02:01 double transgenic mice at 1, 0.1 or 0.01 mg/kg doses. Blood was collected at indicated time points post injection through serial sampling. Plasma was enriched from the blood samples and used for bioanalytical and PK analyses employing coated CGI monomer and detecting antibody GG-conjugated sulfo-tag using MSD methods. PK analyses were performed according to standard non-compartmental analysis using WinNonlin. id="p-40"
[0040] FIG. 14shows that the CGl-bispecific Ab does not inhibit normal hematopoiesis according to certain aspects of the present disclosure. Healthy donor BM was cultured alone (BM) or co-cultured with PBMC at increasing concentrations of CGl-bispecific or control bispecific antibody. Cells were then resuspended in methylcellulose semi-solid matrix on low adhesion 6-well plates and co-cultured for 14 days. On day 14, colonies were counted and imaged using an inverted light microscope. Each group was cultured in triplicate and data represents one of four independent experiments. Cytarabine-treated bone marrow was used as positive control. id="p-41"
[0041] FIGs. 15A-15Cillustrate the construction and design of embodiments of the chimeric antigen receptors (CARs) that were used to transduce healthy donor-derived T cells for testing. The pORBIT Lentivirus plasmid was utilized in combination with either CD28 or 4-IBB 8US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) endodomains for CAR-T cells, followed by the inclusion of the suicide gene EGFR-III via IRES (FIGs. 15A-15B)Details of the sequences for the 4-1BB CAR, CD28 CAR, and Fc- CD28 CAR, as well as the construction of the 9 vectors for CARs with the combination of the top three single chain Fv, are shown in (FIG. 15C). id="p-42"
[0042] FIGs. 16A-16Bare plots of live target cells at difference effector :target ratios of embodiments according to the present disclosure. FIG. 16Ashows the in vitro killing of U937- A2 target cells (U937 cells transduced with HLA-A*0201) at different effectortarget (E:T) ratios after 24 hours, while FIG. 16Bshows the same killing assay after 72 hours. Live U937- A2 cells were assessed using FACS, and parental T-cells (non-transduced) from the same healthy donor were used as the control. The E:T ratio was normalized to the CAR+ T-cells and not the entire population of T-cells to allow for accurate comparisons. id="p-43"
[0043] FIGs. 17A-17Gpresents the results of an efficacy study comparing the in vivo activity of embodiments of T cells (from two healthy donors) transduced with CG1-60-CDCAR and the CGI-176 bbz CAR against ML2 leukemia cells. FIG. 17Aillustrates an experimental design, with female NSG mice aged 6-10 weeks that received a tail vein injection of 1 x 10A5 ML2/Luc (luciferase) human AML cells per mouse. At 11-18 days after tumor inoculation, 1 x 10A7 CAR-T or parental (non-transduced) T cells/mouse were injected IV. FIGs. 17Band 17Epresent the radiance plot of control or CAR-T cell treatment from the two donors. FIGs. 17Cand 17Fillustrate the survival rate of CAR-T treated mice from the two donors, while FIGs. 17Dand 17Gshow the activation of blood T-cells (from the two donors) expressing huCD69+ in the control and CAR-T cell treatment group.
FIGs. 18A-18Bshow hydrophobic interaction chromatography analysis for Binder CGI-compared to Binder CGI-250 and comparted to Binder CGI-251, respectively.
DETAILED DESCRIPTION [0044]The following description recites various aspects and embodiments of the present compositions and methods. No particular embodiment is intended to define the scope of the compositions and methods. Rather, the embodiments merely provide non-limiting examples of various compositions and methods that are at least included within the scope of the disclosed compositions and methods. The description is to be read from the perspective of one of ordinary skill in the art; therefore, information well known to the skilled artisan is not necessarily included. 9US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) 1. TERMINOLOGY id="p-45"
[0045]Unless otherwise defined, all terms of art, notations, and other scientific or medical terms or terminology used herein are intended to have the meanings commonly understood by those of ordinary skill in the art. In some cases, terms with commonly understood meanings are defined herein for clarity and/or for ready reference, and the inclusion of such definitions herein should not be construed as representing a substantial difference over the definition of the term as generally understood in the art. id="p-46"
[0046]Articles "a " and "an " are used herein to refer to one or to more than one (i.e., at least one) of the grammatical object of the article. By way of example, "an element " means at least one element and can include more than one element. id="p-47"
[0047]The use herein of the terms "including, " "comprising, " or "having, " and variations thereof, is meant to encompass the elements listed thereafter and equivalents thereof as well as additional elements. Embodiments recited as "including, " "comprising, " or "having " certain elements are also contemplated as "consisting essentially of ’ and "consisting of those certain elements. " As used herein, "and/or " refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations where interpreted in the alternative ("or "). id="p-48"
[0048]As used herein, the transitional phrase "consisting essentially of ’ (and grammatical variants) is to be interpreted as encompassing the recited materials or steps "and those that do not materially affect the basic and novel characteristic(s) " of the present disclosure or features of the claims. See, for example, In re Herz, 537 F.2d 549, 551-52, 190 U.S.P.Q. 461, 4(CCPA 1976) (emphasis in the original); see also MPEP §2111.03. Thus, the term "consisting essentially of ’ as used herein should not be interpreted as equivalent to "comprising. " id="p-49"
[0049]Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. For example, if a concentration range is stated as 1% to 50%, it is intended that values such as 2% to 40%, 10% to 30%, or 1% to 3%, etc., are expressly enumerated in this specification. These are only examples of what is specifically intended, and all possible combinations of numerical values between and including the lowest value and the highest value enumerated are to be considered to be expressly stated in this disclosure. 10US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-50"
[0050]The terms "about " and "approximately " as used herein shall generally mean an acceptable degree of error for the quantity measured given the nature or precision of the measurements. Exemplary degrees of error are within 20% (%); preferably, within 10%; and more preferably, within 5% of a given value or range of values. Any reference to "about X" or "approximately X" specifically indicates at least the values X, 0.95X, 0.96X, 0.97X, 0.98X, 0.99X, 1.01X, 1.02X, 1.03X, 1.04X, and 1.05X. Thus, expressions "about X" or "approximately X" are intended to teach and provide written support for a claim limitation of, for example, "0.98X." Numerical quantities given herein are approximate unless stated otherwise, meaning that the term "about " or "approximately " can be inferred when not expressly stated. When "about " is applied to the beginning of a numerical range, it applies to both ends of the range. id="p-51"
[0051]As used throughout, the terms "nucleic acid, " "nucleic acid sequence, " "oligonucleotide, " "nucleotides, " or other grammatical equivalents as used herein mean at least two nucleotides, either deoxyribonucleotides or ribonucleotides, or analogs thereof, covalently linked together. Polynucleotides are polymers of any length, including, e.g., 20, 50, 100, 200, 300, 500, 1000, 2000, 3000, 5000, 7000, 10,000, etc. A polynucleotide described herein generally contains phosphodiester bonds, although in some cases, nucleic acid analogs are included that may have at least one different linkage, e.g., phosphoramidate, phosphorothioate, phosphorodithioate, or O-methylphophoroamidite linkages, and peptide nucleic acid backbones and linkages. Mixtures of naturally occurring polynucleotides and analogs can be made; alternatively, mixtures of different polynucleotide analogs, and mixtures of naturally occurring polynucleotides and analogs may be made. The following are non-limiting examples of polynucleotides: a gene or gene fragment, exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, ribozymes, cDNA, cRNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure may be imparted before or after assembly of the polymer. The sequence of nucleotides may be interrupted by non-nucl eotide components. A polynucleotide may be further modified after polymerization, such as by conjugation with a labeling component. The term also includes both double- and single-stranded molecules. Unless otherwise specified or required, the term polynucleotide encompasses both the double-stranded form and each of two complementary single-stranded forms known or predicted to make up 11US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) the double-stranded form. A polynucleotide is composed of a specific sequence of four nucleotide bases: adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) for thymine when the polynucleotide is RNA. Thus, the term "polynucleotide sequence " is the alphabetical representation of a polynucleotide molecule. Unless otherwise indicated, a particular polynucleotide sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions) and complementary sequences as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues. id="p-52"
[0052]Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof, alleles, orthologs, SNPs, and complementary sequences as well as the sequence explicitly indicated. id="p-53"
[0053]The terms "polypeptide " and "peptide " are used interchangeably herein to refer to a polymer of amino acid residues in a single chain. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non- naturally occurring amino acid polymers. Amino acid polymers may comprise entirely L- amino acids, entirely D-amino acids, or a mixture of L- and D-amino acids. The term "protein " as used herein refers to either a polypeptide or a dimer (z.c., two) or multimer (z.c., three or more) of single chain polypeptides. The single chain polypeptides of a protein may be joined by a covalent bond, e.g., a disulfide bond, or non-covalent interactions. The terms "portion " and "fragment " are used interchangeably herein to refer to parts of a polypeptide, nucleic acid, or other molecular construct. id="p-54"
[0054]The amino acids in the polypeptides described herein can be any of the 20 naturally occurring amino acids, D-stereoisomers of the naturally occurring amino acids, unnatural amino acids and chemically modified amino acids. Unnatural amino acids (that is, those that are not naturally found in proteins) are also known in the art, as set forth in, for example, Zhang et al. "Protein engineering with unnatural amino acids, " Curr. Opin. Struct. Biol. 23(4): 581- (2013); Xie et al. "Adding amino acids to the genetic repertoire, "Curr. Opin. Chem. Biol. 9(6): 548-54 (2005); and all references cited therein. Beta and gamma amino acids are known in the art and are also contemplated herein as unnatural amino acids. 12US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-55"
[0055]As used herein, a chemically modified amino acid refers to an amino acid whose side chain has been chemically modified. For example, a side chain can be modified to comprise a signaling moiety, such as a fluorophore or a radiolabel. A side chain can also be modified to comprise a new functional group, such as a thiol, carboxylic acid, or amino group. Post- translationally modified amino acids are also included in the definition of chemically modified amino acids. id="p-56"
[0056]The term "identity " or "substantial identity, " as used in the context of a polynucleotide or polypeptide sequence described herein, refers to a sequence that has at least 60% sequence identity to a reference sequence. Alternatively, percent identity can be any integer from 60% to 100%. Exemplary embodiments include at least: 60%, 65%, 70%, 75%, 80%, 85%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%, as compared to a reference sequence using the programs described herein; preferably BLAST using standard parameters, as described below. One of skill will recognize that these values can be appropriately adjusted to determine corresponding identity of proteins encoded by two nucleotide sequences by taking into account codon degeneracy, amino acid similarity, reading frame positioning and the like. id="p-57"
[0057]For sequence comparison, typically one sequence acts as a reference sequence to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters. id="p-58"
[0058]A "comparison window, " as used herein, includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequences for comparison are well- known in the art. Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith & Waterman Add. APL. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman Proc. Natl. Acad. Set. (U.S.A.) 85: 24 13US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) (1988), by computerized implementations of these algorithms (e.g., BLAST), or by manual alignment and visual inspection. id="p-59"
[0059]Algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al. (1990) J. Mol. Biol. 215: 403-10 and Altschul et al. (1977) Nucleic Acids Res. 25: 3389-402, respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (NCBI) web site. The algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al. (1977)). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative- scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a word size (W) of 28, an expectation (E) of 10, M=l, N=-2, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a word size (W) of 3, an expectation (E) of 10, and the BLOSUMscoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)). id="p-60"
[0060]The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Natl. Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.01, more preferably less than about 105־, and most preferably less than about 1020־. 14US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-61"
[0061]Other terms used in the fields of recombinant nucleic acid technology, microbiology, immunology, antibody engineering, and molecular and cell biology as used herein will be generally understood by one of ordinary skill in the applicable arts.
II. INTRODUCTION id="p-62"
[0062]The present disclosure describes the identification of T cell receptor (TCR)-like antibody that bind to MHC-I restricted tumor specific peptide GG1 derived from Cathepsin G (CG). Various antibodies, chimeric antigen receptors, and associated composition and methods are provided. id="p-63"
[0063]Compositions, pharmaceutical compositions, and methods according to the present disclosure can be utilized, for example, to treat, diagnose, or otherwise detect various cancers, including myeloid malignancies, non-myeloid leukemias, and solid tumor malignancies. Compositions, pharmaceutical compositions, and methods according to the present disclosure can be utilized, for example, to treat, diagnose, or otherwise detect a cancer of which antigens presented by such cancers are also presented (for example CGI or a derivative thereof, in particular, CGI (FLLPTGAEA; SEQ ID NO:61) - a 9-mer peptide derived from cathepsin G protein leader sequence, presented by HLA class I, specifically HLA-A*0201). id="p-64"
[0064]Immunotherapy has shown promise in treating acute myeloid leukemia (AML), as seen with the successful use of allogeneic stem cell transplantation (allo-SCT) in AML patients, even those with relapsed or refractory disease. However, a significant challenge in AML immunotherapy has been the limited number of identified myeloid leukemia antigens suitable for targeting. Most AML immunotherapy targets are surface molecules shared with normal blood cells. Tumor-associated intracellular antigens that appear on the cell surface via human leukocyte antigen (HLA) processing offer a potential source for immunotherapy targets. These antigens can stimulate T cell responses and have proven effective for vaccines and T cell-based therapies. id="p-65"
[0065]While immunotherapy targeting tumor antigens using vaccines and T cell-based approaches has shown potential in solid tumors and hematologic malignancies, a common hurdle is the low affinity of endogenous TCRs for the target antigen. The binding between the TCR and the pMHC is described as a weak interaction, with a KD ranging from 1 to 90 pM. This is in contrast to antibodies, which exhibit a high affinity interaction with a KD that can vary from 109־ nM to 106־ pM. This difference in affinity levels highlights the strong binding of antibodies compared to the TCR. The TCR’s low affinity for pMHC, characterized by slow 15US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) association rate (K-on) and rapid dissociation rate (K-off), enables T-cells to efficiently and rapidly survey a large array of peptides presented by MHC molecules on both normal and diseased cells. This allows the T-cells to establish an immune synapse with the appropriate cells that trigger activation, and bypass non-diseased tissue. However, in the case of cancer immunotherapy with known antigens, the low avidity interaction between pMHC and TCR becomes an obstacle to complete tumor eradication. id="p-66"
[0066]One strategy to overcome this limitation is to develop TCR-like (TCR-L) antibodies (also referred to as TCR-mimic (TCR-m) antibodies) with higher affinity for the peptide/HLA than natural TCRs. TCR-m antibodies not only offer higher affinity but also bypass tumor- mediated mechanisms that impair T cell function. Additionally, they can be administered consistently as drugs, avoiding the delays associated with cell-based therapies. id="p-67"
[0067]The inventors previously identified the myeloid azurophil granule protease cathepsin G (CG), as highly expressed in AML blasts compared to normal myeloid cells, and in particular it has higher expression in leukemia stem cells. Myeloid azurophil granules provide a rich source of intracellular leukemia antigens. FIG. 1is an overview of neutrophil granule proteases. CG is a myeloid azurophil granule serine protease that is involved in host immunity, cleavage of inflammatory mediators and receptors, and degradation of extracellular matrix components and leukemogenesis. CG is highly expressed in acute myeloid leukemia (AML), with a higher expression in leukemia stem cells (LSC). It is further noted that: (1) CG anti- leukemia immunity can be elicited in vitro and in vivo; (2) functional CG-CTL can be detected in AML patients following allogeneic hematopoietic stem cell transplantation (allo-SCT); and (3) in addition to AML, CGI is expressed by lymphoid leukemia, specifically acute lymphoblastic leukemia (ALL) and chronic lymphocytic leukemia (CLL) and may also be detectable in lung cancer. id="p-68"
[0068]Although the inventors previously demonstrated tumor reduction of CGI-expressing AML by poly clonally-expanded CGl-CTL, this approach yielded antigen-specific CTLs with a lower avidity binding of the TCR to the CGl-pMHC. Hence, the TCR-L approach to targeting CG1/HLA-A2 expressed on AML as described in this disclosure was pursued as providing an advantage over conventional expansion of polyclonal CTLs, or CGI-peptide vaccination, which also expands endogenous CTLs with lower avidity TCRs. TCR-L antibodies have been a breakthrough in immunotherapy, as they: (1) target intracellular antigens expressed on HLA; (2) are engineered to have high affinity for HLA; (3) can elicit 16US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) their cytotoxic effect independent of the TCR; and (4) can be produced in large quantities and are easily available for infusion, in contrast with cellular approaches. id="p-69"
[0069]As described in this disclosure, the inventors engineered TCR-like antibodies that target CGI in complex with HLA-A*0201 (also referred to as HLA-A2). The inventors identified CG-derived amino acid sequence FLLPTGAEA (SEQ ID NO:61), hereafter designated as CGI, as a promising target for AML immunotherapy. CGI is a 9-mer peptide derived from CG protein leader sequence and is presented by HLA class I HLA-A*0201 . FIG. 2depicts an overview of aspects of an amino acid sequence of an antigen target according to certain aspects of the present disclosure. FIG. 3depicts processing of CG to produce the CGI peptide, followed by MHC peptide loading, and cell surface presentation of the CG1/HLA-Acomplex. Based on the unique biology of HLA-A*0201, the presentation of leader sequence (LS)-derived peptides is favored. LS peptides are naturally processed and loaded on HLA-A2, providing an abundant source of surface peptide/HLA (pHLA) targets. The inventors eluted CGI from the surface of primary HLA-A2+ AML blasts and AML cell lines, and demonstrated CGI-targeting immunity in leukemia patients following allogeneic stem cell transplant, hence highlighting the potential for CGI to be a promising immunotherapeutic target in AML Clinical and preclinical data suggest HLA-A2 restricted CGI complex could be a good target in development of antibody based anti-tumor therapy, in particular for cancers and tumors related to myeloid malignancies. id="p-70"
[0070]The inventors engineered a novel TCR-like antibody that targets the CG1/HLA-Aantigen. The inventors also incorporated the TCR-L CG1/HLA-A2 Fab into a bispecific antibody platform that also binds CDS - that is a G1 -targeting, T cell-engager, bispecific antibody (Ab) (CGlxCD3e), which incorporates a novel TCR-L construct that recognizes cell surface CG1/HLA-A2 complexes. Preclinical efficacy and safety were also assessed. The CGI bispecific Ab was generated by immunizing H2L2 human transgenic mice with CG1/HLA-A2 monomers. CGl-bispecific antibody showed high binding affinity to CD3-Fc, CG1/HLA-A2, and AML and T cells. CG1/HLA-A2 demonstrated potent killing of AML cell lines and primary AML in vitro and in vivo. This correlated with both tumor- and bispecific antibody-dependent T cell activation and cytokine secretion. Lastly, CFU assays using HLA- A2+ normal donor marrow in the presence of T cells and either CGlxCD3e bispecific antibody or isotype antibody, confirmed specificity of CGlxCD3e bispecific antibody for leukemia. The studies described in this disclosure provides strong evidence supporting the targeting of LS- 17US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) derived peptides, specifically CGI, in the setting of AML using TCR-L-based bispecific antibodies. id="p-71"
[0071]Other TCR like antibodies have been developed with an aim to treat solid tumor malignancies (NY-ESO-1, E75) and leukemia (PR119 and WT1 antigens). There are two characteristics of a CG1/HLA-A2 bispecific antibody that distinguishes it from other TCR-like constructs. Firstly, it was engineered using a humanized mouse model that produced a fully human antibody with high affinity for target antigen. Secondly, CGl-bispecific antibody targets a LS-derived peptide, highlighting the potential for LS-derived peptides to serve as tumor antigens, specifically in the context of HLA-A*0201 and cells with deficiencies in antigen processing machinery (APM), including defects in transporter associated with antigen processing-1 (TAPI), where LS peptides are favored for presentation. Of note, defects/downregulation of TAP and other APM components have been reported in AML and several malignances, and have been correlated with worse outcomes.
III. CANCERS id="p-72"
[0072]While myeloid leukemia, including AML and CML are the primary settings for applying CGl-bispecific antibody therapy, CG was shown to be expressed in non-myeloid malignancies. Specifically, we demonstrated endogenous expression of CG, uptake of CG from the marrow microenvironment, and presentation of CGI in the setting of HLA-A2+ ALL. Alongside the inventors ’ own investigations, there have been three other documented reports indicating the presence of CG in lymphoid malignancies, including ALL, chronic lymphocytic leukemia, and Hodgkin ’s lymphoma. Outside hematologic malignancies, one report documented CG in the setting of non-small cell lung cancer through uptake from the tumor microenvironment. The inventors have previously reported on uptake and cross-presentation of serine proteases by breast cancer, melanoma and lung cancer. It is likely that CG also may be taken up by solid tumors , hence expanding the applicability of CGI-targeting immunotherapy, and specifically CGl-bispecific antibody. id="p-73"
[0073]In some embodiments, the compositions and methods as described in this disclosure will be applicable to cancers that are HLA-A2 positive. Considering that HLA-A2 is the most prevalent HLA-A allele family and its frequency approximates 50% in several ethnic groups, antibodies as described in this disclosure could be applicable to a large number of patients with myeloid malignances as well as other cancers such as leukemia and solid tumor cancers. 18US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) A. Myeloid Malignancies id="p-74"
[0074]Myeloid malignancies are clonal diseases of hematopoietic stem or progenitor cells. These malignancies are primarily present in the bone marrow and peripheral blood but can also be present in non-hematologic tissue. They can result from genetic and epigenetic alterations that perturb key processes such as self-renewal, proliferation and impaired differentiation. id="p-75"
[0075]Myeloid malignancies can be categorized as five types: (l) acute myeloid leukemia (AML); (2) myelodysplastic syndromes (MDS); (3) myeloproliferative neoplasms (MPN); (4) myelodysplastic and myeloproliferative (MDS/MPN) neoplasms; and (5) myeloid neoplasms associated with eosinophilia and abnormalities of growth factor receptors derived from platelets or fibroblasts. id="p-76"
[0076]According to the present disclosure, myeloid malignancies that express antigens contemplated by the present disclosure (CGI, for example) include, for example, AML, MDS, and CML. Compositions and methods according to the present disclosure can detect, diagnose, treat, or otherwise be useful for myeloid malignancies, in particular those characterized by high expression of CGI (high expression compared to a WT or non-pathogenic subject). id="p-77"
[0077]Additional non-myeloid malignancies, for example ALL, CLL, lymphomas, and lung cancer (which also may express high CGI levels), are also contemplated by the present disclosure as cells expressing antigens of interest relating to myeloid malignancies may also be expressed by cells involved in non-myeloid pathologies.
B. Non-Myeloid Leukemias id="p-78"
[0078]Leukemia is classified in two ways. First, the disease can be either chronic (slow- growing) or acute (more aggressive). Second, leukemia is classified based on the types of leukemia cells present. This is determined by where the disease started. Lymphocytic leukemias start in lymphoid cells, and myelogenous leukemias start in myeloid cells. Acute lymphocytic leukemia (ALL) is the most common kind of leukemia. It usually occurs in young children but can also occur in adults. It ’s sometimes called acute lymphoblastic leukemia. ALL starts in the lymphoid cells of the bone marrow. It often spreads quickly to the blood in other parts of the body, such as central nervous system (brain and spinal cord), liver, lymph nodes, spleen, and testicles in male patients. Chronic lymphocytic leukemia (CLL) is the most common type of slow-growing leukemia. It usually affects older adults. CLL starts in the lymphoid (white blood) cells of the bone marrow and progresses slowly. A person with CLL 19US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) may feel fine for several years before experiencing symptoms or seeking treatment. But it can eventually enter the blood and spread to other parts of the body.
C. Solid Tumor Cancers id="p-79"
[0079]In some embodiments, the cancer is a solid tumor, such as a carcina, a sarcoma, or a melanoma. Carcinoma begins in the epithelial tissues, such as the skin or in tissues that compose internal organs (e.g., lung cancer and colorectal cancer). Carcinoma is the most common type of cancer. Sarcoma begins in the connective tissue, such as bone, cartilage, fat, muscle, and blood vessels (e.g., rhabdomyosarcoma, liposarcoma, and Ewing sarcoma). Sarcomas are rare and usually affect children and young adults. Melanomas are cancers that arise in the cells responsible for the pigmentation of the skin. Melanoma is associated with sun exposure. Some people with a family history of melanoma are more at risk for developing the disease. Exemplary solid tumor cancers in the context of the various embodiments of this disclosure include, but are not limited to, breast cancer, prostate cancer, ovarian cancer, glioblastoma, cervical cancer, skin cancer, pancreatic cancer, colorectal cancer, bladder cancer, endometrial cancer, renal cancer, liver cancer, brain cancer, lymphoma, lung cancer, and the like.
IV. ANTIBODIES id="p-80"
[0080]The present disclosure provides compositions that may be useful for treating, diagnosing, or otherwise detecting aspects of myeloid malignancies (for example in a subject having or suspected of having a myeloid malignancy, an animal model, an in vitro tissue culture model, and the like) and other caners. Antibodies or antigen binding portions thereof that specifically or selectively bind antigen targets related to myeloid malignancies are provided herein, in addition to bispecific antibodies that can target more than one unique antigen. In certain aspects, antibodies as described herein are human antibodies. In embodiments of the present disclosure, the provided antibodies and antibody fragments thereof specifically bind to HLA-A2/CG1 as tumor antigen. In further embodiments of the present disclosure, novel antibodies (or antibody fragments) specifically bind to HLA-A2/CG1 as a tumor antigen, and can specifically bind to antigen that can engage T-cells, for example CD3. Antibodies of the present disclosure may also be engineered into other modalities, such as engineered chimeric antigen receptors (CAR), also known as chimeric immunoreceptors, chimeric T cell receptors, or artificial T cell receptors, such as, for example CAR-T, CAR-NK, or CAR macrophage. CARs for CAR T, CAR NK and CAR macrophage have similar structures: the extracellular 20US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) domain including the antigen binding domain and a spacer that is involved in engagement of target cells; a transmembrane domain that docks CAR to immune cells and is also involved in other functions of CAR, such as stability and interaction with other membrane proteins; and an intracellular signaling domain that is involved in signaling transduction and activation of immune cells. In some embodiments, HLA-A2/CG1 is a myeloid malignancy tumor antigen. However, HLA-A2/CG1 may also be a tumor antigen for other types of cancer and, as such, the various compositions and methods provided herein would be useful with respect to other cancers as well. id="p-81"
[0081]As used herein, the terms "specifically binds to, " "specific for, " "selectively binds, " and "selective for " a myeloid malignancy antigen or an epitope on a protein related to a myeloid malignancy mean binding that is measurably different from a non-specific or non-selective interaction. Specific binding can be measured, for example, by determining binding of a molecule compared to binding of a control molecule. Specific binding can also be determined by competition with a control molecule that is similar to the target, such as an excess of non- labeled target. In that case, specific binding is indicated if the binding of the labeled target to a probe is competitively inhibited by the excess non-labeled target id="p-82"
[0082]An antibody, as used herein, can refer to an intact antibody (e.g, an intact immunoglobulin) and antibody fragment, for example, an antigen binding fragment, or a bispecific antibody. Antigen binding fragments can comprise at least one antigen binding domain. One example of an antigen binding domain is an antigen binding domain formed by a Vh-Vl dimer. Antibodies and antigen binding fragments can be described by the antigen to which they specifically bind. In some embodiments, the antigen binding fragments provided herein can comprise any of the antigen binding portions (also referred to as antigen binding domains) described below. id="p-83"
[0083]The Vh and Vl regions can be further subdivided into regions of hypervariability (hypervariable regions (HVRs), also called complementarity determining regions (CDRs)) interspersed with regions that are more conserved. The more conserved regions are called framework regions (FRs). Each Vh and Vl generally comprises three CDRs and four FRs, arranged in the following order (from N-terminus to C-terminus): FRI - CDRI - FR2 - CDR- FR3 - CDR3 - FR4. The CDRs are involved in antigen binding and confer antigen specificity and binding affinity to the antibody. (See Rabat et al. (1991) Sequences of Proteins of Immunological Interest Sth ed., Public Health Service, National Institutes of Health, Bethesda, 21US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) MD.) CDRsequences on the heavy chain (VH) may be designated as CDRH1,2, 3, while CDR sequences on the light chain (Vv) may be designated as CDRL1, 2, 3. id="p-84"
[0084]Provided herein are antibodies or antigen binding portions thereof that specifically bind to antigens related to CG1/HLA-A2 complex. Such antibodies may be, for example, monoclonal antibodies (mAbs) or recombinant/chimeric antibodies (i.e., synthetic antibodies derived from synthetic nucleic acid constructs, such as viral vectors, that may also contain monoclonal Ab sequences as disclosed herein). id="p-85"
[0085]In each case, where a specific amino acid sequence is recited, embodiments comprising a sequence having at least 90% (e.g. 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) identity to the recited sequence (e.g., SEQ ID NOs: 7-9, 15-16, 34-36, 42-43, 55-57, 132-134) are also provided. In some cases, where a specific amino acid sequence is recited, embodiments comprising a sequence having at least 90% (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) identity to the recited sequence (e.g., SEQ ID NOs 1-57, 132-134) are also provided. id="p-86"
[0086]In each case, where a specific amino acid sequence is recited, embodiments consisting essentially of a sequence having at least 90% (e.g. 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) identity to the recited sequence (e.g., SEQ ID NOs: 7-9, 15-16, 34-36, 42- 43, 55-57, 132-134) are also provided. In some cases, where a specific amino acid sequence is recited, embodiments consisting essentially of a sequence having at least 90% (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) identity to the recited sequence (e.g., SEQ ID NOs 1-57, 132-134) are also provided. id="p-87"
[0087]In each case, where a specific amino acid sequence is recited, embodiments consisting of a sequence having at least 90% (e.g. 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) identity to the recited sequence (e.g., SEQ ID NOs: 7-9, 15-16, 34-36, 42-43, 55-57, 132- 134) are also provided. In some cases, where a specific amino acid sequence is recited, embodiments consisting of a sequence having at least 90% (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) identity to the recited sequence (e.g., SEQ ID NOs 1-57, 132- 134) are also provided. id="p-88"
[0088]The disclosure also provides an antibody or antigen binding portion thereof that specifically binds to CG1/HLA-A2 complex, wherein the antibody or antigen binding portion thereof comprises a heavy chain variable region comprising an amino acid sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% 22US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) or 99% identical) to any of SEQ ID NOs: 7, 8, 9, 15, 16, 55, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 34, 35, 36, 42, 43, 56, or 132. Sequence details can be found in the Examples below. In some embodiments, the antibody or antigen binding portion thereof that specifically binds to CG1/HLA-A2 complex comprises a heavy chain variable region comprising an amino acid sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs 1-27, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs 28-54 or 132. id="p-89"
[0089]The disclosure also provides an antibody or antigen binding portion thereof that specifically binds to CG1/HLA-A2 complex, wherein the antibody or antigen binding portion thereof comprises a heavy chain variable region comprising an amino acid sequence that is at least 95% identical (for example, at least 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 7, 8, 9, 15, 16, 55, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 95% identical (for example, at least 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 34, 35, 36, 42, 43, 56, or 132. In some embodiments, the antibody or antigen binding portion thereof that specifically binds to CG1/HLA-Acomplex comprises a heavy chain variable region comprising an amino acid sequence that is at least 95% identical (for example, at least 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs 1-27, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 95% identical (for example, at least 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs 28-54 or 132. id="p-90"
[0090]The disclosure also provides an antibody or antigen binding portion thereof that specifically binds to CG1/HLA-A2 complex, wherein the antibody or antigen binding portion thereof comprises a heavy chain variable region comprising an amino acid sequence that is at least 97% identical (for example, at least 97%, 98% or 99% identical) to any of SEQ ID NOs: 7, 8, 9, 15, 16, 55, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 97% identical (for example, at least 97%, 98% or 99% identical) to any of SEQ ID NOs: 34, 35, 36, 42, 43, 56, or 132. In some embodiments, the antibody or antigen binding portion thereof that specifically binds to CG1/HLA-A2 complex comprises a heavy chain variable region comprising an amino acid sequence that is at least 97% identical (for 23US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) example, at least 97%, 98% or 99% identical) to any of SEQ ID NOs 1-27, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 97% identical (for example, at least 97%, 98% or 99% identical) to any of SEQ ID NOs 28-54 or 132. id="p-91"
[0091]The disclosure also provides an antibody or antigen binding portion thereof that specifically binds to CG1/HLA-A2 complex, wherein the antibody or antigen binding portion thereof comprises a heavy chain variable region comprising an amino acid sequence that is at least 98% identical (for example, at least 98% or 99% identical) to any of SEQ ID NOs: 7, 8, 9, 15, 16, 55, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 98% identical (for example, at least 98% or 99% identical) to any of SEQ ID NOs: 34, 35, 36, 42, 43, 56, or 132. In some embodiments, the antibody or antigen binding portion thereof that specifically binds to CG1/HLA-A2 complex comprises a heavy chain variable region comprising an amino acid sequence that is at least 98% identical (for example, at least 98% or 99% identical) to any of SEQ ID NOs 1-27, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 98% identical (for example, at least 98% or 99% identical) to any of SEQ ID NOs 28-54 or 132. id="p-92"
[0092]The disclosure also provides an antibody or antigen binding portion thereof that specifically binds to CG1/HLA-A2 complex , wherein the antibody or antigen binding portion thereof comprises a heavy chain variable region comprising an amino acid sequence that is at least 99% identical to any of SEQ ID NOs: 7, 8, 9, 15, 16, 55, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 99% identical to any of SEQ ID NOs: 34, 35, 36, 42, 43, 56, or 132. In some embodiments, the antibody or antigen binding portion thereof that specifically binds to CG1/HLA-A2 complex comprises a heavy chain variable region comprising an amino acid sequence that is at least 99% identical to any of SEQ ID NOs 1-27, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 99% identical to any of SEQ ID NOs 28-54 or 132. id="p-93"
[0093]In examples, the antigen is CGI, in particular, a 9-mer peptide derived from cathepsin G protein leader sequence, presented by HLA class I, specifically HLA-A*0201 (SEQ ID NO:61, for example). id="p-94"
[0094]In some embodiments, the antibody or antigen binding portion thereof comprises the heavy chain variable region comprises an amino acid sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 7, 8, 9, 15, 16, 55, 133, or 134. In some embodiments, the antibody or 24US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) antigen binding portion thereof comprises the heavy chain variable region that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 1-27, 133, or 134. id="p-95"
[0095]Provided herein are bi-specific antibodies or antigen binding portions thereof that specifically bind to CG1/HLA-A2 complex as well as another antigen, for example, CD3. id="p-96"
[0096]In each case of a bispecific antibody, where a specific amino acid sequence is recited, embodiments comprising a sequence having at least 90% (e.g. 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) identity to the recited sequence (e.g., SEQ ID NOs: 7-9, 15, 16, 34-36, 42-43, 55-57, 132-134) are also provided. In some cases of the bispecific antibody, where a specific amino acid sequence is recited, embodiments comprising a sequence having at least 90% (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) identity to the recited sequence (e.g., SEQ ID NOs 1-57, 132-134) are also provided. id="p-97"
[0097]In each case of a bispecific antibody, where a specific amino acid sequence is recited, embodiments consisting essentially of a sequence having at least 90% (e.g. 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) identity to the recited sequence (e.g., SEQ ID NOs: 7-9, 15-16, 34-36, 42-43, 55-57, 132-134) are also provided. In some cases of the bispecific antibody, where a specific amino acid sequence is recited, embodiments consisting essentially of a sequence having at least 90% (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) identity to the recited sequence (e.g., SEQ ID NOs 1-57, 132-134) are also provided. id="p-98"
[0098]In each case of a bispecific antibody, where a specific amino acid sequence is recited, embodiments consisting of a sequence having at least 90% (e.g. 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) identity to the recited sequence (e.g., SEQ ID NOs: 7-9, 15-16, 34-36, 42-43, 55-57, 132-134) are also provided. In some cases of the bispecific antibody, where a specific amino acid sequence is recited, embodiments consisting of a sequence having at least 90% (e.g., 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%) identity to the recited sequence (e.g., SEQ ID NOs 1-57, 132-134) are also provided. id="p-99"
[0099]The disclosure also provides a bispecific antibody or antigen binding portion thereof that specifically binds to CG1/HLA-A2 complex, wherein the antibody or antigen binding portion thereof comprises a heavy chain variable region comprising an amino acid sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 7, 8, 9, 15, 16, 55, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 90% identical (for 25US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 34, 35, 36, 42, 43, 56, or 132. Such bispecific antibodies also comprise an antibody or antigen binding portion thereof that specifically binds to a second antigen, such as CD3. In some embodiments, the antibody or antigen binding portion thereof that binds to the second antigen comprises an amino acid sequence that is at least 90% identical to SEQ ID NO:57 (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical). Sequence details can be found in the Examples below. In some embodiments, the bispecific antibody or antigen binding portion thereof that specifically binds to CG1/HLA-Acomplex comprises a heavy chain variable region comprising an amino acid sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 1-27, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 28-54, or 132. id="p-100"
[0100]The disclosure also provides a bispecific antibody or antigen binding portion thereof that specifically binds to CG1/HLA-A2 complex, wherein the antibody or antigen binding portion thereof comprises a heavy chain variable region comprising an amino acid sequence that is at least 95% identical (for example, at least 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 7, 8, 9, 15, 16,55, 133, or 134 and alight chain variable region comprising an amino acid sequence that is at least 95% identical (for example, at least 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 34, 35, 36, 42, 43, 56, or 132. Such bispecific antibodies also comprise an antibody or antigen binding portion thereof that specifically binds to a second antigen, such as CD3. In some embodiments, the antibody or antigen binding portion thereof that binds to the second antigen comprises an amino acid sequence that is at least 95% identical to SEQ ID NO:57 (for example, at least 95%, 96%, 97%, 98% or 99% identical). In some embodiments, the bispecific antibody or antigen binding portion thereof that specifically binds to a myeloid malignancy antigen comprises a heavy chain variable region comprising an amino acid sequence that is at least 95% identical (for example, at least 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 1-27, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 95% identical (for example, at least 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 28-54, 56 or 132. 26US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-101"
[0101]The disclosure also provides a bispecific antibody or antigen binding portion thereof that specifically binds to CG1/HLA-A2 complex, wherein the antibody or antigen binding portion thereof comprises a heavy chain variable region comprising an amino acid sequence that is at least 97% identical (for example, at least 97%, 98% or 99% identical) to any of SEQ ID NOs: 7, 8, 9, 15, 16, 55, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 97% identical (for example, at least 97%, 98% or 99% identical) to any of SEQ ID NOs: 34, 35, 36, 42, 43, 56, or 132. Such bispecific antibodies also comprise an antibody or antigen binding portion thereof that specifically binds to a second antigen, such as CD3. In some embodiments, the antibody or antigen binding portion thereof that binds to the second antigen comprises an amino acid sequence that is at least 97% identical to SEQ ID NO:57 (for example, at least 97%, 98% or 99% identical). In some embodiments, the bispecific antibody or antigen binding portion thereof that specifically binds to CG1/HLA-Acomplexcomprises a heavy chain variable region comprising an amino acid sequence that is at least 97% identical (for example, at least 97%, 98% or 99% identical) to any of SEQ ID NOs: 1-27, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 97% identical (for example, at least 97%, 98% or 99% identical) to any of SEQ ID NOs: 28-54, 56 or 132. id="p-102"
[0102]The disclosure also provides a bispecific antibody or antigen binding portion thereof that specifically binds to CG1/HLA-A2 complex, wherein the antibody or antigen binding portion thereof comprises a heavy chain variable region comprising an amino acid sequence that is at least 98% identical (for example, at least 98% or 99% identical) to any of SEQ ID NOs: 7, 8, 9, 15, 16, 55, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 98% identical (for example, at least 98% or 99% identical) to any of SEQ ID NOs: 34, 35, 36, 42, 43, 56, or 132. Such bispecific antibodies also comprise an antibody or antigen binding portion thereof that specifically binds to a second antigen, such as CD3. In some embodiments, the antibody or antigen binding portion thereof that binds to the second antigen comprises an amino acid sequence that is at least 98% identical to SEQ ID NO:57 (for example, at least 98% or 99% identical). In some embodiments, the bispecific antibody or antigen binding portion thereof that specifically binds to CG1/HLA-A2 complex comprises a heavy chain variable region comprising an amino acid sequence that is at least 98% identical (for example, at least 98% or 99% identical) to any of SEQ ID NOs: 1-27, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 98% identical (for example, at least 98% or 99% identical) to any of SEQ ID NOs: 28-54, 56 or 132. 27US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-103"
[0103]The disclosure also provides a bispecific antibody or antigen binding portion thereof that specifically binds to CG1/HLA-A2 complex, wherein the antibody or antigen binding portion thereof comprises a heavy chain variable region comprising an amino acid sequence that is at least 99% identical to any of SEQ ID NOs: 7, 8, 9, 15, 16, 55, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 99% identical to any of SEQ ID NOs: 34, 35, 36, 42, 43, 56, or 132. Such bispecific antibodies also comprise an antibody or antigen binding portion thereof that specifically binds to a second antigen, such as CD3. In some embodiments, the antibody or antigen binding portion thereof that binds to the second antigen comprises an amino acid sequence that is at least 99% identical to SEQ ID NO:57. In some embodiments the bispecific antibody or antigen binding portion thereof that specifically binds to CG1/HLA-A2 complex comprises a heavy chain variable region comprising an amino acid sequence that is at least 99% identical to any of SEQ ID NOs: 1-27, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 99% identical to any of SEQ ID NOs: 28-54, 56 or 132. id="p-104"
[0104]In examples, the antigen is CGI, in particular, a 9-mer peptide derived from cathepsin G protein leader sequence, presented by HLA class I, specifically HLA-A*0201 (SEQ ID NO:61, for example). In examples, the second antigen can be CD3. id="p-105"
[0105]In some embodiments of a bispecific antibody, the antibody or antigen binding portion thereof comprises the heavy chain variable region comprises an amino acid sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 7, 8, 9, 15, 16, 55, 133, or 134. Such bispecific antibodies also comprise an antibody or antigen binding portion thereof that specifically binds to a second antigen, such as CD3. In some embodiments, the antibody or antigen binding portion thereof that binds to the second antigen comprises an amino acid sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to SEQ ID NO:57. In some embodiments of a bispecific antibody, the antibody or antigen binding portion thereof comprises a heavy chain variable region comprising an amino acid sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 1-27, 133, or 134. id="p-106"
[0106]In some embodiments of a bispecific antibody, the antibody or antigen binding portion thereof comprises the heavy chain variable region comprises an amino acid sequence 28US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to SEQ ID NOs: 7, 55, 133, or 134. and a light chain variable region comprising an amino acid sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to SEQ ID NOs: 34,56, or 132. Such bispecific antibodies also comprise an antibody or antigen binding portion thereof that specifically binds to a second antigen, such as CD3. In some embodiments, the antibody or antigen binding portion thereof that binds to the second antigen comprises an amino acid sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to SEQ ID NO:57. id="p-107"
[0107]In some embodiments of a bispecific antibody, the antibody or antigen binding portion thereof comprises the heavy chain variable region comprises an amino acid sequence that is at least 95% identical (for example, 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 7, 8, 9, 15, 16, 55, 133, or 134. Such bispecific antibodies also comprise an antibody or antigen binding portion thereof that specifically binds to a second antigen, such as CD3. In some embodiments, the antibody or antigen binding portion thereof that binds to the second antigen comprises an amino acid sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to SEQ ID NO:57. In some embodiments of a bispecific antibody, the antibody or antigen binding portion thereof comprises a heavy chain variable region comprising an amino acid sequence that is at least 95% identical (for example, 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 1-27, 133, or 134. id="p-108"
[0108]In some embodiments of a bispecific antibody, the antibody or antigen binding portion thereof comprises the heavy chain variable region comprises an amino acid sequence that is at least 95% identical (for example, at least 95%, 96%, 97%, 98% or 99% identical) to SEQ ID NOs: 7,55, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 95% identical (for example, at least 95%, 96%, 97%, 98% or 99% identical) to SEQ ID NOs: 34,56, or 132. Such bispecific antibodies also comprise an antibody or antigen binding portion thereof that specifically binds to a second antigen, such as CD3. In some embodiments, the antibody or antigen binding portion thereof that binds to the second antigen comprises an amino acid sequence that is at least 95% identical (for example, at least 95%, 96%, 97%, 98% or 99% identical) to SEQ ID NO:57. 29US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-109"
[0109]In some embodiments of a bispecific antibody, the antibody or antigen binding portion thereof comprises the heavy chain variable region comprises an amino acid sequence that is at least 97% identical (for example, at least 97%, 98% or 99% identical) to SEQ ID NOs: 7, 55, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 97% identical (for example, at least 97%, 98% or 99% identical) to SEQ ID NOs: 34, 56, or 132. Such bispecific antibodies also comprise an antibody or antigen binding portion thereof that specifically binds to a second antigen, such as CD3. In some embodiments, the antibody or antigen binding portion thereof that binds to the second antigen comprises an amino acid sequence that is at least 97% identical (for example, at least 97%, 98% or 99% identical) to SEQIDNO:57. id="p-110"
[0110]In some embodiments of a bispecific antibody, the antibody or antigen binding portion thereof comprises the heavy chain variable region comprises an amino acid sequence that is at least 98% identical (for example, at least 98% or 99% identical) to SEQ ID NOs: 7, 55, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 98% identical (for example, at least 98% or 99% identical) to SEQ ID NOs: 34, 56, or 132. Such bispecific antibodies also comprise an antibody or antigen binding portion thereof that specifically binds to a second antigen, such as CD3. In some embodiments, the antibody or antigen binding portion thereof that binds to the second antigen comprises an amino acid sequence that is at least 98% identical (for example, at least 98% or 99% identical) to SEQ ID NO:57. id="p-111"
[0111]The amino acid residue sequences provided herein are set forth in single-letter amino acid code which can be used interchangeably with three-letter amino acid code. An amino acid refers to any monomer unit that can be incorporated into a peptide, polypeptide, or protein. The twenty natural or genetically encoded alpha-amino acids are as follows: alanine (Ala or A), arginine (Arg or R), asparagine (Asn or N), aspartic acid (Asp or D), cysteine (Cys or C), glutamine (Gin or Q), glutamic acid (Glu or E), glycine (Gly or G), histidine (His or H), isoleucine (He or I), leucine (Leu or L), lysine (Lys or K), methionine (Met or M), phenylalanine (Phe or F), proline (Pro or P), serine (Ser or S), threonine (Thr or T), tryptophan (Trp or W), tyrosine (Tyr or Y), and valine (Val or V). The structures of these twenty natural amino acids are shown in, e.g., Stryer et al., Biochemistry, 5th ed., Freeman and Company (2002). The term amino acid also includes unnatural amino acids, modified amino acids (e.g., having modified side chains and/or backbones), and amino acid analogs. 30US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-112"
[0112]The terms identical or percent identity, in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of nucleotides or amino acid residues that are the same (e.g, 90%, or 95% or greater identity over a specified region), when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection. id="p-113"
[0113]Identity or similarity with respect to a sequence is defined as the percentage of amino acid residues in the candidate sequence that are identical (i.e., same residue) with the starting amino acid residues, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Methods of alignment of sequences for comparison are well known in the art. Optimal alignment of sequences for comparison can be conducted, for example, by the local homology algorithm of Smith and Waterman (Adv. Appl. Math. 2:482, 1970), by the homology alignment algorithm of Needleman and Wunsch (J. Mol. Biol. 48:443, 1970), by the search for similarity method of Pearson and Lipman (Proc. Natl. Acad. Set. USA 85:2444, 1988), by computerized implementations of these algorithms (e.g., GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection (see, e.g., Ausubel etal.. Current Protocols in Molecular Biology (1995 supplement)). id="p-114"
[0114]As with all peptides, polypeptides, and proteins, including fragments thereof, it is understood that additional modifications in the amino acid sequence of the CG1/HLA-Acomplex -specific antibodies or antigen binding fragments thereof described herein, for example, in the heavy chain variable region and/or light chain variable region, can occur that do not alter the nature or function of the antibodies or antigen binding fragments thereof. Such modifications include conservative amino acids substitutions, such that each recited sequence optionally contains one or more conservative amino acid substitutions. The list provided below identifies examples of groups that contain amino acids that are conservative substitutions for one another; these groups are exemplary as other conservative substitutions are known to those of skill in the art. 1) Alanine (A), Glycine (G);2) Aspartic acid (D), Glutamic acid (E);3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K); 31US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) ) Isoleucine (I), Leucine (L), Methionine (M), Valine (V);6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W);7) Serine (S), Threonine (T); and8) Cysteine (C), Methionine (M) [0 115]By way of example, when an aspartic acid at a specific residue is mentioned, also contemplated is a conservative substitution at the residue, for example, glutamic acid. Non- conservative substitutions, for example, substituting a proline with glycine, are also contemplated. id="p-116"
[0116]In some instances, the affinity of CG1/HLA-A2 complex-specific antibodies or antigen binding fragments thereof may be optimized through mutations to increase or decrease affinity as desired based on one or more of the known characteristics of the binding interaction with the cognant CGI/HL A-A2 complex, the structure of either or both of the antibodies or fragments thereof, or the CGI/HL A-A2 complex. In some instances, the mutations permit facile elution of purified antibodies or fragments thereof under desirable elution conditions during isolation and purification. id="p-117"
[0117]Methods of generating and screening for antibodies and antigen binding fragments thereof as provided in this disclosure are described in the Examples and are well-known in the art. Methods of further modifying antibodies for enhanced properties (e.g., enhanced affinity, chimerization, humanization) as well as generating antigen binding fragments, as described herein, are also well-known in the art. id="p-118"
[0118]The present disclosure also encompasses antibodies or fragments thereof that bind to the same epitope of the CG1/HLA-A2 complex as the antibodies disclosed herein. Such antibodies can be identified using routine techniques known in the art, including, for example, competitive binding assays. id="p-119"
[0119]The present disclosure also encompasses bi-specific antibodies or fragments thereof that bind to the same epitope of the CG1/HLA-A2 complex as the antibodies disclosed herein, as well as other antigens. Such antibodies can be identified using routine techniques known in the art, including, for example, competitive binding assays. id="p-120"
[0120]The term epitope, as used herein, means a component of an antigen capable of specific binding to an antibody or antigen binding fragment thereof. Such components optionally comprise one or more contiguous amino acid residues and/or one or more non-contiguous 32US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) amino acid residues. Epitopes frequently consist of surface-accessible amino acid residues and/or sugar side chains and can have specific three-dimensional structural characteristics, as well as specific charge characteristics. Conformational and non-conformational epitopes are distinguished in that the binding to the former but not the latter is lost in the presence of denaturing solvents. An epitope can comprise amino acid residues that are directly involved in the binding, and other amino acid residues, which are not directly involved in the binding. The epitope to which an antigen binding protein binds can be determined using known techniques for epitope determination such as, for example, testing for antigen binding protein binding to antigen variants with different point mutations. id="p-121"
[0121]The present disclosure also provides chimeric antibodies. The term chimeric antibody refers to an antibody in which a component of the heavy and/or light chain is derived from a particular source or species, while the remainder of the heavy and/or light chain is derived from a different source or species. id="p-122"
[0122]A human antibody is one that possesses an amino acid sequence corresponding to that of an antibody produced by a human or a human cell, or derived from a non-human source that utilizes a human antibody repertoire or human antibody-encoding sequences (e.g., obtained from human sources, genetically modified non-human sources or designed de novo). Human antibodies specifically exclude humanized antibodies. id="p-123"
[0123]In some embodiments, the antibody or antigen binding fragment thereof provided herein can include a heavy (H) chain variable domain sequence (abbreviated herein as VH), and a light (L) chain variable domain sequence (abbreviated herein as VL). In some embodiments, an antibody molecule comprises or consists of a heavy chain and a light chain (referred to as a half antibody). In another example, an antibody molecule includes two heavy (H) chain variable domain sequences and two light (L) chain variable domain sequence, thereby forming two antigen binding sites, such as Fab, Fab', F(ab')2, Fc, Fd, Fd', Fv, single chain antibodies (scFv, for example), single variable domain antibodies, diabodies (Dab) (bivalent and bispecific), and chimeric (e.g., humanized) antibodies, which may be produced by the modification of whole antibodies or synthesized de novo using recombinant DNA technologies. These functional antibody fragments retain the ability to selectively bind with their respective antigen. Antibodies and antibody fragments can be from any class of antibodies including, but not limited to, IgG, IgA, IgM, IgD, and IgE, and from any subclass (e.g., IgGl, IgG2, IgG3, and IgG4) of antibodies. The preparation of antibody molecules can be 33US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) monoclonal or polyclonal. An antibody molecule can also be a human, humanized, CDR- grafted, or an in vitro generated antibody. The antibody can have a heavy chain constant region chosen from, e.g., IgGl, IgG2, IgG3, or IgG4. The antibody can also have a light chain chosen from either kappa or lambda light chains. id="p-124"
[0124]As used herein, the term monoclonal antibody refers to an antibody from a population of substantially homogeneous antibodies. A population of substantially homogeneous antibodies comprises antibodies that are the same or substantially similar and that bind the same epitope(s), except for variants that can normally arise during production of the monoclonal antibody. Such variants are generally present in only minor amounts. A monoclonal antibody is typically obtained by a process that includes the selection of a single antibody from a plurality of antibodies. For example, the selection process can be the selection of a unique clone from a plurality of clones, such as a pool of yeast clones, phage clones, bacterial clones, mammalian cell clones, hybridoma clones, or other recombinant DNA clones. The selected antibody can be further altered, for example, to improve affinity for the target, for example, by affinity maturation, to humanize the antibody, to improve its production in cell culture, and/or to reduce its immunogenicity in a subject. id="p-125"
[0125]Antigen binding fragments of an antibody molecule are well known in the art, and include, for example, (i) a Fab fragment, a monovalent fragment consisting of the VL, VH, CL and CHI domains; (ii) a F(ab')2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fd fragment consisting of the VH and CHI domains; (iv) a Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a diabody (dAb) fragment, which consists of a VH domain; (vi) a camelid or camelized variable domain; (vii) a single chain Fv (scFv) (see e.g., Bird et al. (1988) Science 242:423-426; Huston et al. (1988) Proc. Natl. Acad. Sci. USA 85:5879-5883); (viii) a single domain antibody. These antibody fragments are obtained using conventional techniques known to those skilled in the art, and the fragments are screened for utility in the same manner as are intact antibodies. id="p-126"
[0126]In certain embodiments, antibodies and antibody compositions as provided herein are distinguishable from naturally occurring antibodies and compositions in one or more respects. Such distinguishable antibodies and compositions may be referred to as "synthetic, " or may be identified by the proviso that the antibody or composition "is not naturally occurring " or affirmatively as "non-naturally occurring. " As used herein the terms "corresponding 34US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) antibody, " and "corresponding to " describes the relationship between (1) an antibody characterized by six specific CDR sequences of the antibodies described in the Examples below and (2) a synthetic antibody comprising the same six CDR sequences. Synthetic antibodies of this disclosure may differ in structure from naturally occurring antibodies with the same CDRs. That is, synthetic antibodies identified by specified CDRs may be structurally different from antibodies comprising the specified CDRs that are described in the Examples below. Possible differences for synthetic antibodies include variable region sequences that differ corresponding naturally occurring antibodies, different light chain sequences (i.e. lambda type instead of kappa type or vice versa), different isotypes, different allotypes, and different constant domain variants. These differences are discussed in more detail below. In some embodiments, the synthetic antibody is an engineered polypeptide, also referred to as a recombinant polypeptide, that is made using conventional protein and antibody engineering molecular biology, chemical, and biochemical methods as described below, including, but not limited to, those described in the Examples below. id="p-127"
[0127]In one approach, an antibody heavy chain of an antibody as provided in this disclosure comprises one or more CDRs of a clone described in Table laand/or Table 1b. 35US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) Table la: Embodiments of Heavy-chain CDRs according to the present disclosure Heavy chain Clone Index Antibody SEQIDNO: VHCDR1 SEQID NO: VHCDR2 SEQID NO: VHCDR3 1 CG1-R-17 67 FTFSSYWMS 79 NIKQDGS EKYYVDSVKG 88 ASALYYYYYYGMDVCG1-R-18 68 GSISSYYWS 80 YIYYSGSTNYNPSLKS 89 ARSLYYYYYYGMDVCG1-6 69 GSVSSYYWN 81 YIYYSESTNYNTSLKS 89 ARSLYYYYYYGMDVCG1-10 70 FTFNNYWMT 82 NI KQDG NEKYYVDSVKG 90 AREGGWYWFDPCG1-12 67 FTFSSYWMS NINQDGSEKNYVDSVKG TKSLYYYYYYGMDVCG1-15 69 GSVSSYYWN 81YIYYSESTNYNTSLKSARSLYYYYYYGMDVד CG1-16 71 FTFSDYWMT 82 NI KQDGS EKYYVDSVKG 90 AREGGWYWFDPCG1-23 67 FTFSSYWMS 83 NIKHDGSEKYYVDSVKG 91 VREGGWYWFDPCG1-27 67 FTFSSYWMS 79 NI KQDGS EKYYVDSVKG 92 AREGGWYWLDPCG1-33 72 FIFSSYWMS 84 NINQDGSEKYYVDSVKG 93 TKSLYYYYYYGMDVCG1-41 73 FTFSDYWMI 79 NI KQDGS EKYYVDSVKG 90 AREGGWYWFDPCG1-44 74 GSVSNYYWN 81 YIYYSESTNYNTSLKS 89 ARSLYYYYYYGMDVCG1-46 74 GSVSNYYWN 81 YIYYSESTNYNTSLKS 89 ARSLYYYYYYGMDVCG1-55 67 FTFSSYWMS 83 NI KHDGSEKYYVDSVKG 91 VREGGWYWFDPCG1-60 75 FTFSNYWMS 79 NI KQDGS EKYYVDSVKG 92 AREGGWYWLDPCG1-61 75 FTFSNYWMS 79 NI KQDGS EKYYVDSVKG 92 AREGGWYWLDPCG1-65 69 GSVSSYYWN 81 YIYYSESTNYNTSLKS 89 ARSLYYYYYYGMDVCG1-68 67 FTFSSYWMS 79 NI KQDGS EKYYVDSVKG 92 AREGGWYWLDPCG1-74 75 FTFSNYWMS 79 NI KQDGS EKYYVDSVKG 92 AREGGWYWLDPCG1-78 70 FTFNNYWMT 85 NI KQDG NEKYYVDSVKG 90 AREGGWYWFDPCG1-104 76 FTFSHYVMH 86 VIWYDGSNINYAESLKG 94 ARGPAPTIFCG1-110 דר FTFSSNAMS 87 AISGRGGNTYYADSVKG 95 ARDSYYDVLTAYYDFCG1-112 72 FIFSSYWMS 84 NINQDGSEKYYVDSVKG 93 TKSLYYYYYYGMDVCG1-176 67 FTFSSYWMS 79 NI KQDGS EKYYVDSVKG 90 AREGGWYWFDPCG1-177 71 FTFSDYWMT 79 NI KQDGS EKYYVDSVKG 90 AREGGWYWFDPCG1-179 78 FTFSSYWMT 79 NI KQDGS EKYYVDSVKG 90 AREGGWYWFDPCG1-189 78 FTFSSYWMT 79 NI KQDGS EKYYVDSVKG 90 AREGGWYWFDP 36US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) Table lb: Embodiments of Light-chain CDRs according to the present disclosure Light chain Clone Index Antibody SEQ ID NO: VLCDR1 SEQ ID NO: VLCDR2 SEQ ID NO: VLCDR3 1 CG1-R-17 96 RSSQSLLHSNGYNYLD 106 LGSIRAS 118 MQALQTPYTCG1-R-18 97 RSSQSLLYSHGYNYLD 106 LGSIRAS 119 MQALQTPWTCG1-6 98 MSSQSLLQSHGYNHLD 107 LGSNRAS 119 MQALQTPWTCG1-10 99 RASQSISSFLN 108 TASSLQS 120 QQSYSTPYTCG1-12 102 RSSQSLLLSHGYNYLD 111 LGSSRAS 121 MQGLQTPWTCG1-15 98MSSQSLLQSHGYNHLD107LGSNRAS119MQALQTPWTד CG1-16 99 RASQSISSFLN 108 AASSFLS 120 QQSYSTPYTCG1-23 100 RASQIISSFLN 109 AASSLQS 120 QQSYSTPYTCG1-27 101 RASQSIASFLN 110 TASSLQG 120 QQSYSTPYTCG1-33 102 RSSQSLLLSHGYNYLD 111 LGSSRAS 121 MQGLQTPWTCG1-41 99 RASQSISSFLN 108 AASSFLS 120 QQSYSTPYTCG1-44 103 RSSQSLLQSHGFNHLD 112 LVSNRAS 119 MQALQTPWTCG1-46 103 RSSQSLLQSHGFNHLD 112 LVSNRAS 119 MQALQTPWTCG1-55 100 RASQIISSFLN 109 AASSLQS 120 QQSYSTPYTCG1-60 101 RASQSIASFLN 113 TASSFQG 120 QQSYSTPYTCG1-61 101 RASQSIASFLN 113 TASSFQG 120 QQSYSTPYTCG1-65 102 RSSQSLLQSHGYNHLD 107 LGSNRAS 119 MQALQTPWTCG1-68 101 RASQSIASFLN 110 TASSLQG 120 QQSYSTPYTCG1-74 101 RASQSIASFLN 113 TASSFQG 120 QQSYSTPYTCG1-78 99 RASQSISSFLN 108 TASSLQS 120 QQSYSTPYTCG1-104 104 RASQSISSWLA 114 KASSLES 122 QQYNSYSYTCG1-110 105 QASQDISNNLN 115 DTSKLED 123 LQHRYLPWTCG1-112 102 RSSQSLLLSHGYNYLD 111 LGSSRAS 121 MQGLQTPWTCG1-176 99 RASQSISSFLN 116 AASSFQS 120 QQSYSTPYTCG1-177 99 RASQSISSFLN 117 AASSLLS 120 QQSYSTPYTCG1-179 99 RASQSISSFLN 116 AASSFQS 120 QQSYSTPYTCG1-189 101 RASQSIASFLN 109 AASSLQS 120 QQSYSTPYT 37US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-128"
[0128]In some embodiments, the antibody comprises a heavy chain variable region sequence and a light chain variable region sequence that are derived from an immunoglobulin producing human B cell, and further comprises a kappa or lambda light chain constant region. In some embodiments, the light chain constant region (kappa or lambda) is from the same type of light chain (i.e., kappa or lambda) as the light chain variable region that was derived from the immunoglobulin producing human B cell; as a non-limiting example, if an IgE-producing human B cell comprises a kappa light chain, then the antibody that is produced can comprise the light chain variable region from the IgE-producing B cell and further comprises a kappa light chain constant region. id="p-129"
[0129]In some embodiments, the antibody comprises a heavy chain variable region sequence and a light chain variable region sequence that are derived from an immunoglobulin- producing human B cell, and further comprises a heavy chain constant region having an IgG isotype (e.g., IgG4), an IgA isotype (e.g, IgAl), an IgM isotype, an IgD isotype, or that is derived from an IgG, IgA, IgM, or IgD isotype (e.g, is a modified IgG4 constant region). It will be appreciated by a person of ordinary skill in the art that the different heavy chain isotypes (IgA, IgD, IgE, IgG, and IgM) have different effector functions that are mediated by the heavy chain constant region, and that for certain uses it may be desirable to have an antibody that has the effector function of a particular isotype (e.g, IgG). id="p-130"
[0130]In some embodiments, the antibody comprises a native (i.e., wild-type) human IgG, IgA, IgM, or IgD constant region. In some embodiments, the antibody comprises a native human IgGl constant region, a native human IgG2 constant region, a native human IgGconstant region, a native human IgG4 constant region, a native human IgAl constant region, a native human IgA2 constant region, a native human IgM constant region, or a native human IgD constant region. In some embodiments, the antibody comprises a heavy chain constant region that comprises one or more modifications. It will be appreciated by a person of ordinary skill in the art that modifications such as amino acid substitutions can be made at one or more residues within the heavy chain constant region that modulate effector function. In some embodiments, the modification reduces effector function, e.g, results in a reduced ability to induce certain biological functions upon binding to an Fc receptor expressed on an effector cell that mediates the effector function. In some embodiments, the modification (e.g, amino acid substitution) prevents in vivo Fab arm exchange, which can introduce undesirable effects and reduce the therapeutic efficacy of the antibody. See, e.g., Silva et al., J Biol Chem, 2015, 280:5462-5469. 38US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-131"
[0131]In some embodiments, the antibody comprises a native (i.e., wild-type) human IgM constant region, human IgD constant region, human IgG constant region that is derived from IgGl, IgG2, IgG3, or IgG4, or human IgA constant region that is derived from IgAl or IgAand comprises one or more modifications that modulate effector function. Ini some embodiments the antibody comprises a human IgM constant region, human IgD constant region, human IgG constant region that is derived from IgGl, IgG2, IgG3, or IgG4, or human IgA constant region that is derived from IgAl or IgA2. In some embodiments, the antibody comprises a native (i.e., wild-type) human IgM constant region, human IgD constant region, human IgG constant region that is derived from IgGl, IgG2, IgG3, or IgG4, or human IgA constant region that is derived from IgAl or IgA2 and comprises one, two, three, four, five, six, seven, eight, nine, ten or more modifications (e.g, amino acid substitutions). In some embodiments the constant regions includes variations (e.g, one, two, three, four, five, six, seven, eight, nine, ten or more amino acid substitutions) that reduce effector function. id="p-132"
[0132]Synthetic antibodies of this disclosure may comprise variations in heavy chain constant regions to change the properties of the synthetic antibody relative to the corresponding naturally occurring antibody. Exemplary changes include mutations to modulate antibody effector function (e.g, complement-based effector function or FcyR-based effector function), alter half-like, modulate co-engagement of antigen and FcyRs, introduce or remove glycosylation motifs (glyco-engineering). See Fonseca et al., 2018, "Boosting half-life and effector functions of therapeutic antibodies by Fc-engineering: An interaction-function review " Int J Biol Macromol. 19:306-311; Wang et al., 2018, "IgGFc engineering to modulate antibody effector functions " Protein Cell 2018, 9(l):63-73; Schlothauer, 2016, "Novel human IgGl and IgG4 Fc-engineered antibodies with completely abolished immune effector functions, " Protein Engineering, Design and Selection 29(10):457-466; Tam et al., 2017, "Functional, Biophysical, and Structural Characterization of Human IgGl and IgG4 Fc Variants with Ablated Immune Functionality " Antibodies 6, 12, each incorporated herein by reference for all purposes. id="p-133"
[0133]In some embodiments, the heavy chain variable region and/or the light chain variable region of the antibody has an identical sequence to the heavy chain variable region and/or the light chain variable region encoded by the immunoglobulin producing single B cell from the human subject having a cancer such as a myeloid malignancy, a non-myeloid leukemia, or a solid tumor cancer. In some embodiments, the heavy chain variable region and/or the light 39US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) chain variable region of the antibody comprises one or more modifications, e.g., amino acid substitutions, deletions, or insertions. id="p-134"
[0134]The heavy chain variable region sequence and/or light chain variable region sequence of an antibody described herein can be engineered to comprise one or more variations in the heavy chain variable region sequence and/or light chain variable region sequence. In some embodiments, the engineered variation(s) improves the binding affinity of the antibody for a cancer such as a myeloid malignancy, a non-myeloid leukemia, or a solid tumor cancer. In some embodiments, the engineered variation(s) improves the cross-reactivity of the antibody for a second cancer such as a myeloid malignancy, a non-myeloid leukemia, or a solid tumor cancer. id="p-135"
[0135]In some embodiments, the engineered variation is a variation in one or more CDRs, e.g., an amino acid substitution in a heavy chain CDR and/or a light chain CDR as described herein. In some embodiments, the engineered variation is a variation in one or more framework regions, e.g., an amino acid substitution in a heavy chain framework region and/or a light chain framework region. In some embodiments, the engineered variation is a reversion of a region of the heavy chain and/or light chain sequence to the inferred naive sequence. Methods for determining an inferred naive immunoglobulin sequence are described in the art. See, e.g., Magnani et al., PLoSNegl Trop Dis, 2017, 11:60005655, doi: 10.1371/journal.pntd. 0005655 id="p-136"
[0136]In some embodiments, affinity maturation is used to engineer further mutations that enhance the binding affinity of the antibody for a cancer (such as a myeloid malignancy, a non- myeloid leukemia, or a solid tumor cancer) or enhance the cross-reactivity of the antibody for a second cancer (such as a myeloid malignancy, a non-myeloid leukemia, or a solid tumor cancer) or other non-myeloid related pathology. Methods for performing affinity maturation are known in the art. See, e.g., Renaut et al., Methods Mol Biol, 2012, 907:451-461. id="p-137"
[0137]Antibody molecules can also be single domain antibodies. Single domain antibodies can include antibodies whose complementary determining regions are part of a single domain polypeptide. Examples include, but are not limited to, heavy chain antibodies, antibodies naturally devoid of light chains, single domain antibodies derived from conventional 4-chain antibodies, engineered antibodies and single domain scaffolds other than those derived from antibodies. Single domain antibodies may be any of the art, or any future single domain antibodies. Single domain antibodies may be derived from any species including, but not limited to mouse, rat, guinea, pig, human, camel, llama, fish, shark, goat, rabbit, and bovine. 40US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) Single domain antibodies are described, for example, in International Application Publication No. WO 94/04678. For clarity reasons, this variable domain derived from a heavy chain antibody naturally devoid of light chain is known herein as a VHH or nanobody to distinguish it from the conventional VH of four chain immunoglobulins. Such a VHH molecule can be derived from antibodies raised in Camelidae species (e.g., camel, llama, dromedary, alpaca and guanaco) or other species besides Camelidae. id="p-138"
[0138]In some embodiments, an antigen binding fragment can also be or can also comprise, e.g., a non-antibody, scaffold protein. These proteins are generally obtained through combinatorial chemistry-based adaptation of preexisting antigen-binding proteins. For example, the binding site of human transferrin for human transferrin receptor can be diversified using the system described herein to create a diverse library of transferrin variants, some of which have acquired affinity for different antigens. See, e.g., Ali et al. (1999) J. Biol. Chern. 274:24066-24073. The portion of human transferrin not involved with binding the receptor remains unchanged and serves as a scaffold, like framework regions of antibodies, to present the variant binding sites. The libraries are then screened, as an antibody library is screened, and in accordance with the methods described herein, against a target antigen of interest to identify those variants having optimal selectivity and affinity for the target antigen. See, e.g., Hey et al. (2005) TRENDS Biotechnol 23(10):514-522. id="p-139"
[0139]Synthetic antibodies of this disclosure may differ from naturally occurring compositions in at least one or more of the following respects: (i) composition comprises antibodies that are purified, i.e., separated from tissue or cellular material with which they are associated in the human body, and optionally in an manufactured excipient or medium; and/or (ii) antibody compositions according to the present disclosure contain a single species of antibody (are monoclonal) such that all antibodies in the composition have the same structure and specificity.
A. Expression and Purification of Antibodies id="p-140"
[0140]The CG1/HLA-A2 complex-specific antibodies or antigen binding fragments thereof disclosed herein may be produced by recombinant expression in a human or non-human cell. Synthetic antibody-producing cells include non-human cells expressing heavy chains, light chains, or both heavy and light chains; human cells that are not immune cells; heavy chains, light chains, or both heavy and light chains; and human B cells that produce heavy chains or light chains, but not both heavy and light chains. Synthetic antibodies of this disclosure may 41US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) be heterologously expressed, in vitro or in vivo, in cells other than human B cells, such as non- human cells and human cells other than B cells, optionally other than immune cells, and optionally in cells other than cells in a B cell lineage. id="p-141"
[0141]The CG1/HLA-A2 complex-specific antibodies or antigen binding fragments thereof disclosed herein (or bispecific antibodies disclosed herein) can be produced using a variety of techniques known in the art of molecular biology and protein chemistry. For example, a nucleic acid encoding the antibody or antigen binding fragment thereof can be inserted into an expression vector that contains transcriptional and translational regulatory sequences, which include, e.g., promoter sequences, ribosomal binding sites, transcriptional start and stop sequences, translational start and stop sequences, transcription terminator signals, polyadenylation signals, and enhancer or activator sequences. The regulatory sequences include a promoter and transcriptional start and stop sequences. In addition, the expression vector can include more than one replication system, such that it can be maintained in two different organisms, for example, in mammalian or insect cells for expression and in a prokaryotic host for cloning and amplification. id="p-142"
[0142]Several possible vector systems are available for the expression of cloned heavy chain and light chain polypeptides from nucleic acids in mammalian cells. One class of vectors relies upon the integration of the desired gene sequences into the host cell genome. Cells that have stably integrated DNA can be selected by simultaneously introducing drug resistance genes such as E. coli gpt (Mulligan and Berg (1981) Proc Natl Acad Sci USA 78:2072) or TnS neo (Southern and Berg (1982) Mol Appl Genet 1:327). The selectable marker gene can be either linked to the DNA gene sequences to be expressed or introduced into the same cell by co- transfection (Wigler et al. (1979) Cell 16:77). A second class of vectors utilizes DNA elements that confer autonomously replicating capabilities to an extrachromosomal plasmid. These vectors can be derived from animal viruses, such as bovine papillomavirus (Sarver et al. (1982) Proc Natl Acad Sci USA, 79:7147), CMV, polyoma virus (Deans et al. (1984) Proc Natl Acad Sci USA 81:1292), or SV40 virus (Lusky and Botchan (1981) Nature 293:79). id="p-143"
[0143]The expression vectors can be introduced into cells in a manner suitable for subsequent expression of the nucleic acid. The method of introduction is largely dictated by the targeted cell type, discussed below. Exemplary methods include CaPO4 precipitation, liposome fusion, cationic liposomes, electroporation, nucleoporation, viral infection, dextran- 42US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) mediated transfection, polybrene-mediated transfection, protoplast fusion, and direct microinjection. id="p-144"
[0144]Appropriate host cells for the expression of antibodies or antigen binding fragments thereof include yeast, bacteria, insect, plant, and mammalian cells. Of particular interest are bacteria such as E. coli, fungi such as Saccharomyces cerevisiae and Pichia pastoris, insect cells such as SF9, mammalian cell lines (e.g., human cell lines), as well as primary cell lines. id="p-145"
[0145]In some embodiments, an antibody or fragment thereof can be expressed in, and purified from, transgenic animals (e.g., transgenic mammals). For example, an antibody can be produced in transgenic non-human mammals (e.g., rodents) and isolated from milk as described in, e.g., Houdebine (2002) Curr Opin Biotechnol 13(6):625-629; van Kuik-Romeijn et al. (2000) Transgenic Res 9(2): 155-159; and Pollock et al. (1999) J Immunol Methods 231(1- 2):147-157. id="p-146"
[0146]The antibodies and fragments thereof can be produced from the cells by culturing a host cell transformed with the expression vector containing nucleic acid encoding the antibodies or fragments, under conditions, and for an amount of time, sufficient to allow expression of the proteins. Such conditions for protein expression vary with the choice of the expression vector and the host cell and are easily ascertained by one skilled in the art through routine experimentation. For example, antibodies expressed in E. coli can be refolded from inclusion bodies (see, e.g., Hou et al. (1998) Cytokine 10:319-30). Bacterial expression systems and methods for their use are known in the art (see Ausubel et al. (1988) Current Protocols in Molecular Biology, Wiley & Sons; and Green and Sambrook (2012) Molecular Cloning—A Laboratory Manual, 4th Ed., Cold Spring Harbor Laboratory Press, New York (2001)). The choice of codons, suitable expression vectors and suitable host cells vary depending on a number of factors and may be easily optimized as needed. An antibody (or fragment thereof) described herein can be expressed in mammalian cells or in other expression systems including but not limited to yeast, baculovirus, and in vitro expression systems (see, e.g., Kaszubska et al. (2000) Protein Expression and Purification 18:213-220). id="p-147"
[0147]In vitro methods are also suitable for preparing monovalent antibodies, or fragments thereof. Digestion of antibodies to produce fragments thereof, particularly, Fab fragments, can be accomplished using routine techniques known in the art. For instance, digestion can be performed using papain. Examples of papain digestion are described in International Application Publication No. WO 94/29348, U.S. Patent No. 4,342,566, and Harlow and Lane, 43US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) Antibodies, A Laboratory Manual, Cold Spring Harbor Publications, New York, (1988). Papain digestion of antibodies typically produces two identical antigen binding fragments, called Fab fragments, each with a single antigen binding site, and a residual Fc fragment. Pepsin treatment yields a fragment, called the F(ab ’)2 fragment that has two antigen combining sites and is still capable of cross-linking antigen. id="p-148"
[0148]The Fab fragments produced in antibody digestion can also contain the constant domains of the light chain and the first constant domain of the heavy chain. Fab ’ fragments differ from Fab fragments by the addition of a few residues at the carboxy terminus of the heavy chain domain including one or more cysteines from the antibody hinge region. The F(ab ’)2 fragment is a bivalent fragment comprising two Fab ’ fragments linked by a disulfide bridge at the hinge region. Fab ’-SH is the designation herein for Fab ’ in which the cysteine residue(s) of the constant domains bear a free thiol group. id="p-149"
[0149]One method of producing proteins comprising the provided antibodies or fragments is to link two or more peptides or polypeptides together by protein chemistry techniques (or recombinant DNA techniques). For example, peptides or polypeptides can be chemically synthesized using currently available laboratory equipment using either Fmoc (9- fluorenylmethyl-oxycarbonyl) or Boc (tert-butyloxycarbonoyl) chemistry (Applied Biosystems, Inc.; Foster City, CA). Those of skill in the art readily appreciate that a peptide or polypeptide corresponding to the antibody provided herein, for example, can be synthesized by standard chemical reactions. For example, a peptide or polypeptide can be synthesized and not cleaved from its synthesis resin whereas the other fragment of an antibody can be synthesized and subsequently cleaved from the resin, thereby exposing a terminal group that is functionally blocked on the other fragment. By peptide condensation reactions, these two fragments can be covalently joined via a peptide bond at their carboxyl and amino termini, respectively, to form an antibody, or fragment thereof. (Grant GA (1992) Synthetic Peptides: A User Guide. W.H. Freeman and Co., N.Y. (1992); Bodansky M and Trost B., Ed. (1993) Principles of Peptide Synthesis. Springer Verlag Inc., NY). Alternatively, the peptide or polypeptide can by independently synthesized in vivo. Once isolated, these independent peptides or polypeptides may be linked to form an antibody or fragment thereof via similar peptide condensation reactions. id="p-150"
[0150]For example, enzymatic ligation of cloned or synthetic peptide segments can allow relatively short peptide fragments to be joined to produce larger peptide fragments, 44US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) polypeptides, or whole protein domains (Abrahmsen et al., Biochemistry, 30:4151 (1991)). Alternatively, native chemical ligation of synthetic peptides can be utilized to synthetically construct large peptides or polypeptides from shorter peptide fragments. This method consists of a two-step chemical reaction (Dawson et al., Science, 266:776 779 (1994)). The first step is the chemo selective reaction of an unprotected synthetic peptide a thioester with another unprotected peptide segment containing an amino terminal Cys residue to give a thioester linked intermediate as the initial covalent product. Without a change in the reaction conditions, this intermediate undergoes spontaneous, rapid intramolecular reaction to form a native peptide bond at the ligation site. Application of this native chemical ligation method to the total synthesis of a protein molecule is illustrated by the preparation of human interleukin 8 (IL-8) (Baggiolini et al., FEES Lett. 307:97-101 (1992); Clark et al., J.Biol. Chern. 269:16075 (1994); Clark et al., Biochemistry 30:3128 (1991); Rajarathnam et al., Biochemistry 33:6623-(1994)). id="p-151"
[0151]Alternatively, unprotected peptide segments can be chemically linked where the bond formed between the peptide segments as a result of the chemical ligation is an unnatural (non- peptide) bond (Schnolzer et al., Science 256:221 (1992)). This technique has been used to synthesize analogs of protein domains as well as large amounts of relatively pure proteins with full biological activity (deLisle et al., Techniques in Protein Chemistry IV. Academic Press, New York, pp. 257-267 (1992)). id="p-152"
[0152]Recombinant techniques can also be used to modify antibodies or antigen binding fragments thereof. For example, amino acids found to not contribute to either the activity or the binding specificity or affinity of the antibody can be deleted without a loss in the respective activity. Insertions, deletions, substitutions, or other selected modifications of particular regions or specific amino acids residues can also be made (and are contemplated by the present disclosure), provided the activity of the fragment is not significantly altered or impaired compared to the non-modified antibody, or antigen binding fragment thereof can be made. Such methods are readily apparent to a skilled practitioner in the art and can include site specific mutagenesis of the nucleic acid encoding the antibody or fragment thereof. (Zoller et al., Nucl. Acids Res. 10:6487-500 (1982)). id="p-153"
[0153]Following expression, the antibodies and fragments thereof can be isolated. An antibody or fragment thereof can be isolated or purified in a variety of ways known in the art depending on what other components are present in the sample. Standard purification methods 45US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) include electrophoretic, molecular, immunological, and chromatographic techniques, including ion exchange, hydrophobic, affinity, and reverse-phase HPLC chromatography. For example, an antibody can be purified using a standard anti-antibody column (e.g., a protein-A or protein- G column). Ultrafiltration and diafiltration techniques, in conjunction with protein concentration, are also useful. See, e.g., Scopes (1994) Protein Purification, 3rd edition, Springer-Verlag, New York City, New York. The degree of purification necessary varies depending on the desired use. In some instances, no purification of the expressed antibody or fragments thereof is necessary. id="p-154"
[0154]Methods for determining the yield or purity of a purified antibody or fragment thereof are known in the art and include, e.g., Bradford assay, UV spectroscopy, Biuret protein assay, Lowry protein assay, amido black protein assay, high pressure liquid chromatography (HPLC), mass spectrometry (MS), and gel electrophoretic methods (e.g., using a protein stain such as Coomassie Blue or colloidal silver stain).
B. Modification of Antibodies id="p-155"
[0155]Any of the antibodies or antigen binding fragments thereof described herein can be modified. The modifications can be covalent or non-covalent modifications, and can include one or more amino acid substitutions that change the properties of the antigen-specific antibodies or antigen binding fragments thereof. Such modifications can be introduced into the antibodies or antigen binding fragments by, e.g., reacting targeted amino acid residues of the polypeptide with an organic derivatizing agent that is capable of reacting with selected side chains or terminal residues, or base-pair mutations in a nucleotide sequence encoding the antigen-specific antibodies or antigen binding fragments thereof. Suitable sites for modification can be chosen using any of a variety of criteria including, e.g., structural analysis or amino acid sequence analysis of the antibodies or fragments. In some instances, the CG1/HLA-A2 complex-specific antibodies or antigen binding fragments may be labeled by a variety of means for use in diagnostic and/or pharmaceutical applications. id="p-156"
[0156]In some embodiments, the antibodies or antigen binding fragments thereof described herein may have a modification comprising one or more amino acid substitutions that provide reduced hydrophobicity and reduce the potential for aggregation, thereby improving the binding or therapeutic capacity of an antibody or an antigen-binding fragment thereof. Such amino acid substitutions can be introduced by changing one or more nucleotides in the polynucleotide encoding the antibody or antigen-binding fragment such that the triplet codon 46US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) for the amino acid residue position where the modification is to be introduced is replaced with the triplet codon encoding the amino acid substitution. In some embodiments, the modification may comprise a single amino acid substitution. In some embodiments, the modification may comprise multiple amino acid substitutions. In some embodiments, the modification may be a substitution of 1 amino acid, 2 amino acids, 3 amino acids, 4 amino acids, or 5 amino acids. In some embodiments, the amino acid substitution may be located in a CDR. For example, the amino acid substitution may be located in heavy chain variable region CDR2 sequence of an antibody or antigen binding fragment provided in this disclosure. In some embodiments, the amino acid substitution can be at the 5th or 6th position (from N terminus to C terminus) of the heavy chain variable region CDR2 sequence of an antibody or antigen binding fragment provided in this disclosure. In some embodiments, the amino acid substitution can be at the 5th or 6th position (from N terminus to C terminus) of the heavy chain variable region CDRsequence of SEQ ID NO:82 of an antibody or antigen binding fragment provided in this disclosure. In some embodiments, the amino acid substitution can be at the 5th or 6th position (from N terminus to C terminus) of the heavy chain variable region CDR2 sequence of SEQ ID NO:82 of an antibody or antigen binding fragment provided in this disclosure, wherein the antibody or antigen binding fragment further comprises a heavy chain variable region CDRI of SEQ ID NO:71 and a heavy chain variable region CDR3 of SEQ ID NO:90. In some embodiments, the amino acid substitution can be at the 5th or 6th position (from N terminus to C terminus) of the heavy chain variable region CDR2 sequence of SEQ ID NO:82 of an antibody or antigen binding fragment provided in this disclosure, wherein the heavy chain variable region comprises at least 90% identity to SEQ ID NO:7. In some embodiments, the amino acid substitution can be at the 5th or 6th position (from N terminus to C terminus) of the heavy chain variable region CDR2 sequence of SEQ ID NO:82 of an antibody or antigen binding fragment provided in this disclosure, wherein the heavy chain variable region comprises at least 90% identity to SEQ ID NO:7, and wherein the antibody or antigen binding fragment comprises a light chain variable region comprising at least 90% identity to SEQ ID NO:34. In some embodiments, the amino acid mutations may include aspartic acid to serine modification. In some embodiments, the modification may include an alanine to glycine. One skilled in the art may understand that any modification to the antibody sequence that reduced the hydrophobicity of an amino acid sequence may fall under the scope of such modifications. Described above modifications are provided herein not to limit the scope of the invention but merely provided as examples of modifying an amino acid sequence for altering the hydrophobicity. 47US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-157"
[0157]In some embodiments, the antibodies or antigen binding fragments thereof can be conjugated to a heterologous moiety. The heterologous moiety can be, e.g., a heterologous polypeptide, a therapeutic agent (e.g., a toxin or a drug), or a detectable label such as, but not limited to, a radioactive label, an enzymatic label, a fluorescent label, a heavy metal label, a luminescent label, or an affinity tag such as biotin or streptavidin. Suitable heterologous polypeptides include, e.g., an antigenic tag (e.g., FLAG (DYKDDDDK) (SEQ ID NO:58), polyhistidine (6-His; HHHHHH (SEQ ID NO:59)), hemagglutinin (HA; YPYDVPDYA (SEQ ID NO:60)), glutathione-S-transferase (GST), or maltose-binding protein (MBP)) for use in purifying the antibodies or fragments. Heterologous polypeptides also include polypeptides (e.g., enzymes) that are useful as diagnostic or detectable markers, for example, luciferase, a fluorescent protein (e.g., green fluorescent protein (GFP)), or chloramphenicol acetyl transferase (CAT). Suitable radioactive labels include, e.g., 32P, 33P, 14c, 125I, 131I, 35s, and 3H. Suitable fluorescent labels include, without limitation, fluorescein, fluorescein isothiocyanate (FITC), green fluorescent protein (GFP), DyLight™ 488, phycoerythrin (PE), propidium iodide (PI), PerCP, PE-Alexa Fluor® 700, Cy5, allophycocyanin, and Cy7 . Luminescent labels include, e.g., any of a variety of luminescent lanthanide (e.g., europium or terbium) chelates. For example, suitable europium chelates include the europium chelate of di ethylene triamine pentaacetic acid (DTPA) or tetraazacyclododecane- 1,4,7,1 O-tetraacetic acid (DOTA). Enzymatic labels include, e.g., alkaline phosphatase, CAT, luciferase, and horseradish peroxidase. Another labeling technique which may result in greater sensitivity consists of coupling the antibodies to low molecular weight haptens. These haptens can then be specifically altered by means of a second reaction. For example, it is common to use haptens such as biotin, which reacts with avidin, or dinitrophenol, pyridoxal, or fluorescein, which can react with specific anti-hapten antibodies. id="p-158"
[0158]Two proteins (e.g., an antibody and a heterologous moiety) can be cross-linked using any of a number of known chemical cross linkers. Examples of such cross linkers are those that link two amino acid residues via a linkage that includes a "hindered " disulfide bond. In these linkages, a disulfide bond within the cross-linking unit is protected (by hindering groups on either side of the disulfide bond) from reduction by the action, for example, of reduced glutathione or the enzyme disulfide reductase. One suitable reagent, 4- succinimidyloxycarbonyl-a-methyl-a(2-pyridyldithio) toluene (SMPT), forms such a linkage between two proteins utilizing a terminal lysine on one of the proteins and a terminal cysteine on the other. Heterobifunctional reagents that cross-link by a different coupling moiety on each 48US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) protein can also be used. Other useful cross-linkers include, without limitation, reagents which link two amino groups (e.g., N-5-azido-2-nitrobenzoyloxysuccinimide), two sulfhydryl groups (e.g., 1,4-bis-maleimidobutane), an amino group and a sulfhydryl group (e.g., m- maleimidobenzoyl-N-hydroxysuccinimide ester), an amino group and a carboxyl group (e.g., 4-[p-azidosalicylamido]butylamine), and an amino group and a guanidinium group that is present in the side chain of arginine (e.g., p-azidophenyl glyoxal monohydrate). id="p-159"
[0159]In some embodiments, a radioactive label can be directly conjugated to the amino acid backbone of the antibody. Alternatively, the radioactive label can be included as part of a larger molecule (e.g., 125I in meta-[ 125I]iodophenyl-N-hydroxysuccinimide ([1251]mIPNHS), which binds to free amino groups to form meta-iodophenyl (mIP) derivatives of relevant proteins (see, e.g., Rogers et al. (1997) JNuclMed 38:1221-1229) or chelate (e.g., to DOTA or DTP A), which is in turn bound to the protein backbone. Methods of conjugating the radioactive labels or larger molecules/chelates containing them to the antibodies or antigen binding fragments described herein are known in the art. Such methods involve incubating the proteins with the radioactive label under conditions (e.g., pH, salt concentration, and/or temperature) that facilitate binding of the radioactive label or chelate to the protein (see, e.g., U.S. Patent No. 6,001,329). id="p-160"
[0160]Methods for conjugating a fluorescent label (sometimes referred to as a fluorophore) to a protein (e.g., an antibody) are known in the art of protein chemistry. For example, fluorophores can be conjugated to free amino groups (e.g., of lysines) or sulfhydryl groups (e.g., cysteines) of proteins using succinimidyl (NHS) ester or tetrafluorophenyl (TFP) ester moieties attached to the fluorophores. In some embodiments, the fluorophores can be conjugated to a heterobifunctional cross-linker moiety such as sulfo-SMCC. Suitable conjugation methods involve incubating an antibody protein or fragment thereof with the fluorophore under conditions that facilitate binding of the fluorophore to the protein. See, e.g., Welch and Redvanly (2003) Handbook of Radiopharmaceuticals: Radiochemistry and Applications, John Wiley and Sons. id="p-161"
[0161]In some embodiments, the antibodies or fragments can be modified, e.g., with a moiety that improves the stabilization and/or retention of the antibodies in circulation, e.g., in blood, serum, or other tissues. For example, the antibody or fragment can be PEGylated as described in, e.g., Lee et al. (1999) Bioconjug Chern 10(6): 973-8; Kinstler et al. (2002) Advanced Drug Deliveries Reviews 54:477-485; and Roberts et al. (2002) Advanced Drug 49US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) Delivery Reviews 54:459-476, or HESylated (Fresenius Kabi, Germany) (see, e.g., Pavisic et al. (2010) Int JPharm 387(1-2): 110-119). The stabilization moiety can improve the stability, or retention of, the antibody (or fragment) by at least 1.5 (e.g., at least 2, 5, 10, 15, 20, 25, 30, 40, or 50 or more) fold. id="p-162"
[0162]In some embodiments, the antibodies or antigen-binding fragments thereof described herein can be glycosylated. In some embodiments, an antibody or antigen-binding fragment thereof described herein can be subjected to enzymatic or chemical treatment, or produced from a cell, such that the antibody or fragment has reduced or absent glycosylation. Methods for producing antibodies with reduced glycosylation are known in the art and described in, e.g., U.S. Patent No. 6,933,368; Wright et al. (1991) EMBO J 10(10):2717-2723; and Co et al. (1993) Mol Immunol 30:1361.
V. CHIMERIC ANTIGEN RECEPTORS id="p-163"
[0163]Also provided herein are chimeric antigen receptors comprising any of the antibodies or antigen-binding fragments described above. Chimeric antigen receptors (CARs, also known as chimeric T cell receptors) are designed to be expressed in host effector cells, e.g., T cells or NK cells, and to induce an immune response against a specific target antigen and cells expressing that antigen. Adoptive T cell immunotherapy, in which a patient ’s own T lymphocytes are engineered to express CARs, has shown great promise in treating hematological malignancies. CARs can be engineered and used as described, for example, in Sadelain et al., 2013, Cancer Discov. 3:388-398. A CAR typically comprises an extracellular target-binding module, a transmembrane (TM) domain, and an intracellular signaling domain (ICD). The CAR domains can be joined via flexible hinge and/or spacer regions. The extracellular target-binding module generally comprises an antibody or antigen binding fragment thereof. In some instances, multiple binding specificities can be included in the extracellular target-binding module. For example, multiple antibodies or antigen binding fragments thereof that target different antigens can be included to produce bi-specific, tri- specific, or quad-specific CARs. Transmembrane (TM) domains are primarily considered a structural requirement, anchoring the CAR in the cell membrane, and are most commonly derived from molecules regulating T cell function, such as CD8 and CD28. The intracellular module typically consists of the T cell receptor CD3(؛ chain and one or more costimulatory domains from either the ig (CD28-like) or TNF receptor (TNFR) superfamilies. CARs containing either CD28 or 4-IBB costimulatory domains have been the most widely used, to 50US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) date, and both of them have yielded dramatic responses in clinical trials. CAR domains are discussed in more detail below. id="p-164"
[0164]Provided herein are chimeric antigen receptors comprising: (a) an extracellular target- binding domain comprising a CG1/HLA-A2 complex-specific antibody or antigen binding portion thereof; (b) a transmembrane domain; and (c) a signaling domain. id="p-165"
[0165]The extracellular target-binding module of a CAR may comprise an antibody or an antigen-binding fragment thereof that specifically binds a target antigen (e.g., CG1/HLA-Acomplex). The extracellular target-binding module of a CAR may comprise a bispecific antibody or an antigen-binding fragment thereof that specifically binds two different target antigens (e.g., CG1/HLA-A2 complex and a second antigen, for example, CD3). In some embodiments, the extracellular target-binding domain of the CARs provided herein can comprise the sequence of any of the antigen binding portions (i.e. domains) described in Section IV of this disclosure. id="p-166"
[0166]In certain embodiments, the extracellular target-binding domain can be a single-chain variable fragment derived from an antibody (scFv), a tandem scFv, a single-domain antibody fragment (VhHs or sdAbs), a single domain bispecific antibody (BsAbs), an intrabody, a nanobody, an immunokine in a single chain format, and Fab, Fab ’, or (Fab ’)2 in a single chain format. In other embodiments, the extracellular target-binding domain can be an antibody moiety that comprises covalently bound multiple chains of variable fragments. In some embodiments, the extracellular target-binding domain comprises any of the antibodies or antigen-binding portions thereof described above. In some embodiments, the extracellular target-binding domain comprises a scFv comprising a heavy chain variable region comprising an amino acid sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 1-27, 133, or 1and a light chain variable region comprising an amino acid sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 28-54, or 132. In some embodiments, the scFv comprises a linker polypeptide between the heavy chain and light chain sequences (e.g., SEQ ID NO:54 or any of the other linkers described herein). In some embodiments, the CAR comprises a scFv comprising an amino acid sequence that is at least 90% identical to SEQ ID NOs: 55-57. In certain embodiments, the extracellular target-binding domain comprises at least one or more VH CDRs of any one of SEQ ID NOs: 67-93 (or any other VH CDR sequence as described 51US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) herein)(or any other VH CDR sequence as described herein, or any combination of any CDRI, CDR2, CDR3 thereof). In certain embodiments, the extracellular target-binding domain comprises at least one or more VL CDRs of any one of SEQ ID NOs: 96-123 (or any other VL CDR sequence as described herein, ior any combination of any CDR1, CDR2, CDR3 thereof). id="p-167"
[0167]In some embodiments, the extracellular target-binding domains of the CARs provided herein further comprise one or more additional antigen-binding domains (i.e., in addition to the CG1/HLA-A2 complex-specific antibody or antigen binding portion thereof, as described above). In some embodiments, the extracellular target-binding domain comprises at least one additional antigen-binding domain. CARs comprising such an extracellular target-binding domain can be referred to as bi-specific CARs. In some embodiments, the additional antigen- binding domains specifically bind to CD3. In embodiments, for example, CAR scFv sequences can be redesigned as a T-cell engaged bi-specific antibody by linking, for example and without intending to be limiting, an anti-CD3 antibody. id="p-168"
[0168]CARs as described herein can comprise a transmembrane domain and an intracellular domain. In certain aspects, the transmembrane domain is a short hydrophobic region that can anchor the CAR in the cell membrane and helps to stabilize its structure. The transmembrane domain of a CAR provided herein may be derived from either a natural or from a synthetic source. Where the source is natural, the domain may be derived from any membrane-bound or transmembrane protein. In some embodiments, the transmembrane domain is derived from (z.e., comprises at least the transmembrane region(s) of) the a, P, 5, y, or £ chain of the T-cell receptor, CD28, CD3e, CD3، CD45, CD4, CDS, CDS, CD9, CD16, CD22, CD30, CD33, CD37, CD64, CD80, CD86, CD134, CD137, or CD154. In embodiments, the transmembrane domain is a CD8a or CD28 transmembrane domain. In some embodiments, a transmembrane domain can be chosen based on, for example, the nature of the various other proteins or trans- elements that bind the transmembrane domain or the cytokines induced by the transmembrane domain. In some embodiments, the transmembrane domain comprises a CD8a transmembrane domain. When a transmembrane domain is synthetic, it may comprise predominantly hydrophobic residues such as leucine and valine. In some embodiments, a triplet of phenylalanine, tryptophan, and valine may be found at each end of a synthetic transmembrane domain. In some embodiments, a short oligo- or polypeptide linker, having a length of, for example, between about 2 and about 10 (such as about any of 2, 3, 4, 5, 6, 7, 8, 9, or 10) amino acids in length may form the linkage between the transmembrane domain and the intracellular 52US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) signaling domain of a CAR described herein. In some embodiments, the linker is a glycine- serine doublet. id="p-169"
[0169]The intracellular signaling domain of the CAR is responsible for activation of at least one of the normal effector functions of the immune cell in which the CAR has been placed in or is designed to be placed in. An effector function of a T cell may be, for example, cytolytic activity or helper activity, including the secretion of cytokines. Thus the term "intracellular signaling domain " refers to the portion of a protein which transduces the effector function signal and directs the cell to perform a specialized function. While usually the entire intracellular signaling domain can be employed, in many cases it is not necessary to use the entire chain. To the extent that a truncated portion of the intracellular signaling domain is used, such truncated portion may be used in place of the intact chain as long as it transduces the effector function signal. The term "intracellular signaling sequence " is thus meant to include any truncated portion of the intracellular signaling domain sufficient to transduce the effector function signal. id="p-170"
[0170]Examples of intracellular signaling domains for use in the CARs provided herein include the cytoplasmic sequences of the T cell receptor (TCR) and co-receptors that act in concert to initiate signal transduction following antigen receptor engagement, as well as any derivative or variant of these sequences and any synthetic sequence that has the same functional capability. In certain aspects, the intracellular signaling domain for use in CARs as described herein is a region of the CAR that can be located inside a T cell and is responsible for transmitting signals to the cell. There can be one or more signaling domains, which can vary depending on the design of the CAR. In certain aspects, the signaling domain is the CD3(؛ domain, which is found in the T cell receptor (TCR) complex and is responsible for activating T cells, and one or more co-stimulatory domains, such as CD28, 4-1BB, or OX40. These co- stimulatory domains can enhance the activation and proliferation of CAR-T cells, as well as improve their persistence and anti-tumor activity. id="p-171"
[0171]It is known that signals generated through the TCR alone are insufficient for full activation of the T cell and that a secondary or costimulatory signal is also required. Thus, T cell activation can be said to be mediated by two distinct classes of intracellular signaling sequence: those that initiate antigen-dependent primary activation through the TCR (primary signaling sequences) and those that act in an antigen-independent manner to provide a secondary or costimulatory signal (costimulatory signaling sequences). 53US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-172"
[0172]Primary signaling sequences regulate primary activation of the TCR complex either in a stimulatory way, or in an inhibitory way. Primary signaling sequences that act in a stimulatory manner may contain signaling motifs which are known as immunoreceptor tyrosine-based activation motifs or ITAMs. In some embodiments, the CARs described herein comprise one or more ITAMs. id="p-173"
[0173]Examples of ITAM containing primary signaling sequences that are of particular use in the invention include those derived from TCRY, FcRy, FeRP, CD3y, CD35, CD3s, CD3، CDS, CD22, CD79a, CD79b, and CD66d. In some embodiments, an ITAM containing primary signaling sequence is derived from CD3؛. id="p-174"
[0174]In some embodiments, the CAR comprises a primary signaling sequence derived from CD3، For example, the intracellular signaling domain of the CAR can comprise the CD3(؛ intracellular signaling sequence by itself or combined with any other desired intracellular signaling sequence(s) useful in the context of the CAR of the invention. In some embodiments, the intracellular signaling domain of a CAR provided herein comprises a CD3(؛ primary intracellular signaling sequence and a 4-IBB costimulatory signaling sequence. id="p-175"
[0175]The CARs provided herein may include additional elements, such a signal peptide to ensure proper export of the fusion protein to the cells surface, a leader sequence, and a hinge domain that imparts flexibility to the recognition region and allows strong binding to the targeted moiety. In some embodiments, a spacer domain may be present between any of the domains of the CAR. The spacer domain can be any polypeptide that functions to link two parts of the CAR. A spacer domain may comprise up to about 300 amino acids, including for example about 10 to about 100, or about 25 to about 50 amino acids. Methods of identifying and selecting suitable spacer domains are known. In certain aspects, signal peptides can be used to direct the expression of the CAR to the cell surface. Embodiments of signal peptides that can be utilized in CAR-T cell design according to the present disclosure include (without intending to be limiting) the human CD8a signal peptide, the IgK signal peptide, and the CMV immediate-early promoter/enhancer signal peptide. In certain aspects, hinge domains can be flexible regions that connect the antigen-recognition domain and the intracellular signaling domains of the CAR. They can have a significant impact on the function and efficacy of the CAR-T cells, by affecting the flexibility and stability of the receptor, as well as its ability to recognize and engage with antigens. Embodiments of hinge domains that can be utilized in 54US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) CAR-T cell designs according to the present disclosure include the IgG4 hinge, the CD8a hinge, and the CD28 hinge. id="p-176"
[0176]In some embodiments, the CAR comprises at least one CG1/HLA-A2 complex- specific scFv domain as described in this disclosure; at least one hinge and/or transmembrane domain comprising CD8a, CD28 and/or, IgG4 Fc-CD28 (as the hinge and transmembrane domain); at least one costimulatory domain comprising CD28, 4-IBB, and/or OX40 (e.g., as described in this disclosure); and a CD3(؛ signaling domain (e.g., as described in this disclosure). In some embodiments, a CAR provided herein comprises a sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% 99%, or 100% identical identical) to SEQ ID NOs: 51, 60, 62, 64, or 66. In some embodiments, a CAR provided herein is encoded by a nucleic acid molecule comprising a nucleotide sequence that is at least 65% identical (for example, at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical) to SEQ ID NOs: 50, 59, 61, 63, or 65.
VI. ANTIBODY EXPRESSION AND PURIFICATION, NUCLEIC ACIDS, VECTORS, AND CELLS [0177]The CG1/HLA-A2 complex antibodies and antigen binding fragments thereof and molecules comprising such antibodies and antigen binding fragments thereof discussed above (e.g., Abs, bi-specific Abs, and CARs) may be produced by recombinant expression in a human or non-human cell. Synthetic antibody-producing cells include non-human cells expressing heavy chains, light chains, or both heavy and light chains; human cells that are not immune cells expressing heavy chains, light chains, or both heavy and light chains; and human B cells that produce heavy chains or light chains, but not both heavy and light chains. Synthetic antibodies of this disclosure may be heterologously expressed, in vitro or in vivo, in cells other than human B cells, such as non-human cells and human cells other than B cells, optionally other than immune cells, and optionally in cells other than cells in a B cell lineage. id="p-178"
[0178]The CG1/HLA-A2 complex antibodies and antigen binding fragments thereof and molecules comprising them described herein can be produced using a variety of techniques known in the art of molecular biology and protein chemistry. For example, a nucleic acid encoding the antibody or antigen binding fragment thereof or CAR can be inserted into an expression vector that contains transcriptional and translational regulatory sequences, which include, e.g., promoter sequences, ribosomal binding sites, transcriptional start and stop 55US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) sequences, translational start and stop sequences, transcription terminator signals, polyadenylation signals, and enhancer or activator sequences. The regulatory sequences include a promoter and transcriptional start and stop sequences. In addition, the expression vector can include more than one replication system, such that it can be maintained in two different organisms, for example, in mammalian or insect cells for expression and in a prokaryotic host for cloning and amplification. id="p-179"
[0179]Several possible vector systems are available for the expression of cloned heavy chain and light chain polypeptides from nucleic acids in mammalian cells. One class of vectors relies upon the integration of the desired gene sequences into the host cell genome. Cells that have stably integrated DNA can be selected by simultaneously introducing drug resistance genes such as E. coli gpt (Mulligan and Berg (1981) Proc Natl Acad Set USA 78:2072) or Tn5 neo (Southern and Berg (1982) Mol Appl Genet 1:327). The selectable marker gene can be either linked to the DNA gene sequences to be expressed or introduced into the same cell by co- transfection (Wigler et al. (1979) Cell 16:77). A second class of vectors utilizes DNA elements that confer autonomously replicating capabilities to an extrachromosomal plasmid. These vectors can be derived from animal viruses, such as bovine papillomavirus (Sarver et al. (1982) Proc Natl Acad Set USA, 79:7147), CMV, polyoma virus (Deans et al. (1984) Proc Natl Acad Set USA 81:1292), or SV40 virus (Lusky and Botchan (1981) Nature 293:79). id="p-180"
[0180]The expression vectors can be introduced into cells in a manner suitable for subsequent expression of the nucleic acid. The method of introduction is largely dictated by the targeted cell type, discussed below. Exemplary methods include CaPO4 precipitation, liposome fusion, cationic liposomes, electroporation, nucleoporation, viral infection, dextran- mediated transfection, polybrene-mediated transfection, protoplast fusion, and direct microinjection. id="p-181"
[0181]Appropriate host cells for the expression of antibodies or antigen binding fragments or CARs thereof include yeast, bacteria, insect, plant, and mammalian cells. Of particular interest are bacteria such as E. coli, fungi such as Saccharomyces cerevisiae and Pichia pastoris, insect cells such as SF9, mammalian cell lines (e.g., human cell lines), as well as primary cell lines. id="p-182"
[0182]In some embodiments, an antibody or fragment thereof or CAR can be expressed in, and purified from, transgenic animals (e.g., transgenic mammals). For example, an antibody can be produced in transgenic non-human mammals (e.g., rodents) and isolated from milk as 56US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) described in, e.g., Houdebine (2002) Curr Opin Biotechnol 13(6):625-629; van Kuik-Romeijn etal. (2000) Transgenic Res 9(2): 155-159; and Pollock et al. (1999) J Immunol Methods 23(- 2):147-157. id="p-183"
[0183]The antibodies and fragments thereof and CARs can be produced from the cells by culturing a host cell transformed with the expression vector containing nucleic acid encoding the antibodies or fragments, under conditions, and for an amount of time, sufficient to allow expression of the proteins. Such conditions for protein expression vary with the choice of the expression vector and the host cell and are easily ascertained by one skilled in the art through routine experimentation. For example, antibodies expressed in E. coli can be refolded from inclusion bodies (see, e.g., Hou et al. (1998) Cytokine 10:319-30). Bacterial expression systems and methods for their use are known in the art (see Ausubel et al. (1988) Current Protocols in Molecular Biology, Wiley & Sons; and Green and Sambrook (2012) Molecular Cloning—A Laboratory Manual, 4th Ed., Cold Spring Harbor Laboratory Press, New York (2001)). The choice of codons, suitable expression vectors and suitable host cells vary depending on a number of factors, and may be easily optimized as needed. An antibody (or fragment thereof) described herein can be expressed in mammalian cells or in other expression systems including but not limited to yeast, baculovirus, and in vitro expression systems (see, e.g., Kaszubska et al. (2000) Protein Expression and Purification 18:213-220). Additional discussion of expression vectors for use in eukaryotic cells (e.g., for treating a subject with cancer), along with suitable delivery systems, is provided in Section VIII. A, below. id="p-184"
[0184]Also provided herein are nucleic acid molecules encoding a CG1/HLA-A2 complex antibody or antigen binding portion thereof or CAR that binds specifically to CG1/HLA-Acomplex as described in this disclosure. id="p-185"
[0185]In some embodiments, provided are nucleic acid molecules encoding a CG1/HLA- A2 complex antibody or antigen binding fragment thereof or CAR comprising a heavy chain variable comprising an amino acid sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 1-27, 133, or 134 and a light chain variable region comprising an amino acid sequence that is at least 90% identical to any one of SEQ ID NOs: 28-54, or 132. In some embodiments, provided are nucleic acid molecules encoding a CG1/HLA-A2 complex antibody or antigen binding fragment thereof or CAR comprising a heavy chain variable comprising an amino acid sequence that is at least 90% identical to any of SEQ ID NOs: 1-27, 133, or 134. In some 57US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) embodiments, provided are nucleic acid molecules encoding a CG1/HLA-A2 complex antibody or antigen binding fragment thereof comprising a light chain variable region comprising an amino acid sequence that is at least 90% identical to any one of SEQ ID NOs: 28-54, or 132. In some embodiments, provided are nucleic acid molecules encoding a CG1/HLA-A2 complex antibody or antigen binding fragment thereof comprising one or more heavy chain CDRs comprising an amino acid sequence that is at least 90% identical to any one of SEQ ID NOs: 67-93. In some embodiments, provided are nucleic acid molecules encoding a CG1/HLA-A2 complex antibody or antigen binding fragment thereof comprising one or more heavy chain CDRs comprising an amino acid sequence that is at least 90% identical to any one of SEQ ID NOs: 67, 71, 75, 79, 82, 90, or 92. In some embodiments, provided are nucleic acid molecules encoding a CG1/HLA-A2 complex antibody or antigen binding fragment thereof comprising one or more light chain CDRs comprising an amino acid sequence that is at least 90% identical to any one of SEQ ID NOs: 99, 101, 108, 113, 116, or 120. In some embodiments, provided are nucleic acid molecules encoding a CG1/HLA-A2 complex antibody or antigen binding fragment thereof comprising one or more light chain CDRs comprising an amino acid sequence that is at least 90% identical to any one of SEQ ID NOs: 28-54, or 132. id="p-186"
[0186]In some embodiments, provided are nucleic acid molecules encoding antibodies or antigen binding fragments thereof or CAR that bind specifically to a CG1/HLA-A2 complex according to the present disclosure, wherein the nucleic acid sequences comprise sequences encoding an amino acid sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to any of the sequences as described herein. id="p-187"
[0187]In some embodiments, provided are nucleic acid molecules comprising a nucleotide sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to any of SEQ ID NOs: 126-128. id="p-188"
[0188]Also provided herein are nucleic acid molecules encoding a molecule comprising a CG1/HLA-A2 complex antibody or antigen binding portion thereof (e.g., a CAR) described above. In some embodiments, provided are nucleic acid molecules encoding any of the CARs described herein. In some embodiments, the nucleic acid molecule encodes a CAR that comprises a sequence that is at least 90% identical (for example, at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical) to SEQ ID NOs: 126-128. In some embodiments, 58US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) the nucleic acid molecule comprises a nucleotide sequence that is at least 65% identical (for example, at least 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical) to SEQ ID NOs: 126-128. id="p-189"
[0189]In some embodiments, the nucleic acid molecules encoding the CG1/HLA-Acomplex antibodies or antigen binding fragments thereof are synthetic sequences designed for expression in a host cell (for example, a human cell). id="p-190"
[0190]In some embodiments, the nucleic acid molecules encoding the CG1/HLA-Acomplex antibodies or antigen binding fragments thereof are operably linked to a promoter capable of directing expression in a bacterial cell or a eukaryotic cell. id="p-191"
[0191]The terms "polynucleotide " and "nucleic acid " interchangeably refer to chains of nucleotides of any length, and include DNA and RNA. The nucleotides can be deoxyribonucleotides, ribonucleotides, modified nucleotides or bases, and/or their analogs, or any substrate that can be incorporated into a chain by DNA or RNA polymerase. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and their analogs. Examples of polynucleotides contemplated herein include single- and double- stranded DNA, single- and double-stranded RNA, and hybrid molecules having mixtures of single- and double-stranded DNA and RNA. id="p-192"
[0192]The amino acid sequences of the CDRs and framework regions can be determined using various well-known definitions in the art, e.g., Rabat, Chothia, international ImMunoGeneTics database (IMGT), AbM, and observed antigen contacts ("Contact "). In some embodiments, CDRs are determined according to the IMGT definition. See, Brochet et al., 2008, Nucl. Acids Rex. 36:W503-508. In some embodiments, CDRs are determined by a combination of Rabat, Chothia, and/or Contact CDR definitions. id="p-193"
[0193]Also provided herein are DNA constructs comprising a promoter that drives expression in a host cell operably linked to a recombinant nucleic acid molecule comprising a nucleotide sequence that encodes a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof or CAR. id="p-194"
[0194]Also provided herein are vectors, discussed further below, comprising a DNA construct comprising a promoter that drives expression in a host cell operably linked to a recombinant nucleic acid molecule comprising a nucleotide sequence that encodes a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof or CAR. 59US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-195"
[0195]Also provided herein are host cells, including bacterial host cells and eukaryotic host cells, comprising a recombinant nucleic acid molecule encoding a CG1/HLA-A2 complex antibody or antigen binding fragment thereof or CAR as described in this disclosure. id="p-196"
[0196]Also provided herein are host cells that have been engineered to express and secrete a CG1/HLA-A2 complex antibody or antigen binding fragment thereof or CAR as described in this disclosure. In some embodiments, the cells are suitable for implanting in a patient with cancer. In some embodiments, the cells are animal or human cells, and can be autologous, heterologous, or xenogeneic. In certain embodiments, the cells can be immortalized. In certain embodiments, in order to decrease the chance of an immunological response, the cells can be encapsulated to avoid infiltration of surrounding tissues. In certain embodiments, the encapsulation materials are typically biocompatible, semi-permeable polymeric enclosures or membranes that allow the release of the protein product(s) but prevent the destruction of the cells by a subject ’s immune system or by other detrimental factors from the surrounding tissues. id="p-197"
[0197]Also provided herein are immune cells (e.g., T cells) expressing any of the CARs described herein. In some embodiments, the immune cell expresses the CAR on its surface. In some embodiments, the immune cell comprises a nucleic acid encoding the CAR, wherein the CAR is expressed from the nucleic acid and localized to the immune cell surface. In some embodiments, the immune cell a B-lymphocyte, T-lymphocyte, thymocyte, dendritic cell, natural killer (NK) cell, monocyte, macrophage, granulocyte, eosinophil, basophil, neutrophil, myelomonocytic cell, megakaryocyte, peripheral blood mononuclear cell, myeloid progenitor cell, or a hematopoietic stem cell. In some embodiments, the immune cell is a T cell. In some embodiments, the T cell is a cytotoxic T cell, a helper T cell, a natural killer T cell, a suppressor T cell, a CD8+T cell, a CD4+T cell, a CD8+/CD4+T cell, 5ץ T cell, or a T-regulatory (T-reg) cell. id="p-198"
[0198]In some embodiments, immune cells expressing a CAR provided herein are obtained from a subject. Where the immune cells are used to treat (e.g., according to the treatment methods described herein below) the same subject from which they are obtained, they are referred to as autologous cells. Where they are obtained from a different subject, they are referred to as heterologous cells or allogeneic (if derived from the same species as the subject). Immune cells can be isolated from peripheral blood using techniques well known in the art, include Ficoll density gradient centrifugation followed by negative selection to remove undesired cells. In some embodiments, heterologous immune cells useful for the methods 60US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) provided herein comprise allogeneic T cells, as described in, e.g., Bedoya et al., 2021, Front. Immunol. 12:640082. id="p-199"
[0199]In vitro methods are also suitable for preparing monovalent antibodies or antigen binding fragments thereof or CARs. Digestion of antibodies to produce fragments thereof, particularly, Fab fragments, can be accomplished using routine techniques known in the art. For instance, digestion can be performed using papain. Examples of papain digestion are described in International Application Publication No. WO 94/29348, U.S. Patent No. 4,342,566, and Harlow and Lane, Antibodies, A Laboratory Manual, Cold Spring Harbor Publications, New York, (1988). Papain digestion of antibodies typically produces two identical antigen binding fragments, called Fab fragments, each with a single antigen binding site, and a residual Fc fragment. Pepsin treatment yields a fragment, called the F(ab ’)2 fragment that has two antigen combining sites and is still capable of cross-linking antigen. id="p-200"
[0200]The Fab fragments produced in antibody digestion can also contain the constant domains of the light chain and the first constant domain of the heavy chain. Fab ’ fragments differ from Fab fragments by the addition of a few residues at the carboxy terminus of the heavy chain domain including one or more cysteines from the antibody hinge region. The F(ab ’)2 fragment is a bivalent fragment comprising two Fab ’ fragments linked by a disulfide bridge at the hinge region. Fab ’-SH is the designation herein for Fab ’ in which the cysteine residue(s) of the constant domains bear a free thiol group. id="p-201"
[0201]One method of producing proteins comprising the provided antibodies or fragments or CARs is to link two or more peptides or polypeptides together by protein chemistry techniques. For example, peptides or polypeptides can be chemically synthesized using currently available laboratory equipment using either Fmoc (9-fluorenylmethyl-oxycarbonyl) or Boc (tert-butyloxycarbonoyl) chemistry (Applied Biosystems, Inc.; Foster City, CA). Those of skill in the art readily appreciate that a peptide or polypeptide corresponding to the antibody provided herein, for example, can be synthesized by standard chemical reactions. For example, a peptide or polypeptide can be synthesized and not cleaved from its synthesis resin whereas the other fragment of an antibody can be synthesized and subsequently cleaved from the resin, thereby exposing a terminal group that is functionally blocked on the other fragment. By peptide condensation reactions, these two fragments can be covalently joined via a peptide bond at their carboxyl and amino termini, respectively, to form an antibody, or fragment thereof. (Grant GA (1992) Synthetic Peptides: A User Guide. W.H. Freeman and Co., N.Y. 61US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) (1992); Bodansky M and Trost B., Ed. (1993) Principles of Peptide Synthesis. Springer Verlag Inc., NY). Alternatively, the peptide or polypeptide can by independently synthesized in vivo. Once isolated, these independent peptides or polypeptides may be linked to form an antibody or fragment thereof via similar peptide condensation reactions. id="p-202"
[0202]For example, enzymatic ligation of cloned or synthetic peptide segments can allow relatively short peptide fragments to be joined to produce larger peptide fragments, polypeptides or whole protein domains (Abrahmsen et al., Biochemistry, 30:4151 (1991)). Alternatively, native chemical ligation of synthetic peptides can be utilized to synthetically construct large peptides or polypeptides from shorter peptide fragments. This method consists of a two-step chemical reaction (Dawson et al., Science, 266:776 779 (1994)). The first step is the chemo selective reaction of an unprotected synthetic peptide a thioester with another unprotected peptide segment containing an amino terminal Cys residue to give a thioester linked intermediate as the initial covalent product. Without a change in the reaction conditions, this intermediate undergoes spontaneous, rapid intramolecular reaction to form a native peptide bond at the ligation site. Application of this native chemical ligation method to the total synthesis of a protein molecule is illustrated by the preparation of human interleukin 8 (IL-8) (Baggiolini et al., FEES Lett. 307:97-101 (1992); Clark et al. ,J. Biol. Chern. 269:16075 (1994); Clark et al., Biochemistry 30:3128 (1991); Rajarathnam et al., Biochemistry 33:6623-(1994)). id="p-203"
[0203]Alternatively, unprotected peptide segments can be chemically linked where the bond formed between the peptide segments as a result of the chemical ligation is an unnatural (non- peptide) bond (Schnolzer et al., Science 256:221 (1992)). This technique has been used to synthesize analogs of protein domains as well as large amounts of relatively pure proteins with full biological activity (deLisle et al., Techniques in Protein Chemistry IV. Academic Press, New York, pp. 257-267 (1992)). id="p-204"
[0204]Following expression, the antibodies and fragments thereof can be isolated. An antibody or fragment thereof can be isolated or purified in a variety of ways known in the art depending on what other components are present in the sample. Standard purification methods include electrophoretic, molecular, immunological, and chromatographic techniques, including ion exchange, hydrophobic, affinity, and reverse-phase HPLC chromatography. For example, an antibody can be purified using a standard anti-antibody column (e.g., a protein-A or protein- Gcolumn). Ultrafiltration and diafiltration techniques, in conjunction with protein 62US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) concentration, are also useful. See, e.g., Scopes (1994) Protein Purification, 3rd edition, Springer-Verlag, New York City, New York. The degree of purification necessary varies depending on the desired use. In some instances, no purification of the expressed antibody or fragments thereof is necessary. id="p-205"
[0205]Methods for determining the yield or purity of a purified antibody or fragment thereof are known in the art and include, e.g., Bradford assay, UV spectroscopy, Biuret protein assay, Lowry protein assay, amido black protein assay, high pressure liquid chromatography (HPLC), mass spectrometry (MS), and gel electrophoretic methods (e.g., using a protein stain such as Coomassie Blue or colloidal silver stain).
VII. KITS AND PACKAGING id="p-206"
[0206]The CG1/HLA-A2 complex antibodies and antigen binding fragments thereof or CAR disclosed herein are ideally suited for the preparation of a kit. In some embodiments, kits are provided for carrying out any of the methods described herein. The kits of this disclosure may comprise a carrier container being compartmentalized to receive in close confinement one or more containers such as vials, tubes, and the like, each of the containers comprising one of the separate elements to be used in the method. id="p-207"
[0207]In some instances, one of the containers may comprise a CG1/HLA-A2 complex antibody or antigen binding fragment thereof or CAR as described in this disclosure that is, or can be, detectably labeled. The kit may also have containers containing buffer(s) and/or a container comprising a reporter-means, such as a biotin-binding protein, such as avidin or streptavidin, bound to a reporter molecule, such as an enzymatic or fluorescent label. For example, a kit for imaging a tumor in a subject with a CG1/HLA-A2 complex antigen- expressing cancer is provided herein. In some embodiments, the kit comprises a container containing a labeled CG1/HLA-A2 complex antibody or antigen binding fragment thereof. In some embodiments, the kit comprises separate containers containing a CG1/HLA-A2 complex antibody or antigen binding fragment thereof and a detectable label. id="p-208"
[0208]A CG1/HLA-A2 complex y antibody or antigen binding fragment thereof or CAR as described in this disclosure for use in treating cancer patients may be delivered in a pharmaceutical package or kit to doctors and cancer patients. Such packaging is intended to improve patient convenience and compliance with the treatment plan. Typically, the packaging comprises paper (cardboard) or plastic. In some embodiments, the kit or pharmaceutical 63US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) package further comprises instructions for use (e.g., for administering according to a method as described herein). id="p-209"
[0209]In some embodiments, a pharmaceutical package or kit comprises unit dose forms of a CG1/HLA-A2 complex antibody or antigen binding fragment or CAR. In some embodiments, the pharmaceutical package or kit further comprises unit dose forms of one or more of a chemotherapeutic agent, a cytotoxic agent, a radiotherapeutic agent, or an immunotherapeutic agent. id="p-210"
[0210]In one embodiment, the kit or pharmaceutical package comprises a CG1/HLA-Acomplex antibody or antigen binding fragment or CAR in a defined, therapeutically effective dose in a single unit dosage form or as separate unit doses. The dose and form of the unit dose (e.g., tablet, capsule, immediate release, delayed release, etc.) can be any doses or forms as described herein. id="p-211"
[0211]In one embodiment, the kit or pharmaceutical package includes doses suitable for multiple days of administration, such as one week, one month, or three months. id="p-212"
[0212]In certain embodiments, kits are provided for producing a single-dose administration unit. In certain embodiments, kits containing single or multi-chambered pre-filled syringes are included. In certain embodiments, kits containing one or more containers of a formulation described in this disclosure are included.
VIII. PHARMACEUTICAL COMPOSITIONS AND FORMULATIONS id="p-213"
[0213]Compositions comprising a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof or CAR of the present disclosure and a pharmaceutically acceptable carrier are also provided. The compositions may further comprise a diluent, solubilizer, emulsifier, preservative, and/or adjuvant to be used with the methods disclosed herein. Such compositions can be used in a subject with a cancer (such as a myeloid malignancy, a non- myeloid leukemia, or a solid tumor cancer) that would benefit from any of the CG1/HLA-Acomplex-specific antibodies or antigen binding fragments thereof described herein. id="p-214"
[0214]In certain embodiments, acceptable formulation materials preferably are nontoxic to recipients at the dosages and concentrations employed. In certain embodiments, the formulation material(s) are for s.c. and/or TV. administration. In certain embodiments, the pharmaceutical composition can contain formulation materials for modifying, maintaining or preserving, for example, the pH, osmolality, viscosity, clarity, color, isotonicity, odor, sterility, 64US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) stability, rate of dissolution or release, adsorption or penetration of the composition. In certain embodiments, suitable formulation materials include, but are not limited to, amino acids (such as glycine, glutamine, asparagine, arginine or lysine); antimicrobials; antioxidants (such as ascorbic acid, sodium sulfite or sodium hydrogen- sulfite); buffers (such as borate, bicarbonate, Tris-HCl, citrates, phosphates or other organic acids); bulking agents (such as mannitol or glycine); chelating agents (such as ethylenediamine tetraacetic acid (EDTA)); complexing agents (such as caffeine, polyvinylpyrrolidone, beta-cyclodextrin or hydroxypropyl-beta- cyclodextrin); fillers; monosaccharides, disaccharides, and other carbohydrates (such as glucose, mannose or dextrins); proteins (such as serum albumin, gelatin or immunoglobulins); coloring, flavoring and diluting agents; emulsifying agents; hydrophilic polymers (such as polyvinylpyrrolidone); low molecular weight polypeptides; salt-forming counterions (such as sodium); preservatives (such as benzalkonium chloride, benzoic acid, salicylic acid, thimerosal, phenethyl alcohol, methylparaben, propylparaben, chlorhexidine, sorbic acid or hydrogen peroxide); solvents (such as glycerin, propylene glycol or polyethylene glycol); sugar alcohols (such as mannitol or sorbitol); suspending agents; surfactants or wetting agents (such as pluronics, PEG, sorbitan esters, polysorbates such as polysorbate 20, polysorbate 80, triton, tromethamine, lecithin, cholesterol, tyloxapal); stability enhancing agents (such as sucrose or sorbitol); tonicity enhancing agents (such as alkali metal halides, preferably sodium or potassium chloride, mannitol sorbitol); delivery vehicles; diluents; excipients and/or pharmaceutical adjuvants. (Allen (2012) Remington - The Science and Practice of Pharmacy, 22d Edition, Lloyd V, Allen, ed., The Pharmaceutical Press). In certain embodiments, the optimal pharmaceutical composition is determined by one skilled in the art depending upon, for example, the intended route of administration, delivery format and desired dosage. See, for example, Allen (2012) Remington - The Science and Practice of Pharmacy, 22d Edition, Lloyd V, Allen, ed., The Pharmaceutical Press. In certain embodiments, such compositions may influence the physical state, stability, rate of in vivo release and/or rate of in vivo clearance of the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof. id="p-215"
[0215]In certain embodiments, the primary vehicle or carrier in a pharmaceutical composition can be either aqueous or non-aqueous in nature. For example, in certain embodiments, a suitable vehicle or carrier can be water for injection, physiological saline solution or artificial cerebrospinal fluid, possibly supplemented with other materials common in compositions for parenteral administration. In certain embodiments, the saline comprises isotonic phosphate-buffered saline. In certain embodiments, neutral buffered saline or saline 65US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) mixed with serum albumin are further exemplary vehicles. In certain embodiments, pharmaceutical compositions comprise a pH controlling buffer such phosphate-buffered saline or acetate-buffered saline. In certain embodiments, a composition comprising a CG1/HLA-Acomplex-specific antibody or antigen binding fragment thereof disclosed herein can be prepared for storage by mixing the selected composition having the desired degree of purity with optional formulation agents (see Allen (2012) Remington - The Science and Practice of Pharmacy, 22d Edition, Lloyd V, Allen, ed., The Pharmaceutical Press) in the form of a lyophilized cake or an aqueous solution. Further, in certain embodiments, a composition comprising a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof disclosed herein can be formulated as a lyophilizate using appropriate excipients. In some instances, appropriate excipients may include a cryo-preservative, a bulking agent, a surfactant, or a combination of any thereof. Exemplary excipients include one or more of a polyol, a disaccharide, or a polysaccharide, such as, for example, mannitol, sorbitol, sucrose, trehalose, and dextran 40. In some instances, the cryo-preservative may be sucrose or trehalose. In some instances, the bulking agent may be glycine or mannitol. In one example, the surfactant may be a polysorbate such as, for example, polysorbate-20 or polysorbate-80. id="p-216"
[0216]In certain embodiments, the pharmaceutical composition can be selected for parenteral delivery. In certain embodiments, the compositions can be selected for inhalation or for delivery through the digestive tract, such as orally. The preparation of such pharmaceutically acceptable compositions is within the ability of one skilled in the art. id="p-217"
[0217]In certain embodiments, the formulation components are present in concentrations that are acceptable to the site of administration. In certain embodiments, buffers are used to maintain the composition at physiological pH or at a slightly lower pH, typically within a pH range of from about 5 to about 8. For example, the pH may be 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8. 6.9, 6.9, 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, or 8.5. In some instances, the pH of the pharmaceutical composition may be in the range of 6.6-8.5 such as, for example, 7.0-8.5, 6.6-7.2, 6.8-7.2, 6.8- 7.4, 7.2-7.8, 7.0-7.5, 7.5-8.0, 7.2-8.2, 7.6-8.5, or 7.8-8.3. In some instances, the pH of the pharmaceutical composition may be in the range of 5.5-7.5 such as, for example, 5.5-5.8, 5.5- 6.0, 5.7-6.2, 5.8-6.5, 6.0-6.5, 6.2-6.8, 6.5-7.0, 6.8-7.2, or 6.8-7.5. In some instances, the pH of the pharmaceutical composition may be in the range of 4.0-5.5 such as, for example, 4.0-4.3, 4.0-4.5, 4.2-4.8, 4.5-4.8, 4.5-5.0, 4.8-5.2, or 5.0-5.5. In an embodiment, the pH is 7.2. 66US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-218"
[0218]In certain embodiments when parenteral administration is contemplated, a therapeutic composition can be in the form of a pyrogen-free, parenterally acceptable aqueous solution comprising a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof in a pharmaceutically acceptable vehicle. In certain embodiments, a vehicle for parenteral injection is sterile distilled water in which a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof is formulated as a sterile, isotonic solution and properly preserved. In certain embodiments, the preparation can involve the formulation of the desired molecule with an agent, such as injectable microspheres, bio-erodible particles, polymeric compounds (such as polylactic acid or polyglycolic acid), beads or liposomes, that can provide for the controlled or sustained release of the product which can then be delivered via a depot injection. In certain embodiments, hyaluronic acid can also be used, and can have the effect of promoting sustained duration in the circulation. In certain embodiments, implantable drug delivery devices can be used to introduce the desired molecule. id="p-219"
[0219]In certain embodiments, a pharmaceutical composition can be formulated for inhalation. In certain embodiments, a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof can be formulated as a dry powder for inhalation. In certain embodiments, an inhalation solution comprising a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof can be formulated with a propellant for aerosol delivery. In certain embodiments, solutions can be nebulized. Pulmonary administration is further described in International Application Publication No. WO/1994/020069, which describes pulmonary delivery of chemically modified proteins. id="p-220"
[0220]In certain embodiments, it is contemplated that formulations can be administered orally. In certain embodiments, a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof that is administered in this fashion can be formulated with or without carriers customarily used in compounding solid dosage forms, such as tablets and capsules. In certain embodiments, a capsule can be designed to release the active portion of the formulation at the point in the gastrointestinal tract when bioavailability is maximized, and pre-systemic degradation is minimized. In certain embodiments, at least one additional agent can be included to facilitate absorption of a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof. In certain embodiments, diluents, flavorings, low melting point waxes, vegetable oils, lubricants, suspending agents, tablet disintegrating agents, and binders can also be employed. 67US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-221"
[0221]In certain embodiments, a pharmaceutical composition can involve an effective quantity of a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof in a mixture with non-toxic excipients suitable for the manufacture of tablets. In certain embodiments, by dissolving the tablets in sterile water or other appropriate vehicle, solutions can be prepared in unit-dose form. In certain embodiments, suitable excipients include, but are not limited to, inert diluents, such as calcium carbonate, sodium carbonate or bicarbonate, lactose, or calcium phosphate; or binding agents, such as starch, gelatin, or acacia; or lubricating agents such as magnesium stearate, stearic acid, or talc. id="p-222"
[0222]Additional pharmaceutical compositions can be selected by one skilled in the art, including formulations involving a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof in sustained- or controlled-delivery formulations. In certain embodiments, techniques for formulating a variety of other sustained- or controlled-delivery means, such as liposome carriers, bio-erodible microparticles or porous beads and depot injections, are also known to those skilled in the art. See for example, International Application Publication No. WO/1993/015722, which describes the controlled release of porous polymeric microparticles for the delivery of pharmaceutical compositions. In certain embodiments, sustained-release preparations can include semipermeable polymer matrices in the form of shaped articles, e.g., films, or microcapsules. Sustained release matrices can include polyesters, hydrogels, polylactides (see, e.g., U.S. Patent No. 3,773,919; U.S. Patent No. 5, 594,091; U.S. Patent No. 8,383,153; U.S. Patent No. 4,767,628; International Application Publication No. WO1998043615, Calo, E. et al. (2015) Eur. Polymer J 65.252-261 and European Patent No. EP 058,481), including, for example, chemically synthesized polymers, starch based polymers, and polyhydroxyalkanoates (PHAs), copolymers of L-glutamic acid and gamma ethyl-L-glutamate (Sidman et al. (1993) Biopolymers 22:547-556), poly (2-hydroxyethyl-methacrylate) (Langer et al. (1981) J Biomed Mater Res. 15: 167-277; and Langer (1982) Chern Tech 12:98-105), ethylene vinyl acetate (Hsu and Langer (1985) J Biomed Materials Res 19(4):445-460) or poly- D(-)-3-hydroxybutyric acid (European Patent No. EP0133988). In certain embodiments, sustained release compositions can also include liposomes, which can be prepared by any of several methods known in the art. (See, e.g., Eppstein et al. (1985) Proc. Natl. Acad. Sci. USA 82:3688-3692; European Patent No. EP 036,676; and U.S. Patent Nos. 4,619,794 and 4,615,885). id="p-223"
[0223]The pharmaceutical composition to be used for in vivo administration typically is sterile. In certain embodiments, sterilization is accomplished by filtration through sterile 68US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) filtration membranes. In certain embodiments, where the composition is lyophilized, sterilization using this method can be conducted either prior to or following lyophilization and reconstitution. In certain embodiments, the composition for parenteral administration can be stored in lyophilized form or in a solution. In certain embodiments, parenteral compositions generally are placed into a container having a sterile access port, for example, an intravenous solution bag or vial having a stopper pierceable by a hypodermic injection needle. id="p-224"
[0224]In certain embodiments, once the pharmaceutical composition has been formulated, it can be stored in sterile vials as a solution, suspension, gel, emulsion, solid, or as a dehydrated or lyophilized powder. In certain embodiments, such formulations can be stored either in a ready-to-use form or in a form (e.g., lyophilized) that is reconstituted prior to administration. id="p-225"
[0225]In certain embodiments, kits are provided for producing a single-dose administration unit. In certain embodiments, the kit can contain both a first container having a dried protein and a second container having an aqueous formulation. In certain embodiments, kits containing single and multi-chambered pre-filled syringes are included. id="p-226"
[0226]In certain embodiments, the effective amount of a pharmaceutical composition comprising a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof to be employed therapeutically depends, for example, upon the therapeutic context and objectives. One skilled in the art will appreciate that the appropriate dosage levels for treatment, according to certain embodiments, vary depending, in part, upon the molecule delivered, the indication for which a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof is being used, the route of administration, and the size (body weight, body surface or organ size) and/or condition (the age and general health) of the patient. The clinician can titer the dosage and modify the route of administration to obtain the optimal therapeutic effect. id="p-227"
[0227]The clinician also selects the frequency of dosing, taking into account the pharmacokinetic parameters of the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof in the formulation used. In certain embodiments, a clinician administers the composition until a dosage is reached that achieves the desired effect. In certain embodiments, the composition can therefore be administered as a single dose or as two or more doses (which may or may not contain the same amount of the desired molecule) over time, or as a continuous infusion via, for example, an implantation device or catheter. Further refinement of the appropriate dosage is routinely made by those of ordinary skill in the art and 69US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) is within the ambit of tasks routinely performed by them. In certain embodiments, appropriate dosages can be ascertained through use of appropriate dose-response data. id="p-228"
[0228]In certain embodiments, the route of administration of the pharmaceutical composition is in accord with known methods, e.g., orally, through injection by intravenous, intraperitoneal, intracerebral (intra-parenchymal), intracerebral, intraventricular, intramuscular, subcutaneously, intra-ocular, intraarterial, intraportal, or intralesional routes; by sustained release systems or by implantation devices. In certain embodiments, the compositions can be administered by bolus injection or continuously by infusion, or by implantation device. In certain embodiments, individual elements of a combination therapy may be administered by different routes. id="p-229"
[0229]In certain embodiments, the composition can be administered locally, e.g., during surgery or topically. Optionally local administration is via implantation of a membrane, sponge, or another appropriate material onto which the desired molecule has been absorbed or encapsulated. In certain embodiments, where an implantation device is used, the device can be implanted into any suitable tissue or organ, and delivery of the desired molecule can be via diffusion, timed-release bolus, or continuous administration. id="p-230"
[0230]In certain embodiments, it can be desirable to use a pharmaceutical composition comprising a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof in an ex vivo manner. In such instances, cells that have been removed from a subject may be exposed to a pharmaceutical composition comprising a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof after which the cells are subsequently implanted back into the subject. id="p-231"
[0231]In certain embodiments, a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof can be delivered by implanting certain cells that have been genetically engineered, using methods such as those described herein, to express and secrete the polypeptides. In certain embodiments, such cells can be animal or human cells, and can be autologous, heterologous, or xenogeneic. In certain embodiments, the cells can be immortalized. In certain embodiments, in order to decrease the chance of an immunological response, the cells can be encapsulated to avoid infiltration of surrounding tissues. In certain embodiments, the encapsulation materials are typically biocompatible, semi-permeable polymeric enclosures or membranes that allow the release of the protein product(s) but prevent 70US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) the destruction of the cells by a subject ’s immune system or by other detrimental factors from the surrounding tissues.
IX. METHOD OF USE OF CG1/HLA-A2 COMPLEX -SPECIFIC ANTIBODIES A. In Vitro Detection and Diagnostics id="p-232"
[0232]The CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof provided in this disclosure are suited for in vitro use, for example, in immunoassays in which they can be utilized in liquid phase or bound to a solid phase carrier. In addition, the antibodies or fragments thereof in these immunoassays can be detectably labeled in various ways. Examples of types of immunoassays which can utilize the antibodies according to the present disclosure are competitive and non-competitive immunoassays in either a direct or indirect format. Examples of such immunoassays are the radioimmunoassay (RIA) and the sandwich (immunometric) assay. Detection of antigens using the antibodies according to the present disclosure can be done utilizing immunoassays which are run in either the forward, reverse, or simultaneous modes, including immunohistochemical assays on physiological samples. Those of skill in the art will know, or can readily discern, other immunoassay formats without undue experimentation. id="p-233"
[0233]The antibodies according to the present disclosure can be bound to many different carriers and used to detect the presence of a cancer (such as a myeloid malignancy, non-myeloid leukemia, or solid tumor cancer). In some embodiments, the cancer is a HLA-A2 positive cancer. Examples of well-known carriers include glass, polystyrene, polypropylene, polyethylene, dextran, nylon, amylase, natural and modified cellulose, polyacrylamide, agarose and magnetite. The nature of the carrier can be either soluble or insoluble for purposes according to the present disclosure. Those skilled in the art will know of other suitable carriers for binding antibodies according to the present disclosure, or will be able to ascertain such, using routine experimentation. id="p-234"
[0234]For purposes of this disclosure, a cancer may be detected by the provided antibodies fragments thereof when the virus is present in biological fluids and tissues from a subject that may contain cancer cells. Any sample containing a detectable amount of cancer cells can be used. A sample can be a liquid such as urine, saliva, cerebrospinal fluid, blood, serum or the like; a solid or semi-solid such as tissues, feces, or the like; or, alternatively, a solid tissue such as those commonly used in histological diagnosis. 71US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-235"
[0235]Another approach to assessing whether a subject has a cancer (such as a myeloid malignancy, non-myeloid leukemia, or solid tumor cancer) is to determine if the B cell receptor (BCR) repertoire of the subject includes a coding sequence for one of the CG1/HLA-Acomplex-specific antibodies provided in this disclosure. An exemplary method of this type of sequence analysis is described in the art. For example, RNA from whole blood or B cells (PBMCs) can be used as the template for the amplification of CDR sequences. CDRs of the heavy chain, light chain, or both may be sequenced, with analysis of either or both of lambda or kappa chain sequences. Primer pools are designed to result in wide-spread amplification of the BCR V(D)JC sequences in the sample. Reverse transcription is then performed to create cDNA sequences corresponding to the BCR coding sequences, which may be amplified for subsequent sequence analysis. Next generation sequencing of the amplified cDNA library can then be performed. Sequence analysis is used to assess the identity of the the BCR V(D)JC sequences in the sample and to determine the percent identity thereof to the antibodies described herein. Various commercial services are also available for performing BCR repertoire analysis (e.g., Magic™ BCR Repertoire Analysis by Creative Biolabs). The presence of BCR sequences encoding the antibodies described in this disclosure in the subject ’s sample may be indicative that the subject has a cancer or has previously been affected by a cancer (such as a myeloid malignancy, non-myeloid leukemia, or solid tumor cancer).
B. In Vivo Detection id="p-236"
[0236]In using the provided antibodies and fragments thereof for the in vivo detection of CG1/HLA-A2 complex complex , the detectably labeled antibody or fragment thereof is given in a dose which is diagnostically effective. The term "diagnostically effective " means that the amount of detectably labeled antibody is administered in sufficient quantity to enable detection of a site having the CG1/HLA-A2 complex for which the antibodies are specific. id="p-237"
[0237]The concentration of detectably labeled antibody or fragment thereof which is administered should be sufficient such that the binding to a cancer cell is detectable compared to the background. Further, it is desirable that the detectably labeled antibody or fragment thereof be rapidly cleared from the circulatory system in order to give the best target-to- background signal ratio. id="p-238"
[0238]As a rule, the dosage of detectably labeled antibody or fragment thereof for in vivo diagnosis will vary depending on such factors as age, sex, and extent of disease of the individual. The dosage of antibody can vary from about 0.01 mg/kg to about 50 mg/kg, 72US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) preferably 0.1 mg/kg to about 20 mg/kg, most preferably about 0.1 mg/kg to about 2 mg/kg. Such dosages may vary, for example, depending on whether multiple injections are given, on the tissue being assayed, and other factors known to those of skill in the art. id="p-239"
[0239]For in vivo diagnostic imaging, the type of detection instrument available is a major factor in selecting an appropriate radioisotope. The radioisotope chosen must have a type of decay which is detectable for the given type of instrument. Still another important factor in selecting a radioisotope for in vivo diagnosis is that the half-life of the radioisotope be long enough such that it is still detectable at the time of maximum uptake by the target, but short enough such that deleterious radiation with respect to the host is acceptable. Ideally, a radioisotope used for in vivo imaging will lack a particle emission but produce a large number of photons in the 140-250 keV range, which may be readily detected by conventional gamma cameras. For in vivo diagnosis, radioisotopes may be bound to immunoglobulin either directly or indirectly by using an intermediate functional group. Intermediate functional groups which often are used to bind radioisotopes which exist as metallic ions are the bifunctional chelating agents such as diethylenetriaminepentacetic acid (DTPA) and ethylenediaminetetra-acetic acid (EDTA) and similar molecules. Typical examples of metallic ions which can be bound to the antibodies according to the present disclosure are 111In, 97Ru, 67Ga, 68Ga, 72As, 89Zr and 201T1. id="p-240"
[0240]The CG1/HLA-A2 complex-specific antibodies and antigen binding fragments thereof can also be labeled with a paramagnetic isotope for purposes of in vivo diagnosis, as in magnetic resonance imaging (MRI) or electron spin resonance (ESR). In general, any conventional method for visualizing diagnostic imaging can be utilized. Usually, gamma and positron emitting radioisotopes are used for camera imaging and paramagnetic isotopes for MRI. Elements which are particularly useful in such techniques include 157Gd, 55Mn, 162Dy, 52Cr and 56Fe. id="p-241"
[0241]The provided antibodies and antigen binding fragments can be used in vitro and in vivo to monitor the course of cancer therapy. Thus, for example, by measuring the increase or decrease in the number of cancer cells or changes in the amount of cancer present in the body or in various body fluids, it would be possible to determine whether a particular therapeutic regimen aimed at ameliorating the cancer is effective. 73US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) C. Therapeutic Methods id="p-242"
[0242]As described herein, the present disclosure provides a method of treating a subject with a cancer (such as a myeloid malignancy, non-myeloid leukemia, or solid tumor cancer), comprising administering to the subject a therapeutically effective amount of a myeloid malignancy antigen-specific antibody or antigen binding fragment thereof of the present disclosure. In some embodiments, the subject has or is determined to have a cancer. In some embodiments, the cancer is a HLA-A2 positive cancer. id="p-243"
[0243]The compositions described herein are useful in, inter alia, methods for treating a cancer (such as a myeloid malignancy, non-myeloid leukemia, or solid tumor cancer) in a subject. As used herein, the term subject means a mammalian subject. Exemplary subjects include, but are not limited to humans, monkeys, dogs, cats, mice, rats, cows, horses, camels, goats and sheep. In some embodiments, the subject is a human. In some embodiments, the subject has or is suspected to have a cancer. In some embodiments, the subject is diagnosed with a myeloid malignancy. In some embodiments, the subject is diagnosed with a non- myeloid leukemia. In some embodiments, the subject is diagnosed with a solid tumor cancer. In some embodiments, the subject is a human that is suspected of having a cancer as described herein. id="p-244"
[0244]As used herein, administer or administration refers to the act of injecting or otherwise physically delivering a substance as it exists outside the body (e.g., a CG1/HLA-A2 complex- specific antibody or antigen binding fragment provided herein or a construct encoding same) into a patient, such as by mucosal, intradermal, intravenous, intramuscular, subcutaneous delivery and/or any other method of physical delivery described herein or known in the art. When a disease, or a symptom thereof, is being treated, administration of the substance typically occurs after the onset of the disease or symptoms thereof. When a disease, or symptoms thereof, are being prevented, administration of the substance typically occurs before the onset of the disease or symptoms thereof. id="p-245"
[0245]The compositions can be administered to a subject, e.g., a human subject, using a variety of methods that depend, in part, on the route of administration. The route can be, e.g., intravenous injection or infusion (IV), subcutaneous injection (SC), intraperitoneal (IP) injection, intramuscular injection (IM), intradermal injection (ID), subcutaneous, transdermal, intracavity, oral, intracranial injection, or intrathecal injection (IT). The injection can be in a bolus or a continuous infusion. Techniques for preparing inj ectate or infusate delivery systems 74US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) containing antibodies are well known to those of skill in the art. Generally, such systems should utilize components which will not significantly impair the biological properties of the antibodies, such as the paratope binding capacity (see, for example, Remington's Pharmaceutical Sciences, l^th edition, 1990, Mack Publishing). Those of skill in the art can readily determine the various parameters and conditions for producing antibody injectates or infusates without resort to undue experimentation. id="p-246"
[0246]Administration can be achieved by, e.g., topical administration, local infusion, injection, or by means of an implant. The implant can be of a porous, non-porous, or gelatinous material, including membranes, such as sialastic membranes, or fibers. The implant can be configured for sustained or periodic release of the composition to the subject. See, e.g., U.S. Patent Application Publication No. 20080241223; U.S. Patent Nos. 5,501,856; 5,164,188; 4,863,457; and 3,710,795. The composition can be delivered to the subject by way of an implantable device based on, e.g., diffusive, erodible, or convective systems, e.g., osmotic pumps, biodegradable implants, electrodiffusion systems, electroosmosis systems, vapor pressure pumps, electrolytic pumps, effervescent pumps, piezoelectric pumps, erosion-based systems, or electromechanical systems. In some embodiments, a CG1/HLA-A2 complex- specific antibody or antigen binding fragment of the present disclosure is therapeutically delivered to a subject by way of local administration. id="p-247"
[0247]Preparations for parenteral administration include sterile aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer ’s dextrose, dextrose and sodium chloride, lactated Ringer ’s or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer ’s dextrose), and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, antioxidants, chelating agents, and the like. id="p-248"
[0248]Treating or treatment of any disease or disorder refers to ameliorating a disease or disorder that exists in a subject or a symptom thereof. The term ameliorating refers to any therapeutically beneficial result in the treatment of a disease state, e.g., a cancer, lessening in the severity or progression, promoting remission or durations of remission, or curing thereof. Thus, treating or treatment includes ameliorating at least one physical parameter or symptom. 75US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) Treating or treatment includes modulating the disease or disorder, either physically (e.g., stabilization of a discernible symptom) or physiologically (e.g., stabilization of a physical parameter) or both. Treating or treatment includes delaying or preventing metastasis. Thus, in the disclosed methods, treatment can refer to a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% reduction in the severity of an established disease or condition or symptom of the disease or condition. For example, a method for treating a cancer in a subject by administering an antibody as described in this disclosure is considered to be a treatment if there is a 10% reduction in one or more symptoms of the cancer in a subject as compared to a control. Thus the reduction can be a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any percent reduction in between 10% and 100% as compared to native or control levels. It is understood that treatment does not necessarily refer to a cure or complete ablation of the disease, condition, or symptoms of the disease or condition. id="p-249"
[0249]In some embodiments, the symptoms of a myeloid malignancy can include (without intending to be limiting) bone pain, nausea, constipation, loss of appetite, mental fogginess or confusion, fatigue, frequent infections, weight loss, weakness or numbness in the legs, excessive thirst, easily fractured or broken bones, anemia, leukopenia, thrombocytopenia, excessive urination, hypercalcemia, spinal cord compression, kidney dysfunction, hyperviscosity, and the like. id="p-250"
[0250]As used herein, the term "therapeutically effective amount " or effective amount refers to an amount of a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof that, when administered to a subject, is effective to treat a disease or disorder such that the symptoms of cancer are ameliorated, or the likelihood of cancer developing or progressing is decreased. A therapeutically effective amount is not, however, a dosage so large as to cause adverse side effects, such as hyperviscosity' syndromes, pulmonary edema, congestive heart tai lure, and the like. A suitable dose of an antibody or fragment thereof described herein, which dose is capable of treating a cancer in a subject, can depend on a variety of factors including the particular construct used and whether it is used concomitantly with other therapeutic agents. For example, a different dose of a whole CG1/HLA-A2 complex-specific antibody may be required to treat a subject with a camcer as compared to the dose of a fragment of a CG1/HLA- A2 complex-specific antibody (e.g., Fab ’ antibody fragment) required to treat the same subject. Other factors affecting the dose administered to the subject include, e.g., the type or extent of cancer. For example, a subject that has had a previous cancer may require administration of a different dosage of CG1/HLA-A2 complex-specific antibody or antigen binding fragment 76US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) thereof than a subject who has not previously had a cancer. Generally, a therapeutically effective amount may vary with the subject ’s age, condition, and sex, as well as the extent of the disease in the subject and can be determined by one of skill in the art. Other factors can include, e.g., other medical disorders concurrently or previously affecting the subject, the general health of the subject, the genetic disposition of the subject, diet, time of administration, rate of excretion, drug combination, and any other additional therapeutics that are administered to the subject. It should also be understood that a specific dosage and treatment regimen for any particular subject also depends upon the judgment of the treating medical practitioner (e.g., doctor or nurse). A therapeutically effective amount is also one in which any toxic or detrimental effects of the composition are outweighed by the therapeutically beneficial effects. The dosage of the therapeutically effective amount may be adjusted by the individual physician or veterinarian in the event of any complication. In some instances, a therapeutically effective amount may vary from about 0.01 mg/kg to about 50 mg/kg, preferably from about 0.1 mg/kg to about 20 mg/kg, most preferably from about 0.2 mg/kg to about 2 mg/kg, in one or more dose administrations daily, for one or several days. In some instances, the CG1/HLA-Acomplex-specific antibody or antigen binding fragment thereof is administered for 2 to 5 or more consecutive days in order to avoid "rebound" of virus replication from occurring. id="p-251"
[0251]A pharmaceutical composition can include a therapeutically effective amount of a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof described herein. Such effective amounts can be readily determined by one of ordinary skill in the art as described above. Considerations include the effect of the administered CG1/HLA-A2 complex- specific antibody or antigen binding fragment thereof, or the combinatorial effect of the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof with one or more additional active agents, if more than one agent is used in or with the pharmaceutical composition. In certain aspects, the doses can be about 1, about 0.5, about 0.1, about 0.05, or about 0.01 mg/kg, or any intervening dose between about 0.01 mg/kg and 1 mg/kg. id="p-252"
[0252]Suitable human doses of any of the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof described herein can further be evaluated in, e.g., Phase I dose escalation studies. See, e.g., van Gurp et al. (2008) Am J Transplantation 8(8): 1711-1718; Hanouska et al. (2007) Clin Cancer Res 13(2, part !):523-531; and Hetherington et al. (2006) Antimicrobial Agents and Chemotherapy 50(10): 3499-3500. 77US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-253"
[0253]Toxicity and therapeutic efficacy of such CG1/HLA-A2 complex-specific antibodies or antigen binding fragments thereof can be determined by known pharmaceutical procedures in cell cultures or experimental animals (e.g., animal models of any of the cancers described herein). These procedures can be used, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index, and it can be expressed as the ratio LD50/EDso. A CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof that exhibits a high therapeutic index is preferred. While constructs that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such constructs to the site of affected tissue and to minimize potential damage to normal cells and, thereby, reduce side effects. id="p-254"
[0254]The data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. The dosage of a CG1/HLA-A2 complex- specific antibody or antigen binding fragment thereof lies generally within a range of circulating concentrations of the CG1/HLA-A2 complex-specific antibody or antigen binding fragment that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. For CG1/HLA-A2 complex-specific antibodies or antigen binding fragments thereof described herein, the therapeutically effective dose can be estimated initially from cell culture assays. A dose can be formulated in animal models to achieve a circulating plasma concentration range that includes the EC50 (i.e., the concentration of the construct - e.g., antibody - which achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans. Levels in plasma may be measured, for example, by high performance liquid chromatography. In some embodiments, e.g., where local administration is desired, cell culture or animal models can be used to determine a dose required to achieve a therapeutically effective concentration within the local site. id="p-255"
[0255]In some embodiments, a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof described herein can be administered to a subject as a monotherapy. Alternatively, the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof can be administered in conjunction with other therapies for cancer (combination therapy). For example, the composition can be administered to a subject at the same time, prior to, or after, a second therapy. In some embodiments, the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof and the one or more additional active agents are 78US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) administered at the same time. Optionally, the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof is administered first in time and the one or more additional active agents are administered second in time. In some embodiments, the one or more additional active agents are administered first in time and the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof is administered second in time. Optionally, the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof and the one or more additional agents are administered simultaneously in the same or different routes. For example, a composition comprising the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof optionally contains one or more additional agents. id="p-256"
[0256] ACG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof described herein can replace or augment a previously or currently administered therapy. For example, upon treating with a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof, administration of the one or more additional active agents can cease or diminish, e.g., be administered at lower levels or dosages. In some embodiments, administration of the previous therapy can be maintained. In some embodiments, a previous therapy is maintained until the level of the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof reaches a level sufficient to provide a therapeutic effect. id="p-257"
[0257]Also provided are cancer treatment methods using a CAR comprising a CG1/HLA- A2 complex-specific antibody or antigen binding fragment thereof antibody or antigen binding fragment thereof as described in this disclosure. In some embodiments, these methods comprise using the CAR to redirect the specificity of an immune effector cell (e.g., a T cell) to target a cancer cell (e.g., a CG1/HLA-A2 complex-expressing cancer cell). Thus, provided herein are methods of stimulating an effector cell-mediated response (such as a T cell-mediated immune response) to a target cell population or tissue comprising cancer cells in a mammal, comprising the step of administering to the mammal an effector cell (such as a T cell) that expresses a CAR as described herein. In some embodiments, "stimulating " an immune cell refers to eliciting an effector cell-mediated response (such as a T cell-mediated immune response), which is different from activating an immune cell. CAR-expressing effector cells described herein can be infused to a subject in need of treatment (e.g., a cancer patient). In some embodiments, the infused cell is able to kill (or lead to the killing of) cancer cells in the subject. Formulations and methods for making CAR-expressing effector cells and using them in therapeutic methods are known in the art (see, e.g., Feins et al., 2019, Am. J. Hematol. 94(S1):S3-S9). 79US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-258"
[0258]Monitoring a subject (e.g., a human patient) for an improvement of cancer (such as a myeloid malignance, a non-myeloid leukemia, or a solid tumor cancer), as defined herein, means evaluating the subject for a change in a disease parameter, e.g., a reduction in one or more symptoms of a cancer exhibited by the subject. In some embodiments, the evaluation is performed at least one (1) hour, e.g., at least 2, 4, 6, 8, 12, 24, or 48 hours, or at least 1 day, days, 4 days, 10 days, 13 days, 20 days or more, or at least 1 week, 2 weeks, 4 weeks, 10 weeks, weeks, 20 weeks or more, after an administration. The subject can be evaluated in one or more of the following periods: prior to beginning of treatment; during the treatment; or after one or more elements of the treatment have been administered. Evaluation can include evaluating the need for further treatment, e.g., evaluating whether a dosage, frequency of administration, or duration of treatment should be altered. It can also include evaluating the need to add or drop a selected therapeutic modality, e.g., adding or dropping any of the treatments for a cancer described herein. id="p-259"
[0259]In some instances, the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof can be administered via virus-like particles. Virus-like particles (VLPs) comprise viral protein(s) derived from the structural proteins of a virus. Methods for making and using virus like particles are described in, for example, Garcea and Gissmann, Current Opinion in Biotechnology 15:513-7 (2004). id="p-260"
[0260]In some instances, the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof can be administered by subviral dense bodies (DBs). DBs transport proteins into target cells by membrane fusion. Methods for making and using DBs are described in, for example, Pepperl-Klindworth et al., Gene Therapy 10:278-84 (2003). id="p-261"
[0261]In some instances, the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof can be administered by tegument aggregates. Methods for making and using tegument aggregates are described in International Publication No. WO 2006/110728. id="p-262"
[0262]In another aspect, provided is a method of treating a subject with cancer, the method comprising administering to the patient cells that have been genetically engineered, using methods such as those described herein, to express and secrete a CG1/HLA-A2 complex- specific antibody or antigen binding fragment thereof as described in this disclosure. id="p-263"
[0263]In another aspect, provided is a method of treating a subject with cancer, the method comprising administering to the patient immune cells that express a CAR comprising a 80US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof as described herein. id="p-264"
[0264]In another aspect, provided is a method of treating a subject with cancer, the method comprising administering to the patient a vector comprising a nucleic acid sequence encoding a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof as described in this disclosure. id="p-265"
[0265]There are a number of compositions and methods which can be used to deliver the nucleic acid molecules and/or polypeptides to cells, either in vitro or in vivo via, for example, expression vectors. These methods and compositions can largely be broken down into two classes: viral based delivery systems and non-viral based delivery systems. Such methods are well known in the art and readily adaptable for use with the compositions and methods described herein. id="p-266"
[0266]As used herein, plasmid or viral vectors are agents that transport the disclosed nucleic acids into the cell without undesired degradation and include a promoter yielding expression of the nucleic acid molecule and/or adapter polypeptide in the cells into which it is delivered. Viral vectors are, for example, Adenovirus, Adeno-associated virus, herpes virus, Vaccinia virus, Polio virus, Sindbis, and other RNA viruses, including these viruses with the HIV backbone. Also preferred are any viral families which share the properties of these viruses which make them suitable for use as vectors. Retroviral vectors, in general are described by Coffin et al., Retroviruses, Cold Spring Harbor Laboratory Press (1997), which is incorporated by reference herein for the vectors and methods of making them. The construction of replication-defective adenoviruses has been described (Berkner et al., J. Virology 61:1213-(1987); Massie et al., Mol. Cell. Biol. 6:2872-83 (1986); Haj-Ahmad et al., J. Virology 57:267- (1986); Davidson et al., J. Virology 61:1226-39 (1987); Zhang et al., BioTechniques 15:868- (1993)). The benefit and the use of these viruses as vectors is that they are limited in the extent to which they can spread to other cell types, since they can replicate within an initial infected cell, but are unable to form new infections viral particles. Recombinant adenoviruses have been shown to achieve high efficiency after direct, in vivo delivery to airway epithelium, hepatocytes, vascular endothelium, CNS parenchyma, and a number of other tissue sites. Other useful systems include, for example, replicating and host-restricted non-replicating vaccinia virus vectors. In some instances, the nucleic acid molecules encoding the CG1/HLA-A 81US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) complex-specific antibody or antigen binding fragment thereof can be delivered via virus-like particles. id="p-267"
[0267]Non-viral based delivery methods, can include expression vectors comprising nucleic acid molecules and nucleic acid sequences encoding the adapter polypeptides, wherein the nucleic acids are operably linked to an expression control sequence. Suitable vector backbones include, for example, those routinely used in the art such as plasmids, artificial chromosomes, BACs, YACs, orPACs. Numerous vectors and expression systems are commercially available from such corporations as Novagen (Madison, WI), Clonetech (Pal Alto, CA), Stratagene (La Jolla, CA), and Invitrogen/Life Technologies (Carlsbad, CA). Vectors typically contain one or more regulatory regions. Regulatory regions include, without limitation, promoter sequences, enhancer sequences, response elements, protein recognition sites, inducible elements, protein binding sequences, 5’ and 3’ untranslated regions (UTRs), transcriptional start sites, termination sequences, polyadenylation sequences, and introns. id="p-268"
[0268]Preferred promoters controlling transcription from vectors in mammalian host cells may be obtained from various sources, for example, the genomes of viruses such as polyoma, Simian Virus 40 (SV40), adenovirus, retroviruses, hepatitis B virus, and most preferably cytomegalovirus (CMV), or from heterologous mammalian promoters (e.g, P־actin promoter or EFla promoter), or from hybrid or chimeric promoters (e.g., CMV promoter fused to the P־ actin promoter). Of course, promoters from the host cell or related species are also useful herein. id="p-269"
[0269]Enhancer generally refers to a sequence of DNA that functions at no fixed distance from the transcription start site and can be either 5’ or 3’ to the transcription unit. Furthermore, enhancers can be within an intron as well as within the coding sequence itself. They are usually between 10 and 300 bp in length, and they function in cis. Enhancers usually function to increase transcription from nearby promoters. Enhancers can also contain response elements that mediate the regulation of transcription. While many enhancer sequences are known from mammalian genes (globin, elastase, albumin, fetoprotein, and insulin), typically one will use an enhancer from a eukaryotic cell virus for general expression. Preferred examples are the SV40 enhancer on the late side of the replication origin, the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers. 82US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-270"
[0270]The promoter and/or the enhancer can be inducible (e.g, chemically or physically regulated). A chemically regulated promoter and/or enhancer can, for example, be regulated by the presence of alcohol, tetracycline, a steroid, or a metal. A physically regulated promoter and/or enhancer can, for example, be regulated by environmental factors, such as temperature and light. Optionally, the promoter and/or enhancer region can act as a constitutive promoter and/or enhancer to maximize the expression of the region of the transcription unit to be transcribed. In certain vectors, the promoter and/or enhancer region can be active in a cell type specific manner. Optionally, in certain vectors, the promoter and/or enhancer region can be active in all eukaryotic cells, independent of cell type. Preferred promoters of this type are the CMVpromoter, the SV40 promoter, the beta-actin promoter, the EFla promoter, and the retroviral long terminal repeat (LTR). id="p-271"
[0271]The vectors also can include, for example, origins of replication and/or markers. A marker gene can confer a selectable phenotype, e.g, antibiotic resistance, on a cell. The marker product is used to determine if the vector has been delivered to the cell and once delivered is being expressed. Examples of selectable markers for mammalian cells are dihydrofolate reductase (DHFR), thymidine kinase, neomycin, neomycin analog G418, hygromycin, puromycin, and blasticidin. When such selectable markers are successfully transferred into a mammalian host cell, the transformed mammalian host cell can survive if placed under selective pressure. Examples of other markers include, for example, the E. coli lacZ gene, green fluorescent protein (GFP), and luciferase. In addition, an expression vector can include a tag sequence designed to facilitate manipulation or detection (e.g, purification or localization) of the expressed polypeptide. Tag sequences, such as GFP, glutathione S- transferase (GST), polyhistidine, c-myc, hemagglutinin, or FLAG™ tag (Kodak; New Haven, CT) sequences typically are expressed as a fusion with the encoded polypeptide. Such tags can be inserted anywhere within the polypeptide including at either the carboxyl or amino terminus. id="p-272"
[0272]In certain embodiments, the effective amount of a pharmaceutical composition comprising a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof to be employed therapeutically depends, for example, upon the therapeutic context and objectives. One skilled in the art will appreciate that the appropriate dosage levels for treatment, according to certain embodiments, vary depending, in part, upon the molecule delivered, the indication for which a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof is being used, the route of administration, and the size (body weight, body surface or organ size) 83US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) and/or condition (the age and general health) of the patient. The clinician can titer the dosage and modify the route of administration to obtain the optimal therapeutic effect. id="p-273"
[0273]The clinician also selects the frequency of dosing, taking into account the pharmacokinetic parameters of the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof in the formulation used. Such pharmacokinetic parameters are well known in the art, i.e., the rate of absorption, bioavailability, metabolism, clearance, and the like (see, e.g., Hidalgo-Aragones (1996) J. Steroid Biochem. Mol. Biol. 58:611-617; Groning (1996) Pharmazie 51:337-341; Fotherby (1996) Contraception 54:59-69; Johnson (1995) J. Pharm. Sci. 84:1144-1146; Rohatagi (1995) Pharmazie 50:610-613; Brophy (1983) Ear. J. Clin. Pharmacol. 24:103-108; the latest Remington's, supra). In certain embodiments, a clinician administers the composition until a dosage is reached that achieves the desired effect. In certain embodiments, the composition can therefore be administered as a single dose or as two or more doses (which may or may not contain the same amount of the desired molecule) over time, or as a continuous infusion via, for example, an implantation device or catheter. Further refinement of the appropriate dosage is routinely made by those of ordinary skill in the art and is within the ambit of tasks routinely performed by them. In certain embodiments, appropriate dosages can be ascertained through use of appropriate dose-response data. id="p-274"
[0274]In some cases, the dosage (of the active component) ranges from about 0.0001 to 1mg/kg, and more usually 0.01 to 20 mg/kg, of the patient ’s body weight. For example, dosages can be 0.3 mg/kg body weight, 1 mg/kg body weight, 3 mg/kg body weight, 5 mg/kg body weight, 10 mg/kg body weight or within the range of 0.1-20 mg/kg. In certain examples, the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof can be administered at a dose of 1 mg/kg, 2 mg/kg, 3 mg/kg, 4 mg/kg, or 5 mg/kg once every other day at least four times. An exemplary treatment regime may include administration once per day, once per week, twice a week, once every two weeks, once every three weeks, once every four weeks, once a month, once every 3 months, or once every three to 6 months. In some cases, the treatment comprises administering CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof according to one of the aforementioned dosing regimens for a first period and another of the aforementioned dosing regimens for a second period. In some cases, the treatment discontinues for a period of time before the same or a different dosing regimen resumes. For example, a patient may be on a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof -specific antibody dosing regimen for two weeks, off for a week, on for another two weeks, and so on. Dosage regimens for CG1/HLA-A 84US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) complex-specific antibodies or antigen binding fragments thereof of this disclosure include 0.mg/kg body weight, 0.3 mg/kg body weight, 2 mg/kg body weight, 3 mg/kg body weight, or mg/kg via intravenous administration, with the CG1/HLA-A2 complex-specific antibodies or antigen binding fragments thereof being given using one of the following dosing schedules: (i) every four weeks for six dosages, then every three months; (ii) every three weeks; (iii) mg/kg body weight once followed by 1 mg/kg body weight every three weeks. id="p-275"
[0275]In certain embodiments, the route of administration of the pharmaceutical composition is in accord with known methods, e.g., orally, through injection by intravenous, intraperitoneal, intracerebral (intra-parenchymal), intracerebral, intraventricular, intramuscular, subcutaneously, intra-ocular, intraarterial, intraportal, or intralesional routes; by sustained release systems or by implantation devices. In certain embodiments, the compositions can be administered by bolus injection or continuously by infusion, or by implantation device. In certain embodiments, individual elements of a combination therapy may be administered by different routes. id="p-276"
[0276]In certain embodiments, the composition can be administered locally, e.g., during surgery or topically. Optionally local administration is via implantation of a membrane, sponge, or another appropriate material onto which the desired molecule has been absorbed or encapsulated. In certain embodiments, where an implantation device is used, the device can be implanted into any suitable tissue or organ, and delivery of the desired molecule can be via diffusion, timed-release bolus, or continuous administration. id="p-277"
[0277]In certain embodiments, it can be desirable to use a pharmaceutical composition comprising a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof in an ex vivo manner. In such instances, cells that have been removed from a subject may be exposed to a pharmaceutical composition comprising a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof after which the cells are subsequently implanted back into the subject. id="p-278"
[0278]In some instances, the provided methods may include administering to the subject a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof that is conjugated to a therapeutic agent. The therapeutic agent may be at least one of a cytotoxic agent, a chemotherapeutic agent, or an immunosuppressive agent. Such therapeutic agents are described below. 85US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-279"
[0279]In some instances, the provided methods may include administering a CG1/HLA-Acomplex-specific antibody or antigen binding fragment thereof and a second form of cancer therapy to the subject. The second form of cancer therapy may include a cytotoxic agent, a chemotherapeutic agent, an immunosuppressive agent (including immune checkpoint inhibitors), or radiation therapy. In some embodiments, the second form of cancer therapy is an antibody (e.g., a monoclonal antibody). Monoclonal antibodies which may be administered as a second form of cancer therapy include, but are not limited to, rituximab (e.g., for treatment of B-cell lymphomas), trastuzumab (e.g., for treatment of breast cancer), and cetuximab (e.g., for treatment of lung cancer). id="p-280"
[0280]In some instances, the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof can be labeled, conjugated, or fused with a therapeutic agent or diagnostic agent (such as an imaging agent). The linkage can be covalent or noncovalent (e.g., ionic). Such antibodies and antibody fragments are referred to antibody-drug conjugates (ADC) or immunoconjugates. The antibody conjugates are useful for the local delivery of therapeutic agents, particularly cytotoxic or cytostatic agents, i.e. drugs to kill or inhibit tumor cells in the treatment of cancer allows targeted delivery of the drug moiety to tumors, and intracellular accumulation therein, where systemic administration of these unconjugated drug agents may result in unacceptable levels of toxicity to normal cells as well as the tumor cells sought to be eliminated. Therapeutic agents include but are not limited to toxins, including but not limited to plant and bacterial toxins, small molecules, peptides, polypeptides and proteins. Genetically engineered fusion proteins, in which genes encoding for an antibody, or fragments thereof including the Fv region, or peptides can be fused to the genes encoding a toxin to deliver a toxin to the target cell are also provided. As used herein, a target cell or target cells are myeloid malignancy antigen- positive cells. id="p-281"
[0281]In some embodiments, the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof is conjugated to a moiety that specifically binds to an immune cell. In some embodiments, provided is abispecific antibody comprising a CG1/HLA-A2 complex- specific antibody or antigen binding fragment thereof as described herein and an antibody or antigen binding fragment thereof that specifically binds to an immune cell. In some embodiments, the bispecific antibody comprises a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof and an antibody moiety that specifically binds to T cells. Such a molecule is referred to as a bispecific T cell engager and may induce T cell-mediated cytotoxicity of CG1/HLA-A2 complex-expressing cancer cells (see, e.g., Zhou et al., 2021, 86US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) Biomarker Research 9:38). In some embodiments, the bispecific antibody comprises a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof and an antibody moiety that specifically binds to natural killer cells (NK cells). Such a molecule is referred to as a NK cell engager and may induce NK cell-mediated cytotoxicity of CG1/HLA-Acomplex-expressing cancer cells (see, e.g., Demaria et al., 2021, European Journal of Immunology 51(8): 1934-1942). id="p-282"
[0282]In certain aspects, a CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof and CARs (or cells comprising CARs as described herein) according to the present disclosure can be administered as a co-therapy with other therapeutic agents. Other examples of therapeutic agents include chemotherapeutic agents, a radiotherapeutic agent, and immunotherapeutic agent, as well as combinations thereof. In this way, the antibody or peptide complex or CAR (or cell comprising a CAR) delivered to the subject can be multifunctional, in that it exerts one therapeutic effect by binding to the CG1/HLA-A2 complex and a second therapeutic effect by delivering a supplemental therapeutic agent. id="p-283"
[0283]The therapeutic agent can act extracellularly, for example by initiating or affecting an immune response, or it can act intracellularly, either directly by translocating through the cell membrane or indirectly by, for example, affecting transmembrane cell signaling. The therapeutic agent is optionally cleavable from the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof. Cleavage can be autolytic, accomplished by proteolysis, or affected by contacting the cell with a cleavage agent. id="p-284"
[0284]In some instances, the therapeutic agent is a cytotoxic agent. A cytotoxin or cytotoxic agent includes any agent that is detrimental to cells. Examples of toxins or toxin moieties include diphtheria, ricin, streptavidin, and modifications thereof. Additional examples include paclitaxel, cisplatin, carboplatin, cytochalasin B, gramicidin D, ethidium bromide, emetine, etoposide, tenoposide, colchicin, dihydroxy anthracin dione, mitoxantrone, mithramycin, actinomycin D, 1- dehydrotestosterone, glucocorticoids, procaine, tetracaine, lidocaine, propranolol, puromycin and analogs or homologs thereof. Therapeutic agents include, but are not limited to, antimetabolites (e.g, methotrexate, 6-mercaptopurine, 6-thioguanine, cytarabine, 5-fluorouracil, decarbazine), alkylating agents (e.g, mechlorethamine, thiotepa, chlorambucil, melphalan, carmustine (BSNU) and lomustine (CCNU), cyclothosphamide, busulfan, dibromomannitol, streptozotocin, mitomycin C, and cis-dichlorodiamine platinum (II) (DDP) cisplatin), anthracyclines (e. g., daunorubicin (formerly daunomycin) and 87US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) doxorubicin), antibiotics (e.g. , dactinomycin (formerly actinomycin), bleomycin, mithramycin, and anthramycin (AMC)), and anti-mitotic agents (e.g, vincristine and vinblastine). Cytotoxic peptides such as auristatin (antineoplastic) peptides auristatin E (AE) and monomethylauristatin (MMAE), which are synthetic analogs of dolastatin, may also be conjugated to the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof. In some instances, the CG1/HLA-A2 complex-specific antibody or antigen binding fragment thereof may be conjugated to a radioactive metal ion. id="p-285"
[0285]As referred to herein, a chemotherapeutic agent is a chemical compound useful in the treatment of cancer. Examples of chemotherapeutic agents include erlotinib (such as TARCEVA®, Genentech/OSI Pharm.), bortezomib (such as VELCADE®, Millenium Pharm.), fulvestrant (such as FASLODEX®, AstraZeneca), sutent (such as SUI 1248, Pfizer), letrozole (such as FEMARA®, Novartis), imatinib mesylate (such as GLEEVEC®, Novartis), PTK787/ZK222584 (Novartis), oxaliplatin (such as ELOXATIN®, Sanofi), 5-fluorouracil (5- FU), leucovorin, rapamycin (also known as sirolimus) (such as RAPAMUNE®, Wyeth), lapatinib (such as TYKERB®, GSK572016, GlaxoSmithKline), lonafarib (such as SCH 66336), sorafenib (such as BAY43-9006, Bayer Labs.), capecitabine (such as XELODA®, Roche), docetaxel (such as TAXOTERE®), and gefitinib (such as IRESSA®, Astrazeneca), AG1478, AG1571 (such as SU 5271; Sugen Inc.), alkylating agents such as thiotepa and cyclosphosphamide (such as CYTOXAN®); alkyl sulfonates such as busulfan, improsulfan and piposulfan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamines including altretamine, triethylenemelamine, triethylenephosphoramide, triethylenethiophosphoramide and trimethylomelamine; acetogenins (especially bullatacin and bullatacinone); a camptothecin (including the synthetic analogue topotecan); bryostatin; callystatin; CC-1065 (including its adozelesin, carzelesin and bizelesin synthetic analogues); cryptophycins (particularly cryptophycin 1 and cryptophycin 8); dolastatin; duocarmycin (including the synthetic analogues, KW-2189 and CB1-TM1); eleutherobin; pancratistatin; a sarcodictyin; spongistatin; nitrogen mustards such as chlorambucil, chlomaphazine, cholophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard; nitrosoureas such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, and ranimnustine; antibiotics such as the enediyne antibiotics (e.g, calicheamicin, particularly calicheamicin yi 1 and calicheamicin Or 1); dynemicin, including dynemicin A; bisphosphonates, such as clodronate; an esperamicin; as well as neocarzinostatin 88US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) chromophore and related chromoprotein enediyne antibiotic chromophores), aclacinomysins, actinomycin, anthramycin, azaserine, bleomycins, cactinomycin, carabicin, carminomycin, carzinophilin, chromomycinis, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L- norleucine, doxorubicin (such as ADRIAMYCIN®, including morpholino-doxorubicin, cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin and deoxydoxorubicin), epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins such as mitomycin C, mycophenolic acid, nogalamycin, olivomycins, peplomycin, potfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, zorubicin; anti-metabolites such as methotrexate and 5-fluorouracil (5-FU); folic acid analogues such as denopterin, methotrexate, pteropterin, trimetrexate; purine analogs such as fludarabine, 6-mercaptopurine, thiamiprine, thioguanine; pyrimidine analogs such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine; androgens such as calusterone, dromostanolone propionate, epitiostanol, mepitiostane, testolactone; anti- adrenals such as aminoglutethimide, mitotane, trilostane; folic acid replenisher such as frolinic acid; aceglatone; aldophosphamide glycoside; aminolevulinic acid; eniluracil; amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diaziquone; elfornithine; elliptinium acetate; an epothilone; etoglucid; gallium nitrate; hydroxyurea; lentinan; lonidainine; maytansinoids such as maytansine and ansamitocins; mitoguazone; mitoxantrone; mopidanmol; nitraerine; pentostatin; phenamet; pirarubicin; losoxantrone; podophyllinic acid; 2-ethylhydrazide; procarbazine; Trametes Versicolor polysaccharide-K (Krestin, PSK) (JHS Natural Products, Eugene, OR); razoxane; rhizoxin; sizofiran; spirogermanium; tenuazonic acid; triaziquone; 2,2', 2"-trichlorotriethylamine; trichothecenes (especially T-2 toxin, verracurin A, roridin A and anguidine); urethan; vindesine; dacarbazine; mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine; cytarabine (cytosine arabinoside, "Ara-C"); cyclophosphamide; thiotepa; taxoids, e.g., paclitaxel (such as TAXOL®, Bristol-Myers Squibb Oncology, Princeton, N.J.), ABRAXANETM (a Cremophor-free, albumin-engineered nanoparticle formulation of paclitaxel (American Pharmaceutical Partners, Schaumberg, IL)), and doxetaxel (such as TAXOTERE®, Rhone-Poulenc Rorer, Antony, France); chloranbucil; gemcitabine (such as GEMZAR®); 6-thioguanine; mercaptopurine; methotrexate; platinum analogs such as cisplatin and carboplatin; vinblastine; platinum; etoposide (VP-16); ifosfamide; mitoxantrone; vincristine; vinorelbine (such as NAVELBINE®); novantrone; teniposide; edatrexate; daunomycin; aminopterin; xeloda; ibandronate; CPT-11; topoisomerase inhibitor RFS 2000; difluorometlhylomithine (DMFO); retinoids such as retinoic acid; capecitabine; and pharmaceutically acceptable salts, acids or derivatives of any of the above. 89US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-286"
[0286]Chemotherapeutic agents, as used herein, also refers to (i) anti-hormonal agents that act to regulate or inhibit hormone action on tumors such as anti-estrogens and selective estrogen receptor modulators (SERMs), including, for example, tamoxifen (including NOLVADEX® tamoxifen), raloxifene, droloxifene, 4-hydroxytamoxifen, trioxifene, keoxifene, LY 117018, onapristone, and toremifene (such as FARESTON®); (ii) aromatase inhibitors that inhibit the enzyme aromatase, which regulates estrogen production in the adrenal glands, such as, for example, 4(5)-imidazoles, aminoglutethimide, megestrol acetate (such as MEGASE®), exemestane (such as AROMASIN®), formestanie, fadrozole, vorozole (such as RIVISOR®), letrozole (such as FEMARA®), and anastrozole (such as ARIMIDEX®); (iii) anti-androgens such as flutamide, nilutamide, bicalutamide, leuprolide, and goserelin; as well as troxacitabine (a 1,3-dioxolane nucleoside cytosine analog); (iv) aromatase inhibitors; (v) protein kinase inhibitors; (vi) lipid kinase inhibitors; (vii) antisense oligonucleotides, particularly those which inhibit expression of genes in signaling pathways implicated in aberrant cell proliferation, such as, for example, PKC-alpha, Ralf and H-Ras; (viii) VEGF receptor and angiogenesis inhibitors (including ribozymes such as ANGIOZYME®) and a HER2 expression inhibitor; (ix) vaccines such as gene therapy vaccines, for example, ALLOVECTIN-7® vaccine (plasmid/lipid complex containing the DNA sequences encoding HLA-B7 and 132 microglobulin), LEUVECTIN® vaccine (plasmid DNA expression vector encoding interleukin-2 (IL-2) complexed with a lipid delivery vehicle (DMRIE/DOPE)), and VAXID® vaccine (patient-specific naked DNA vaccine); IL-2 or aldesleukin (such as PROLEUKIN®); topoisomerase 1 inhibitors (such as TOPOTECAN®); gonadotropin- releasing hormone antagonists (such as ABARELIX®); (x) anti-angiogenic agents such as bevacizumab (such as AVASTIN®, Genentech); and (xi) pharmaceutically acceptable salts, acids or derivatives of any of the above. id="p-287"
[0287]In some instances, the treatment methods provided herein may further comprise administering an immunosuppressive agent such as an immune checkpoint inhibitor as part of the method. These treatments work by "taking the brakes off ’ the immune system (are immunosuppressive), allowing it to mount a stronger and more effective attack against cancer. Several different types of checkpoint inhibitors, targeting different checkpoints or "brakes " on immune cells, are currently in use. Exemplary immunosuppressive agents are PD-1 inhibitors (such as nivolumab and pembrolizumab), PD-L1 inhibitors (such as atezolizumab, durvalumab, and avelumab), and CTLA-4 inhibitors (such as ipilimumab). In one example, the second form of cancer therapy comprises a PD-L1 inhibitor, a PD-1 inhibitor, or a CTLA 90US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) inhibitor. In some instances, combinations of such inhibitors can be administered. In some instances, the PD-LI inhibitor, the PD-1 inhibitor, and/or the CTLA4 inhibitor may be an inhibitory antibody that binds specifically to PD-LI, PD-1, or CTLA4, respectively. id="p-288"
[0288]In some instances, the treatment methods provided herein may further comprise administering radiation therapy to the subject. Radiation therapy uses high-energy radiation to shrink tumors and kill cancer cells. X-rays, gamma rays, and charged particles are types of radiation used for cancer treatment. The radiation may be delivered by a machine outside the body (external-beam radiation therapy), or it may come from radioactive material placed in the body near cancer cells (internal radiation therapy, also called brachytherapy). Systemic radiation therapy uses radioactive substances, such as radioactive iodine, that travel in the blood to kill cancer cells.
EXAMPLES EXAMPLE 1: CGI IS PRESENTED ON SURFACE HLA-A2+ MYELOID LEUKEMIA. [0289]We first aimed to verify whether the CGIpeptide is indeed found on the surface of HLA-A2+ myeloid leukemia cells.
A. Materials and Methods id="p-290"
[0290] Cell lines.Healthy donor and patient samples were obtained after appropriate informed consent through an institutional review board approved protocol at the University of Texas MD Anderson Cancer Center. The AML samples were collected between 2006 and 20and were selected based on their AML subtype, percent blasts, sample viability and HLA status. U-937 (myelomonoblastic leukemia), Jurkat human T lymphocyte cell line were purchased from American Type Culture Collection (ATCC); MML-2 acute myelomonocytic leukemia cell line and EM-2 chronic myeloid leukemia cell line was purchased from Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ). Cell lines were cultured in standard media composed of RPMI-1640 with 25 mM HEPES+L-Glutamine (Hyclone) supplemented with 10% fetal bovine serum (FBS) (Gemini Bio-Products), and Penicillin (1U/mL)/ Streptomycin (100 ug/mL) (Cellgro). Cells were cultured at 37 °C and were kept in 5% CO2. Prior to cell line use, DNA finger-printing was performed at MD Anderson Cancer Center within six months to authenticate cell lins. Healthy donor and patient PBMC, bone marrow and granulocytes, were enriched using standard Histopaque 1077 or 1119 (Sigma) gradient centrifugation. 91US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-291"
[0291] Peptide elution for mass spectrometry analysis.For peptide elution, >1 x 10A7- x 10A8 leukemia cells and normal donor PBMCs underwent sonication in standard buffer containing protease inhibitors (Sigma). Cell lysate was subjected to ultra-centrifugation to remove cellular debris. Triton X-100 was added to the supernatant (1%), which were placed on a shaker overnight. Protein G magnetic beads were premixed with anti-HLA-A2 antibody BB7.2 (Santa Cruz), cell lysate was then added, and the lysate-bead mixture was placed on shaker at room temperature for 2 hours to precipitate HLA-A2-peptide complexes. Samples were washed, eluted and analyzed using Time-of-Flight (ToF) MS (Waters™, Milford, MA). Intact protein MS analysis was performed with a ACQUITY H-Class chromatography system coupled to a Xevo G2-XS QT0F Time-of-Flight MS (Waters™, Milford, MA). Samples were loaded on the ACQUITY Premier BEH C4 Column (Waters™). Formic acid (0.1%, v/v) in water and acetonitrile with 0.1% formic acid were used as eluents. The intact MS was deconvoluted by Unifi software from Waters. A heavy isotype labelled peptide (F)LLPTGAEA (F+10) was synthesized as the absolute quantification standard in the assay. Mascot algorithm was used to search acquired MS/MS spectra against the SwissProt complete human protein database. Search results were cross-referenced with the appropriate HLA-binding specificities using NetMHC 3.4 (website: cbs.dtu.dk/services/NetMHC ). Peptides eluted were compared to synthetic peptides by obtaining retention-time windows for the synthetic peptide, and then by targeted methods that were constructed using mass windows of 1 Da around each m/z.
B. Results id="p-292"
[0292]The anti-HLA-A2*0201 antibody BB7.2 (Santa Cruz) was used to perform immunoprecipitation (IP) of HLA-A2 molecules present in the cell lysate, along with their associated peptides. Following IP, the HLA-A2/peptide/p2m complexes were dissociated using an organic solution, and the fraction containing the peptides was analyzed using targeted ToF- MS with high sensitivity. This analysis involved the examination of cells from seven myeloid leukemia cell lines, including six acute myeloid leukemia cell lines, and one chronic myeloid leukemia in blast crisis cell line. Additionally, we examined CGI expression by T cell leukemia, solid tumor malignancies, including lung, breast, colon and ovarian carcinoma, as well as HLA-A2+ normal donor PBMC and neutrophils. Since U937 and MOLM13 cell lines are HLA-A2, these cell lines were transduced with HLA-A2 as previously described (Zhang M, et al. Clin Cancer Res. 2013;19(l):247-257; Rodriguez-Cruz TG, et al. PLoS One. 2011;6(8):e22939). The results are shown in Table A. 92US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-293"
[0293]In the eluted fractions, CGI was identified in all of the HLA-A2+ myeloid leukemia cell lines, confirming what we reported previously (Alatrash G, et al. Leukemia. 2017;31(l):234-237). Consistent with the known lack of endogenous expression of CG by non-myeloid malignancies, CGI was not eluted from solid tumor cell lines. Similarly, since CG is primarily expressed by normal granulocytes, we did not elute CGI from the surface of normal PBMC. Taken together, these findings provide confirmation that CGI is naturally processed and presented on the surface of HLA-A2+ myeloid leukemia blasts, thus highlighting its potential as an antigen associated with leukemia.
Table A. CGI peptide is eluted from cell surface of HLA-A2+ myeloid leukemia.
Cell line/type Disease HLA-A Genotype CGl/cell A2/Cell U937-A2 Acute Myeloid Leukemia03:01, 03:01; ATransduced 2300 12000TH P I Acute Myeloid Leukemia 02:01, 02:01 320 34000M0LM13-HAGE-A2 Acute Myeloid Leukemia A2 Transduced 2500 51000OCI-AML3 Acute Myeloid Leukemia 23:01, 02:01 750 11000ME2 Acute Myeloid Leukemia 02:01, 02:01 3700 63000SKM1 Acute Myeloid Leukemia 33:03, 02:07 10 17000 EM2Chronical Myelogenous Leukemia 02:01, 03:01 950 17000CCRF-CEM T cell leukemia AO2+ ND 10000DEC 1032 NSCLC AO2+ ND 160000H441 NSCLC 03:01, 02:01 ND 140000BT-549 Ductal Breast Carcinoma 01:01, 02:01 ND 9500MDA-MB-231 Breast Adenocarcinoma 02:17, 02:17 ND 540000Colo 205 Colon Adenocarcinoma 01:01, 02:01 ND 31000OVCAR3 Ovarian Carcinoma 02:01, 29:02 ND 5200HD Neutrophils Normal AO2 + ND 9500HD PBMC#1 Normal AO2 + ND 4900HD PBMC#2 Normal AO2 + ND 1500 EXAMPLE 2: MATERIALS AND METHODS [0294]The following example includes the various materials and methods used in developing and assessing the antibodies of this disclosure. The data from these experiments is subsequently described in Example 3. 93US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) 1. Quantitative and qualitative characterization of CGI peptide presented by HLA-A02 from various sources id="p-295"
[0295]Time of Flight-Multiple Reaction Monitor-mass spectrometry (TOF-MRM) analyses were performed from a Waters Xevo G2-XS QT of Quadrupole Time-of-Flight Mass instrument (Waters) with the analytical column, ACQUITY UPLC BEH C18 1.7 pm 1.0 x 150 mm (Waters). Fifteen microliters of all samples were loaded. Formic acid (0.1%, v/v) in water was used as eluent A, and ACN with 0.1% formic acid was used as eluent B. The flow rate was set to 0.1 ml/min and the column temperature was set to 65°C. The gradient of eluent B was increased from 0-50% for 70 min, followed by an increase to 90% for 10 min for the wash and 0% eluent B for 10 min for re-equilibration. IP samples from W6/32 or BB7.2 from different cell lines with stable isotope labelled peptides were spiked as the positive control and quantitative standards were injected into the system. Each peptide ’s collision energy and scheduled windows were optimized by stable isotope labelled CGI peptides (AQUA peptides with 95% concentration accuracy synthesized from Thermo Scientific), and samples of CGI peptide copy number per cell were calculated based on the ratio to AQUA CGI peptides and the whole cell number in the IP samples. id="p-296"
[0296]The availability analysis of CGI peptides presented to CML and AML patients was analyzed based on the LC-MS/MS DDA data of W6/32 IP samples from CML, AML patients Blasts (website: ebi.ac.uk/pride/ ). Analysis was run on PEAKs Studio with 10 ppm parental and 0.25 Da Daugher ion windows (website: bioinfor.com ). 2. Antibody discovery, top clinical lead selection and BsAb construction id="p-297"
[0297]CGI (FLLPTGAEA (SEQ ID NO:61)) was refolded with recombinant HLA-A2 and p2-microglobulin. H2L2 human transgenic mice were purchased from Harbour BioMed (Boston, MA) and immunized with CG1/HLA-A2 monomers subcutaneously in a 1:1 volume mix of monomer (50 g) and Ribi adjuvant (S6322-lvl, Sigma). Mice were immunized 5- times at 2-week intervals, followed by the last boost injection of antigen alone 3-days prior to splenocyte harvest. id="p-298"
[0298]Single B-cell Cloning (SBCC) technology was utilized to amplify variable heavy and variable light gene regions from the cDNA of CGI monomer immunized H2L2 mouse memory B cells. The naturally paired variable regions were cloned into pcDNA3.1+ human (h) immunoglobulin (Ig)Gl and hKappa expression vectors for subsequent ExpiCHO (Thermo Scientific) high throughput transient expression in 96-well format. 94US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-299"
[0299]High-throughput production of mAbs was performed by micro-scale transfection (mL) of paired heavy and light chain antibody sequences cloned into single expression vector in Chinese Hamster Ovary (CHO) cells using the deep 96-well plate Gibco™ ExpiCHOTM Expression System. (ThermoFisher Scientific). Briefly, synthesized antibody-encoding DNA (0.8 pg per transfection) was diluted in OptiPro serum free medium (OptiPro SFM), incubated with ExpiFectamine CHO Reagent and added to 750 pL of ExpiCHO cell cultures into sterile deep well plates using a ViaFlo 96 liquid handler (Integra Biosciences). Plates were placed in an Infors HT Multitron Pro incubator shaking at 1,000 rpm with 3 mm orbital diameter at 37°C in 8% CO2 and 80% humidity. The day after transfection, ExpiFectamine CHO Enhancer and ExpiCHO Feed reagents were added to the cells, followed by 6 days incubation at 32°C in 5% CO2 and 80% humidity. id="p-300"
[0300]Cells were harvested by centrifugation at 1500 x g for 10 min. Supernatants were then transferred to new deep 96-well plates for high throughput micro-scale purification. Briefly, clarified culture supernatants were incubated with 15 pL MabSelect resin (Cytiva, formerly GE Healthcare Life Sciences) on a 3mm orbital shaker at lOOOrpm at RT to capture mAb. The mixture was then transferred to pre-equilibrated fritted deep well filter plates, washed with PBS, eluted with 100 pL 50mM phosphoric acid pH 3.0 into 96-well plates containing 15 pL neutralization buffer (20X PBS pH 11.0). id="p-301"
[0301]After Protein-A magnet beads purification, binding affinities of each clone were assayed by Bio-Layer Interferometry (BLI) with anti-human IgGFc capture (AHC) biosensors to CGI monomer. The specificity of antibodies was determined by screening HLA-Amonomer presenting different sequence peptides. Positive clones were then expressed at mg levels for further cell surface EC50, cross-reactivity, epitope binning, specificity, and stability assays. id="p-302"
[0302]To generate bispecific CGl-16xCD3e, CGI-16 heavy and light chain gene regions were cloned into hlgGl or hKappa pcDNA3 .1+ expression vectors respectively. Xencor CD3e antibody and heterodimeric Fc technology was applied for the bispecific antibody (BsAb). CGl-16xCD3e was expressed in ExpiCHO cells through transient transfection, and then purified using Protein-A column (AKTA FPLC system). Binding of CGl-16xCD3e with CGI monomer and CD3e antigen were also tested by BLI. 95US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) 3. Mid or large-scale mAb production and purification id="p-303"
[0303]For larger scale mAb or bispecific antibody expression, we performed transfections of CHO cell cultures using the Gibco™ ExpiCHOTM Expression System in 125 mL Erlenmeyer vented cap flasks (Corning) containing 35 mL (Mid-scale) of ExpiCHO cells or 2000 ml Erlenmeyer vented cap flasks (Corning) containing 500 mL of ExpiCHO cells (Large-Scale) following the manufacturer ’s protocol. Antibodies were purified from filtered culture supernatants by fast protein liquid chromatography (FPLC) on an AKTA Pure instrument using a 1 mL HiTrap MabSelect PrismA column (Cytiva, formerly GE Healthcare Life Sciences). Purified mAbs were concentrated and buffer exchanged into PBS using Amicon® Ultra-50KDa Centrifugal Filter Units (Millipore Sigma), filtered using sterile 0.2-um pore size filter devices (Millipore), and stored in aliquots at 4°C until future use. 4. Biolayer Interferometry (BLI) for Anti-CGI monoclonal antibody screening id="p-304"
[0304]BLI assays were performed on the Octet Red384 instrument at 30°C with shaking at 1,000 RPM. The monoclonal antibody (mAb) high throughput (HTP) binding screen was performed after 96-well high-throughput expression and protein A purification. 100 nM of different anti-CGl monomer clones were loaded to either AHC Biosensors for 600 seconds . After loading, the baseline signal was then recorded for 60 seconds in 10X Kinetics Buffer from the vendor (10X Buffer comprises phosphate-buffered saline with 0.2% IgG free, Protease free BSA and 0.01% Azide). The sensors were then immersed in 10X Kinetics Buffer containing different concentrations of CGI monomer or other control monomers (Baylor Tetramer Core), for 600 seconds. The dissociation was then measured for 600 seconds by immersing sensors in 10X Kinetics Buffer. As a control for non-specific binding, the background signal of empty sensors with loading BSA was subtracted at each time point. For kinetic analyses for either mid or large-scale antibodies were captured on AHC sensors, ligands were diluted to 100 nM in 1 Oxkinetics Buffer and loaded for 600 seconds. After loading, the baseline signal was then recorded for 1 min in 1 Oxkinetics Buffer. The sensors were immersed into wells containing CGI monomer, CGI monomer with Ala replacement, or controlled monomers with 100 nM and 20 nM in 1 OX Kinetics Buffer for 600 seconds (association phase), followed by immersion in 10X Kinetics Buffer for an additional 600 seconds (dissociation phase). The background signal from each analyte-containing well was measured using empty reference sensors coated with same concentrations of BSA and subtracted from the signal obtained with each corresponding mAb loaded sensor. Kinetic analyses were performed at least twice with an independently prepared analyte dilution series. Curve fitting was performed using 96US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) a 1:1 binding model and the ForteBio data analysis software. Mean kon, koff values were determined by averaging all binding curves that matched the theoretical fit with an R2 value of >=0.95. The germlines of each clone was calculated by IgBlast (ncbi.nlm.nih.gov/igblast/ ).
. BLI binding assays for for CGI-16 x CD3e bispecific antibody screening id="p-305"
[0305]Binding of CGI-16 x CD3e with CG1/HLA-A2 monomers and CD3e antigen was tested using Octet® BLI using AR2G biosensors and cellular binding assays. BLI assays were performed on the Octet® Red384 instrument at 30°C with shaking at 1,000 RPM Bispecific antibodies were captured on AR2G sensors, ligands were diluted to 100 nM in lOx Kinetics buffer and loaded for 600 seconds. After loading and quenching of the active AR2G surface by M ethanolamine, the baseline signal was then recorded for 1 minute in lOx Kinetics buffer. Different concentrations (100 nM and 20 nM) of CG1/HLA-A2 or CD3e antigens in lOx Kinetics buffer were bound to the sensors for 300 seconds and dissociated in lOx Kinetics buffer for the other 300 seconds. The kinetics values were fitted using Octet® software. id="p-306"
[0306]For cellular binding assays, EM2 cells (HLA-A2 positive) or Jurkat T-cells (HLA- A2 negative) cells were placed in a 96-well plate. Cells were blocked with FcR Blocker (TruStain FcX) and serum, and stained with the following Alexa-647 conjugated antibodies: CGI-16 x CD3 bispecific antibody, CGI-16 hlgGl, Velo 8CD138LC x CD3 bispecific antibody, and isotype control antibody. Flow cytometry was done on live cells using a BD LSR Fortessa, and data were analyzed using FlowJo software (FlowJo). 6. CGl-16xCD3 BsAb functional assays id="p-307"
[0307]For functional assay, GFP+ U937-A2, ML2 or EM2 cells were incubated with CGI- 16xCD3 BsAb or a control BsAb (CGI-16 arm disabled, but anti-CD3 arm still active) before addition of human T cells (2:1 E:T ratioT) followed by culture for 48 hrs. The levels of activation marker CD69 were measured on CD3+ GFP- cells. The killing efficiency were detected by GFP+ tumor cell lines after 48 h incubation at 37°C, 5% CO2 condition by Flow cytometry with different concentrations of CGl-16xCD3 BsAb or control mAb. The cytokines (IFNy, IL2 and TNFa) concentrations after bispecific engaged T-cells killing assay after 48h were detected by MSD standard protocol following its manual instructions (MSD, MD). id="p-308"
[0308]A flow cytometry-based T cell-dependent cellular cytotoxicity (TDCC) assay was used to evaluate CG1-16/CD3 bispecific antibody killing of target cells. For bispecific antibody cytotoxicity, 1 x 10A4 GFP- or mCherry-expressing target cells were co-cultured with 5 x 10A 97US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) normal donor T cells in the presence of increasing concentrations of CG1-16/CD3 or a negative control bispecific antibody. The negative control antibody was created as a human bispecific antibody with Vel08 heavy chain and CD138 light chain, employing the same CD3e (Xencor) used in the bispecific construct, which binds to CD3 but not any other human molecules. After incubation for 24 and 72 hours, flow cytometry was used to quantify live/dead target cells by using light scatter to determine viability, and GFP and mCherry to exclude target cells. 7. Cell line and patient-derived xenograft models id="p-309"
[0309]All animal experiments were approved by and conformed to the relevant regulatory standards of the Institutional Animal Care and Use Committee at the MDACC. NOD/SCID gamma (NSG™) mice (NOD.CgPrkdcscid I12rgtmlWjl/SzJ, Jackson Laboratory) at 6-weeks old were used. Primary AML samples or luciferase-expressing human AML cell lines (ML2/Luc, U937-A02; Perkin Elmer) were administered via tail vein at a dose of 1 x 10A6 to x 10A7 cells to sub-lethally irradiated (250 eGy) mice. Engraftment was assessed by imaging using IVIS (PerkinElmer). Peripheral blood was analyzed by flow cytometer to determine the percentage of AML cells. Once the tumor was established, I x 10A7 PBMC/mouse were administered via tail vein injection for humanization. Three to four days after humanization, mice were randomized into control and bispecific treatment groups and mice were either treated with vehicle control or CGl-16xCD3 weekly at different doses. Leukemia was monitored using peripheral blood analysis for human leukemia blasts or bioluminescence imaging, the latter was used only for cell lines (Provasi E,. et al. Nat Med. 2012; 18(5):807-815). Mice were sacrificed at approximately 4 weeks following antibody treatment, or when mice became moribund. Bone marrow (BM) was processed using standard methodology and analyzed for residual human AML by flow cytometry as previously described (Provasi et al. 2012; Sergeeva A, et al. Leukemia. 2016 Jul; 30(7): 1475-1484). The following flow cytometry antibodies were used to identify the leukemia: CD13, CD33 (BD Biosciences, Sparks, MD), CD3, hCD(BioLegend, San Diego, CA), mouse (m)CD45 (eBioscience, San Diego, CA) and GFP. 8. Histology id="p-310"
[0310]Immunohistochemistry was used to determine the effects of CGl-bispecific Ab on residual AML. Mouse bone marrow and spleen was harvested and fixed in 10% formalin. The fixed marrow was stained with myeloperoxidase (MPO) and hematoxylin and eosin prior to histologic examination. 98US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) 9. Pharmacokinetics (PK) in mice id="p-311"
[0311]Single dose PK of CGl-16xCD3 was studied in human CGI and HLA-Atransgenic mice (the Jackson Laboratory). For the PK in NSG mice, animals were randomized into treatment groups, and were i.p. injected with 1B7/CD3 at 0.1, 0.3 and 1 mg/kg (n=5). For PK in humanized NSG mice, lx 107 PBMC were IV injected into the mice 10 days prior to randomization for dosing. Blood samples were collected at indicated time points post injection through serial sampling and processed to plasma for bioanalytical and PK analyses. Concentrations of 1B7/CD3 in plasma samples were measured using antigen coated ECL based ELISA (MSD, MD). PK analyses were performed according to standard non-compartmental analysis using WinNonlin package (v. 6.3, Pharsight, Certara Company).
. Statistical analysis id="p-312"
[0312]Statistical significance in drug-treated versus control in tumor xenograft models was determined by using the Student ’s t test or One-way ANOVA. 11. In vitro T cell activation and phenotyping assays id="p-313"
[0313]Target leukemia cells (1 x 10A4) were co-cultured with normal donor T cells (5 x 10A4) and bispecific antibodies (1 ug/mL) for 48 hours. Cells were then surface stained with CD3 (BD Biosciences) and CD69 (Biolegend) and analyzed using flow cytometry. In addition, secreted IFN-y, IL-2 and TNF-a were detected using Meso Scale Discovery assay (Meso Scale Diagnostics, LLC). 12. Colony Forming Unit (CFU) Assay id="p-314"
[0314]CFU assays using HLA-A2+ bone marrow from healthy donors were used to investigate the effects of CGl/HLA-A2-CD3e bispecific antibody on normal hematopoiesis, as previously done (Alatrash G, et al. Leukemia. 2017; 31(l):234-237; Alatrash G, et al. Clin Cancer Res. 2019; 25(8):2610-2620). Healthy donor marrow was cultured in RPMI with 1% penicillin/streptomycin for 24 hours. PBMCs were added to bone marrow cells and co-cultured at a ratio of 1:5 in 500 pL RPMI supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin for 4 hours in a 48-well plate. After incubation, the cultures were suspended in 350 pL of Iscove ’s Modified Dulbecco's Media (IMDM) with 2% FBS and added to settled 3.2 mL of MammoCult™ H4034 Optimum Human Medium (STEMCELL Technologies, Cambridge, MA). These mixtures were then transferred to 6-well plates and incubated for 10-14 days. On Day 14, the CPUs were visualized and counted using a Leica 99US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) DMi8 microscope. To confirm the phenotype of the cells, the wells were incubated at 4°C for hours and washed with 2 mL of IMDM and phosphate-buffered saline (PBS) for antibody staining. The cells were stained with fluorescently conjugated antibodies against CD3, CD4, CDS, CD14, CD16, CD19, CD33, CD34, and live/dead Aqua using products from BD Biosciences (Sparks, MD) and eBioscience (San Diego, CA).
EXAMPLE 3: DEVELOPMENT OF BISPECIFIC T CELL RECEPTOR (TCR)-LIKE ANTIBODIES TARGETING A2/CG1 FOR MYELOID MALIGNANCY [0315] Overview.In general, there is a direct correlation between the affinity and activity of an antibody, with higher affinity antibodies demonstrating more potent anti-tumor activities. To generate high affinity antibodies, the inventors used a vaccination approach in the generation of the CG1/HLA-A2 Fab, rather than an antibody display library, with an aim to obtaining more potent antibodies for use in cancer immunotherapy. Specifically, humanized mice (i.e. Harbour mice) were immunized with CGl/pMHC monomers to generate antibodies that target CGl/pHLA. First, the immunization approach utilizes the physiologic affinity maturation processes that yield antibodies with high affinity for antigen. Secondly, using Harbour mice, allows for the direct generation of humanized antibodies, bypassing the requirement for humanizing antibodies after their generation. Antibodies that are not fully humanized can cause major immune complications when infused to humans, urthermore humanizing murine antibodies runs the risk of interfering with the tumor antigen binding moiety and altering the originally generated affinity of the murine antigen binding domain for its target. id="p-316"
[0316]A bispecific antibody approach was chosen because bispecific antibodies provide an off-the-shelf product that can be readily infused into patients. Furthermore, there is minimal engineering required for bispecific antibodies (vs. cell therapies), and considering that AML can be a rapidly fatal disease, a bispecific antibody approach may be ideal in the AML setting. The optimal timing of bispecific antibodies in AML would be in the post induction setting where there is a lower disease burden and an adequate immune system, specifically T cells, to be engaged by the bispecific antibody. Another potential setting for CGI bispecific antibody may be the post stem cell transplant setting, where there is a potent donor-derived immune system with functional donor-derived T cells that could be recruited to sites of AML through engagement with CGl-bispecific. 100US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-317"
[0317] Table 2shows CGI peptides dominantly presented on CML/AML HLA-A*O2+, but not HLA-A*02- Samples from both MRM assays quantitively and characterization of peptide LD. from CML and AML patients. Rows 1-17 were identified from TOF-MRM Quantification; rows 18-20 were identified from ProteomeXchange Open Proteomics Database for Peptide I.D.).
Table 2. CML/AML HLA-A*02+ dominantly presented CGI peptides Cells/Tissue Diseases A*O2 Positive/Negative CGl-HLA- A*O2 Copies Source 1Healthy Neutrophil Neutrophil AO2+ NDHealthy DonorsHealthy PBMC#P98Healthy PBMC AO2+ NDHealthy DonorsHealthy PBMC#881Healthy PBMC AO2+ NDHealthy DonorsDFC1032 Lung cancer A*02:01 NDNon- AML/CML Cell linesBT-549Breast AdenocarcinomaA*O2:17 NDNon- AML/CML Cell linesH441Lung AdenocarcinomaA*02:01 NDNon- AML/CML Cell linesC0102O5Colon AdenocarcinomaA*02:01 NDNon- AML/CML Cell linesOVCAR3Ovarian CarcinomaA*02:01 NDNon- AML/CML Cell linesCCRE-CEM T cell leukemia AO2+ NDNon- AML/CML Cell linesHL60-A2AcutePromyelocyticLeukemiaA*02:TransducedNDNon- AML/CML Cell linesTHP-1Acute Myeloid LeukemiaA*02:01 320AML/CML Cell linesMOLM13-HAGEAcute Myeloid LeukemiaA*02:Transduced2500AML/CML Cell linesOCI-AML3Acute Myeloid LeukemiaA*02:01 750AML/CML Cell linesU937/A2Acute Myeloid LeukemiaA*02:Transduced2300AML/CML Cell linesEM2Chronical Myelogenous LeukemiaA*02:01 950AML/CML Cell linesSKM1Acute Myeloid LeukemiaA*02:07 10AML/CML Cell lines 101US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) 17ML2Acute Myeloid LeukemiaA*02:01 3700AML/CML Cell lines Patients CML(20)Chronical Myelogenous LeukemiaA02+ (10); A02- (10)ND A02+: 7 of Caught CGI Signal;A02-:0oflCaught CGI Signal Patients AML(14, Stanford Studies)Acute Myeloid LeukemiaA02+ (2); A02- (12)ND A02+: 1 of Caught CGI Signal;A02-: 0 of Caught CGI Signal Patients AML(29, Tubingen Studies)Acute Myeloid LeukemiaAO2+ (16); A02- (13)ND A02+: 6 of Caught CGI Signal;A02-:0oflCaught CGI Signal A. Statistics of CG1-HLA-AO2 TCR mimic antibody campaign. [0318]Twenty-seven unique antibodies were developed and then screened against peptides-HLA-AO2 monomer to determine their specificities. Three different groups of antibodies were identified according to antibody binding domain classification. Group #antibodies covered only the N-terminal of CGI (CGI-46, CGI-44, CGI-65, CGI-33, CGI- 15, CGI-12, CGI-6, CGI-182, CGI-183, CGI-194). Group #2 antibodies covered the N- terminal and Middle of CGI (CGI-61, CGI-68, CGI-33, CGI-189, CGI-177). Group #antibodies covered the N-terminal, middle, and C-terminal of CGI (CGI-55, CGI-27, CGI- 23, CGI-16, CGI-41, CGI-10, CGI-60, CGI-74, CGI-78, CGI-176, CGI-179). Of these antibodies, 12 had a KD of < I nM, 13 had a KD of greater than or equal to I nM but less than 10 nM, I had a KD of greater than or equal to 10 nM but less than 100 nM, and I had a KD of greater than or equal to 100 nM . The germline distributions of the 27 antibodies is shown in FIG. 4C. id="p-319"
[0319] Table 3provides details for the affinity and specificity to HLA-A2/CG1 for a panel of selected anti-CGl/A2 antibody leads. Table 4shows that selected top lead antibodies specifically bind to CG1/HLA-A2 complex. Specifically, the 6 top leads from group #3 (16, 23, 27, 55, 60, 61) and Group #1 antibody 46 binding specificities to different monomer showed. Table 5shows a sequence alignment of the antigens against which the lead antibody candidates were tested. 102US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) Table 3: A panel of selected anti-CGl/A2 leads affinity and specificity to HLA-A2/CG1 Orbit Name IgG hCGl- A2 monomer KD(M) Affinity CGI Cross- reactive to non-specific peptide CMA Cross- reactive to non-specific peptide PI3K Cross- reactive to non-specific peptide CMV Cross- reactive to non-specific peptide MIF4G CGI-16 1.42E-10 NO NO NO NOCGI-23 3.44E-09 NO NO NO NOCGI-27 5.68E-10 NO NO NO NOCGI-60 2.20E-10 NO NO NO NOCGI-61 2.53E-10 NO NO NO NO Table 4: Selected leads specifically bind to CG1/HLA-A2 complex Leads CGI CMAI PI3K MIF CMV Papl35 CGI-16 +++ - + + - - CGI-23 +++ - + - - - CGI-27 +++ - + + - - CGI-46 +++ - +++ +++ +++ - CGI-55 +++ - + - - - CGI-60 +++ - + + - - CGI-61+++ - + ++ - - Table 5: Sequence Alignment of Antigens of the Present Disclosure Antigen Sequences (consensus sequences w/ CGI bold and underlined) SEQ ID NO: CGI FL L P T G A E A FL L C S R A E A FL L P T G V ¥ L FL L P T G L S S LNLVPMVATVIL L W Q P I P V 61CMAI 62P13 63MIF 64CMV 65PAP135 66 id="p-320"
[0320] Table 6shows a Protein Profile Panel (3P) for CGI Top leads in a Specificity Assay. MSD was applied in the assay with anti-Human Fc CH3 monoclonal antibody GG-5 with sulfo- tag conjugated as the detection antibody. Herceptin, Keytruda, Tecentiq were applied as the control antibodies. Coated CGI monomer, Her2, PD-L1 or PDI recombinant proteins as the positive signal control in the assays (emphasized = PC ratio to blank, ratio of the positive coated antigen signal the negative control (bovine serum albumin (BSA) coated)). 103US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) Table 6 - Part 1: Protein Profile Panel (3P) for CGI Top leads Specificity Assay: CGI- 16, CG1-23, CG1-27, CGI-46.
CGI-16 CGI-23 CGI-27 CG11-46 lOOnM lOnM lOOnM lOnM lOOnM lOnM lOOnM lOnMserum albumin (human)1 4 0 0 0 0 0 serum albumin (bovine)0 0 0 0 0 0 0 fibrinogen (bovine plasma)0 0 0 0 0 0 0 hemoglobin (human)0 0 0 0 0 0 0 apo-transferrin (bovine)0 0 0 0 0 1 0 Al-antitrypsin (human)0 0 0 0 0 0 0 lysozyme (chicken egg)0 0 0 0 0 0 0 pepsinogen (porcine)0 0 0 0 0 0 0 amyloglycosidase (fungus)0 0 0 0 0 0 0 trypsin inhibitor (soybean)0 0 0 0 0 0 0 cytochrome c (bovine)0 0 0 0 0 0 0 myoglobin (horse)0 0 0 0 0 0 0 lectin (lentil) 19 1 1 0 1 0 22 3ovalbumin (chicken egg)0 0 0 0 0 0 0 blank 0 0 0 0 0 0 0 0trypsinogen (bovine)0 0 0 0 0 0 0 Rnase A (bovine) 1 0 0 0 0 0 0 0Rnase B (bovine) 1 0 0 0 0 0 1 0milk powder 0 0 0 0 0 0 0 0CGI monomer 1239 1196 548 558 210 222 590 617CMV monomer 1 0 0 0 0 0 4 2Pap3 monomer 0 0 0 0 0 0 0 0Her2 3 1 1 0 6 1 0 0PD-1 1 1 0 0 2 3 0 0PD-LI 26 2 3 0 1 1 1 0Streptavidin- Epitopes0 0 0 1 1 0 0 CGI monomer 1048 898 549 471 755 767 407 389blank 0 0 0 0 0 0 0 0CBR(100, lOnM)7 10 0 10 7 29 4 2CBR 76 11 17 34 104US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) Table 6 - Part 2: Protein Profile Panel (3P) for CGI Top leads Specificity Assay: CGI- 60, CG1-61, Herceptin™, Keytruda™.
CGI-60 CGI-61 Herceptin™ (trastuzumab) Keytruda™ (pembro izumab) lOOnM lOnM lOOnM lOnM lOOnM lOnM lOOnM lOnMserum albumin (human)0 1 0 15 2 0 0 serum albumin (bovine)0 0 0 0 0 0 0 fibrinogen (bovine plasma)0 0 0 0 0 0 0 hemoglobin (human)0 0 0 0 0 0 0 apo-transferrin (bovine)0 0 0 0 0 0 0 Al-antitrypsin (human)0 0 0 0 0 0 0 lysozyme (chicken egg)0 0 0 0 0 0 0 pepsinogen (porcine)0 0 0 0 0 0 0 amyloglycosidase(fungus)0 0 0 0 0 0 0 trypsin inhibitor (soybean)0 0 0 0 0 0 0 cytochrome c (bovine)0 0 0 0 0 0 0 myoglobin (horse)0 0 0 0 0 0 0 lectin (lentil) 1 1 1 0 0 0 4 0ovalbumin (chicken egg)0 0 0 0 0 0 0 blank 0 0 0 0 0 0 0 0trypsinogen (bovine)0 0 0 0 0 0 0 Rnase A (bovine) 0 0 0 0 0 0 2 0Rnase B (bovine) 0 0 0 0 0 0 0 0milk powder 0 0 0 0 0 0 0 0CGI monomer 1467 1127 831 791 0 1 0 0CMV monomer 0 0 0 0 1 1 1 0Pap3 monomer 0 0 0 0 0 0 0 0Her2 0 0 0 0 18241 16291 6 2PD-1 0 0 0 0 200 23 17883 17009PD-LI 1 0 2 1 14 3 6 3Streptavidin- Epitopes0 0 0 1 1 1 1 CGI monomer 1110 856 730 756 1 1 1 0blank 0 0 0 0 1 0 0 0 105US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) CBR(100, lOnM)2 5 1 234 32 23 8 2CBR 3 6 266 31 Table 6 - Part 3: Protein Profile Panel (3P) for CGI Top leads Specificity Assay: Tecentriq™.
Tecentriq™ (atezolizumab) lOOnM lOnMserum albumin (human) 6 1serum albumin (bovine) 0 0fibrinogen (bovine plasma) 0 0hemoglobin (human) 0 0apo-transferrin (bovine) 0 0Al-antitrypsin (human) 0 0lysozyme (chicken egg) 0 0pepsinogen (porcine) 0 0amyloglycosidase (fungus) 0 0trypsin inhibitor (soybean) 0 0cytochrome c (bovine) 0 0myoglobin (horse) 0 0lectin (lentil) 1 1ovalbumin (chicken egg) 1 0blank 0 0trypsinogen (bovine) 0 0Rnase A (bovine) 0 0Rnase B (bovine) 0 0milk powder 0 0CGI monomer 1 0CMV monomer 3 0Pap3 monomer 3 0Her2 10 2PD-1 3 1PD-LI 3039 2617Streptavidin-Epitopes 0 0CGI monomer 1 0blank 0 0CBR(100, lOnM) 30 62CBR 3 6 B. T2 cell surface binding specificity analysis for top lead antibody candidates. id="p-321"
[0321]Lead antibodies only bound to CGI spiked T2 cells, and did not bind to the control peptides. Clone 46 from Group #1 is applied as the control. As can be seen in FIGs. 5A-5F, lead compounds CGI-16 (FIG. 5A),CG1-23 (FIG. 5B),CG1-27 (FIG. 5C),CG1-46 FIG. 5D),CGI-60 (FIG. 5E),and CGI-61 (FIG. 5F)show specificity to HLA-A2/CG1. 106US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-322"
[0322] FIGs. 5G-5Nare plots showing lead Anti-HLA-A2/CG1 compounds recognize their target on leukemia cell lines: U937-A2 (FIG. 5G),MV4-11-A2 (FIG. 5H),THP-1 (FIG. 51), MOLM-13-A2 (FIG. 5 J),OCI-AML3 (FIG. 5K),EM2 (FIG. 5L),SKM-1 (FIG. 5M),and ML-2 (FIG. 5N).Clone 46 has higher MFI from different A02+ leukemia cell lines for its non- specific binding.
C. Characterization of specificities of the top lead CGI-16 to HLA-A*02-CGl with different techniques. id="p-323"
[0323]A cartoon depiction of the CGI-bispecific antibody CGI-16 is shown in FIG. 8A. The structure of the bispecific antibody was confirmed using SDS-page gel electrophoresis (data not shown). Two bands were observed under reducing conditions, consistent with heavy chain and light chain, the latter composed of the CG1-HLA-A2 binding moiety light chain, as the CD3e binding moiety is composed of scFv. As expected, non-reducing conditions demonstrated primarily a single band representing the intact bispecific antibody. id="p-324"
[0324]In silico docking data was generated using Molecular Operating Environment (MOE). This analysis indicated that the CGI-16 antibody variable region fully covers CGI peptide and HLA-A02 surface (data not shown). id="p-325"
[0325]Hydrogen Deuterium Exchange (HDX) mass spectrometry in amino acids resolution indicates CGI-16 binding epitope covers most of CGI peptide. This data is shown in FIGS. 6A-6B.Characterized Peptide area was quantified from LC-MS/MS after CGI-immunoprecipitation from 1 x 10A7 ML2 cell plasma membrane pellet (graph not shown). None of the HLA-A02 presenting peptides tested from ML2 cell lines bind significantly to the CGI-16 antibody. id="p-326"
[0326]Alanine replacement analysis indicates that CGI-16 binds to 4-8 amino acids of the CGI peptide. This data is summarized in Table7. Table 8:summarizes CGI-16 binding affinities to CGI monomer as assessed by BEI assays using different formats. 107US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) Table 7: Ala replacement assay indicates that CGI-16 Binding to 4-8 AAs of CGI peptide.
Sequences/Affinity Changes CGI-16 Fold Change FLLPTGAEA 1.0ALLPTGAEA 3.0 <3 timesFALPTGAEA 3.0 <3 timesFLAPTGAEA 1.9 <3 timesFLLATGAEA 20.2 12-24 timesFLLPAGAEA 17.0 12-24 timesFLLPTAAEA 41.2 >24 timesFLLPTAAEA 10.3 12-24 timesFLLPTGAAA 33.5 >24 timesFLLPTGAEG 6.0 6-12 times Table 8: CGI-16 affinities to CGI monomer with different format of BLI assays.
Loading Analyte KD (M) Kon (1/Ms) Kdis (l/s) CGI-16 IgG CGI Monomer 1.40E-10 2.01E+05 2.86E-05 CGI Monomer CGl16 ־xCD3e 7.50E-10 2.25E+05 1.69E-04 CGI Monomer CGl-16Fab 8.07E-09 1.23E+04 9.91E-05 D. CGl-16xCD3e Bispecific antibody design and characterization. id="p-327"
[0327]Octet® Bio-Layer Interferometry (BLI) technology was used to determine the binding avidity and affinity of the bispecific antibody to CD3 and to CG1/HLA-A2 monomers, respectively (FIGS. 8A-8B).After coating AR2G biosensor with bispecific antibody, CD3e- Fc was added at 100 nM and 20 nM concentrations. The binding avidity of the bispecific antibody to CD3e was high (KD= 7.52 x 1010־ M; K-on=2.25 x 105 1/Molar x seconds [Ms]; K-off= 1.69 x 101 4־/second [s]). The same methodology using CG1/HLA-A2 monomer at 1nM and 20 nM was used to calculate the binding affinity of the bispecific antibody to CG1/HLA-A2, which was also high (KD= 1.28 x 1010־ M; K-on=1.25 x 105 l/Ms; K-off= 1.x 104־ l/s). Of note, the data show that the affinity of CGI bispecific to G1/HLA-A2 is much higher than the affinity of the CD3e arm for its cognate ligand. id="p-328"
[0328]Cellular assays were also performed using flow cytometry to show the binding kinetics of the bispecific antibody to cell lines. The CGI-expressing EM2 HLA-A2+ CML cell line (Table A) was used, and it was found that CGl-CD3e and CGI Fab showed high 108US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) affinity for CG1/HLA-A2 (FIGs. 8C-8D).Similarly, CGl-CD3e for CD3 demonstrated high avidity using Jurkat T cell line, as Jurkat cells lack HLA-A2, CG and CGI. id="p-329"
[0329]Intact protein mass spectrometry (MS)was performed to assess the expressed CGI- 16xCD3e bispecific antibody, which indicated that the antibody was intact (no detectable fragments; data not shown). id="p-330"
[0330]UHPLC-SEC was performed to assess the purity of monomer bispecific antibody. This analysis showed that the preparation was a highly pure, homogenous preparation (FIG. 8E). id="p-331"
[0331]Stability assay of CGlxCD3e bispecific antibody at 4° and 37° C in the concentration of img/ml with 20 mM arginine in PBS solution. The CD3e sequence is further described in U.S. Patent Publication No. US2014/0377270A1, which is incorporated by reference as if set forth herein regarding the nucleotide and/or amino sequence of antibody CD3e. This data is shown in FIG. 8F.
E. In vitro killing and T-cells activation assay of CGl-16xCD3e Bispecific antibody indicate A02 and CGI-16 arm dependent killing and T-cell activation. id="p-332"
[0332]To assess the ability of CGl-bispecific Ab to activate T cells, flow cytometry staining of T cells after co-culturing normal PBMC with target myeloid leukemia was performed: AML (U937-A2 and ML2) and CML (EM2) cell lines. T cell activation (FIGs. 9D, 9H, 9L)and cytokine secretion (FIGs. 9E-9G, 9I-9K, 9M-9O)was higher in the CGl-CD3e bispecific antibody-treated groups, in comparison with the groups that were treated with the control bispecific antibody. Furthermore, ability of CGl-CD3e bispecific antibody to kill HLA-A2+ myeloid leukemia was assesses using in vitro flow cytometry-based cytotoxicity assays (FIGs. 9A-9C). After co-culturing fluorescently-labeled AML (U937-A2 and ML2) and CML (EM2) cell lines with normal donor T cells and CGl-CD3e bispecific antibody for 24 hours, flow cytometry analysis demonstrated high killing of target cells by T cells in the groups that were treated with CGl-CD3e bispecific, in comparison with control bispecific antibody (FIGs. 9A- 9C).Cytotoxicity was HLA-A2 dependent, as shown by the lack of killing of the HLA-Anegative cell line U937.
F. Efficacy of CG1XCD3 bispecific antibody in xenograft mouse models. id="p-333"
[0333]The CGl-bispecific antibody was assessed as an immunotherapeutic in vivo (Figure 3). After engrafting HLA-A2+ ML2 CML cell line, normal donor PBMC (I x 10A7 cells) were 109US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) administered intravenously to NSG mice. Four days following PBMC infusion, mice received weekly doses of CGl-bispecific antibody (0.01 mg/Kg, 0.05 mg/Kg, and 0.1 mg/Kg) or PBS via IP injection. An overview of the protocol is shown in FIG. 10A.Bioluminescence imaging showed that the mice treated with PBMC + CGl-bispecific antibody had a significantly lower levels of ML2 cells in the bone marrow compared to the mice treated with PBMC alone. The imaging showed a dose dependent decrease in bioluminescence after treatment with CGI- bispecific antibody in comparison with PBS. Similar potent anti-leukemia activity was seen at all dose levels (FIG. 10B)A higher percentage of human T cells (hCD45-/hCD3+) was seen in all treatment groups in comparison with PBS-treated group (FIG. 10C).Histologic analysis of bone marrow confirmed BLI and flow cytometry results, showing a smaller leukemia burden as shown using MPO and H&E staining, and higher bone marrow restoration and normal hematopoiesis in the CGl-bispecific Ab-treated groups (FIGs. 10D-10F).Similar results were demonstrated when mice were engrafted with primary AML patient blasts, with results showing a decreased AML burden and longer survival in the mice treated with CGl-bispecific Ab (FIGs. 10G-10H) id="p-334"
[0334]In a similar experiment, the CGIxCD3 bispecific antibody was assessed in a U937- A02 xenograft. The same protocol was followed except that the mice were engrafted with U937-A02/Luc cells. Mice were either treated with vehicle control or CGl-16xCD3 at 1 mg/kg IP. The radiance plot from the bioluminescence imaging of control or CGI-16xCD3-treated mice is shown in FIG. 11 A.The percentage of CD3+ T cells in blood, BM, and spleen in the humanized mice is shown in FIGs. 11B-11D,respectively. Activated T-cells (detection of CD69) in the control and bispecific treatment group in blood is shown in FIG. HE.
G. Anti-tumor activity of CGl-16xCD3 BsAb in AML patient derived xenograft model across donors. id="p-335"
[0335]Female NSG mice at 6-10 weeks old received tail vein injection with 5 x 10A6 of AML patient cells per mouse. Once blood tumor cell levels reached ~2%, 1 x 10APBMC/mouse were IV injected for humanization. Four days after PBMC injection mice were randomized into control and treatment groups. Mice were either treated with vehicle control or CGl-16xCD3 at 1.0, 0.1, or 0.01 mg/kg IV. The radiance plot from the bioluminescence imaging of control or CGl-16xCD3 treated mice is shown in FIG. 12A.Survival curves of mice from different treatment groups is shown in FIG. 12B. 110US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) H. Pharmacokinetics of 1B7/CD3 BsAb. id="p-336"
[0336]Single dose CGl-16xCD3 PK analysis in human CGI & HLA-A02:01 double transgenic mice at 1, 0.1 or 0.01 mg/kg doses was perfomed. Blood was collected at indicated time points post injection through serial sampling and processed to plasma for bioanalytical and PK analyses with coated CGI monomer and detecting antibody GG-5 conjugated sulfo- tag using MSD methods. PK analyses were performed according to standard non- compartmental analysis using WinNonlin. The data is shown in FIG. 13and Table 9below.
Table 9: Pharmacokinetics of 1B7/CD3 BsAb Dose Lamdbaz Tl/2 Tmax Cmax AUCINFobs Vzobs Clobs (l/hr) (hr) (hr) (ng/mL) (hr*ng/mL) (ml/kg) (ml/hr/ kg) 1 mg/kg 0.0044±0.0005160.2±19.40.2500 2288.9±106.2226484.2±32510.31029.3±128.44.5 ±0.7 0.1 mg/kg 0.0060±0.0009118.4±17.30.2500 185.3 ±18.4 12974.8±2249.31346.1±283.77.898±1.386 0.01 mg/kg 0.0060±0.0008117.1±14.40.2500 19.5 ±4.2 1131.5 ±220.0 1528.3±300.79.104±1.750 1. CGI bispecific antibody does not inhibit healthy donor HPC. id="p-337"
[0337]Although CGexpression is expected on normal hematopoietic progenitors, the inventors previously reported that primary AML blasts and CD34+38- leukemia stem cells have higher levels of CG expression compared to normal HPC (Zhang M, et al. Clin Cancer Res. 2013; 19(l):247-257). The effects of CGl-bispecific antibody on the formation of typical colonies from HD BM progenitor cells was investigated using a standard CPU assay (Alatrash G, et al. Leukemia. 2017; 31(l):234-237; Alatrash G, et al. Clin Cancer Res. 2019; 25(8):2610- 2620). HD BM were cultured in a semi-solid matrix of methylcellulose either alone or in the presence of PBMC and either CGI-biospecific antibody or isotype antibody (FIG. 14).After days, the average number of colony-forming units (CPUs) was similar between the untreated, and the bispecific-, and isotype-treated groups, irrespective of the doses used. As expected, the cytarabine (ara-c) treated group showed a significantly lower number of CPUs. illUS2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) Based on these findings, treatment with CGl-bispecific antibody does not significantly impair normal hematopoiesis. id="p-338"
[0338]Sequences of the present example can be found in Examples and 5 below.
EXAMPLE 4: ADDITIONAL ASPECTS OF THE PRESENT DISCLOSURE [0339]As described in the present example, vectors encoding CARs were constructed utilizing embodiments of sequences encoding CGI-monomer binding antibodies heavy and light chain variable regions linked single chain Fv (in particular, scFv sequences of CGI, CGI- 60, and CGI-176 according to the present disclosure were applied to the CAR-T sequences; full-length VH and VL sequences can be found in Example 4 below, and CDRs can be found in at least Table la above), in combination with embodiments of sequences of hinge, transmembrane, signaling domain encoding 4-1BB, Fc-CD28, and CD28 endodomains plus common CD3(؛ signaling domain. Various combinations of the sequences were utilized to create and test CAR polypeptide constructs comprising single-chain Fv (ScFv) extracellular CGI polypeptides (for example CGI-16, CGI-60, and CGI-176 polypeptides as described herein) operatively linked (at their C-terminus) to polypeptides comprising CAR endodomains (for example, CAR endodomain polypeptides 4-1BB, Fc-CD28, and CD28) at their N- terminus, respectively. The following CAR polypeptides were expressed and tested in T-cells (CAR T): CGI-16 antigen/4-lBB endodomain; CGI-16 antigen/Fc-CD28 endodomain; CGI- antigen/CAR endodomain; CGI-60 antigen/4-lBB endodomain; CGI-60 antigen/Fc-CDendodomain; CGI-60 antigen/CAR endodomain; CGI-176 antigen/4-lBB endodomain; CGI- 176 antigen/Fc-CD28 endodomain; and CGI-176 antigen/CAR endodomain. id="p-340"
[0340]Alanine screening of various antibody clones was assessed. OCTET BEI assay was used to assess binding of the different peptide/HLA-A2 monomers to the lead antibodies. The affinities of each monomer were calculated based on BEI data. The monomer is prepared by UV-exchange protocol. The results are shown below in Table 10.In silico docking of CG1/HLA-A2 complex interaction with a representative CGI-16 antibody was performed, with cCGl-46 used as a non-specific control in the assay. The primary interactions appear to be with Pr04, Leu3, Thr5, Gly6, Ala7, Glu8, Ala9. 112US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) Table 10: Ala replacement assay assessing binding of different antibody clones.
Affinity Changes Sequences CGI- CGI- CGI- CGI- CGI- CGI- CGI- 176 CGI- 179 FLEPTGAEA 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00ALLPTGAEA 0.34 0.39 0.90 1.52 0.34 0.37 0.38 0.32FALPTGAEA 0.34 0.25 0.38 0.59 0.31 0.38 0.40 0.23FLAPTGAEA 0.53 0.20 0.50 0.58 0.44 0.71 0.40 0.35FLLATGAEA 0.05 0.12 0.41 0.61 0.51 0.93 0.47 0.39FLEPAGAEA 0.06 0.07 0.14 0.71 0.06 0.06 0.00 0.14FELPTAAEA 0.02 0.02 0.11 1.07 0.07 0.00 0.00 0.00FELPTAAEA 0.10 0.07 0.10 0.41 0.12 0.30 0.09 0.12FLLPTGAAA 0.03 0.07 0.06 0.50 0.16 0.00 0.00 0.00FLLPTGAEG 0.17 0.18 0.16 0.34 0.03 0.12 0.14 0.48 id="p-341"
[0341] FIGs. 15A-15Cillustrate the construction and design of embodiments of the chimeric antigen receptors (CARs) that were used to transduce healthy donor-derived T cells for testing. The pORBIT Lentivirus plasmid was utilized in combination with either CD28 or 4-IBB endodomains for CAR-T, followed by the inclusion of the suicide gene EGFR-III via IRES (FIGs. 15A-15B)Details of the sequences for the 4-1BB CAR, CD28 CAR, and Fc ־CDCAR, as well as the construction of the 9 vectors for CARs with the combination of the top three CGI single chain Fv, are shown in (FIG. 15C),and listed below. >4-lBB CAR Sequence(according to the embodiment: the underlined sequence is the CDhinge domain; the bold domain is the CD8 transmembrane domain; the Italic sequence is 4- IBB signaling domain; and the remainder (starting with RVK and ending with PPR) is the CD3(؛ costimulatory domain) EcoRi —gccgccacc —Single Chain Fv: rZZ ؛ ، gr^//yz^،7p^rpv ؛ tlvcAT ؛ waplagtcgvlllslv ؛ v ؛ tttpaprpptpaptiasqplslrpeacrpaaggavhtrgldfacd^et/gcscrj^eeeeggce/RVKFSRSADAPAYQQGQNQLYNELNLGRREEYDVLDKRRGRD PEMGGKPRRKNPQEGLYNELQKDKMAEAYSEIGMKGERRRGKGHDGLYQGLSTAT KDTYDALHMQALPPR (SEQ ID NO:126)— TAATAG—BamHI >CD28 CAR Sequence(according to the embodiment: the underlined sequence is the CDhinge domain; the bold domain is the CD28 transmembrane domain; the Italic sequence is 113US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) CD28 signaling domain; and the remainder (starting with RVK and ending with PPR) is the CD3(؛ costimulatory domain) EcoRi —gccgccacc —Single Chain Fv: AAALDNEKSNGTIIHVKGKHLCPSPLFPGPSKPFWVLVVVGGVLACYSLLVTVAFII ^NRSKRSRLLHSDYMNMTPRRPGPTRKHYQPYAPPRDFAAYRSKVKY^SNDNPNXQ QGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPRRKNPQEGLYNELQKDKMA EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPR (SEQ ID NO: 127)— TAATAG—BamHl >Fc-CD28 CAR Sequence(according to the embodiment: the underlined sequence is the Fc hinge domain; the bold domain is the CD28 transmembrane domain; the Italic sequence is CD28 signaling domain; and the remainder (starting with RVK and ending with PPR) is the CD3(؛ costimulatory domain) EcoRi —gccgccacc —Single Chain Fv: SDPAEPKSPDKTHTCPPCPAPPVAGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDP EVKFNWYVDGVEVHNAKTKPREEQYOSTYRVVSVLTVLHODWLNGKEYKCKVSN KALPAPIEKTISKAKGQPREPOVYTLPPSRDELTKNOVSLTCLVKGFYPSDIAVEWES NGOPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWOOGNVFSCSVMHEALHNHYTO I id="p-343"
[0343] FIGs. 16A-16Bare plots of live target cells at difference effector :target ratios of embodiments according to the present disclosure. FIG. 16Ashows the in vitro killing of U937- A2+ target cells (U937 cells transduced with HLA-A*0201) at different effectortarget (E:T) ratios after 24 hours, while FIG. 16Bshows the same killing assay after 72 hours. Live U937- A2+ cells were assessed using FACS, and parental T-cells (non-transduced) from the same healthy donor were used as the control. The E:T ratio was normalized to the CAR+ T-cells and not the whole T-cells to allow for accurate comparisons. 114US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) id="p-344"
[0344] FIGs. 17A-17Gpresents the results of an efficacy study comparing the in vivo activity of embodiments of T cells (from two healthy donors) transduced with CG1-60-CDCAR and the CGI-176 bbz CAR against ML2 leukemia cells. Table 11summarizes characterization of the CAR-T cells. FIG. 17Aillustrates an experimental design, with female NSG mice aged 6-10 weeks that received a tail vein injection of 0.1 M of ML2/Luc (luciferase) human AML cells per mouse. At 11-18 days after tumor inoculation, 10 million CAR-T or parental (non-transduced) T cells/mouse were injected IV. FIGs. 17Band 17Epresent the radiance plot of the bioluminescence imaging for control or CAR-T treated mice. FIGs. 17C and 17Fillustrate the survival rate of CAR-Ttreated mice, while FIGs. 17Dand 17Gshow the activation of T-cells (from the two donors) expressing huCD69+ in blood in the control and CAR-T treatment groups. id="p-345"
[0345] CAR T Experiments.The pORBIT Lentivirus plasmid was utilized in combination with either CD28 or 4-1BB CAR-T against ML2 cells from two healthy donors.
Table 11: Characterization of CAR-T cells CAR-T Donor Car% CNV in total cells CNV in car+ cells Harvest Day CGI-60 28z 117 51.8 1.57 3.03 9697 75.8 2.17 2.86 9CGI-1bbz117 53.5 2.20 3.78 9697 2.16 2.16 2.90 9 EXAMPLE 4: ANALYSIS OF ANTIBODY VARIANTS [0346]MOE (Molecular Operating Environment) software, specifically, the BioMOE "annotate PTM and liabilities " tool, was used to identify amino acid residues DG in the H- CDR2 region of binder CGI-16 as a high-risk Asp isomerization site. Next in MOE, the "antibody database statistics " tool was used to determine the most common AA in that position, by first-filtering the database by human sequences, and second- using the "UID" feature, which identified that at the DG position the most common amino acid residue was serine (Table 12). This was the rationale behind mutating DG to SG. The rationale for the mutation of DG to DA was to change the other residue responsible for the PTM to ablate the liability. Both SG and DA mutants were created via site-directed mutagenesis using mutagenic primers in a polymerase chain reaction (PCR) based methodology. 115US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) Table 12:MOE antibody database statistics tool analysis AA Residue % prevalence at UID #59 aka DG position Alanine 3.4Arginine 3.8Asparagine 8.4Aspartic Acid 12.2Cysteine 0.0Glutamine 0.7Glutamic Acid 2.4Glycine 20.4Histidine 0.9Isoleucine 3.5Leucine 2.1Lysine 4.3Methionine 0.6Phenylalanine 0.9Proline 0.6 Serine 22.0 Threonine 3.7Tryptophan 0.1Tyrosine 7.6 id="p-347"
[0347]Two modified variants of binder CGI-16 (see Example 2, heavy and light chains being SEQ ID NO: 7 and 34, respectively, and bi-specific heavy and light sequences SEQ ID NOs: and 56, respectively) were made having specific mutations in the heavy chain CDR2 region. The H-CDR2 region (Imgt annotation) of the original binder CGI-16 is: IKODGSEK (SEQ ID NO:129). The H-CDR2 region (Imgt annotation) of the first modified binder, CGI-250, is: IKOSGSEK (SEQ ID NO: 130). The H-CDR2 region (Imgt annotation) of the second modified binder, CGI-251 is: IKODASEK (SEQ ID NO: 131). The light and heavy chain variable region sequences for binders CGI-250 and CGI-251 are SEQ ID NO: 132 (light) and 133-134 (heavy, respectively). For the potential isomerization consideration, two more variants, CD1-250 and CG1-251 with just one amino acid mute from H-CDR2 were created. id="p-348"
[0348]Hydrophobic interaction chromatography analysis was performed for Binder CGI-compared to Binder CGI-250 (FIG. 18A)and comparted to Binder CGI-251 (FIG. 18B). Molecules with higher hydrophobicity will elute later resulting in higher retention time. All 116US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) molecules were analyzed in the same format and have the same structural domains, thus the difference in hydrophobicity is caused by the introduction of a single mutation in CDR2. id="p-349"
[0349]Hydrophobic interaction chromatography (HIC) was performed by analyzing samples in high salt to low salt gradient. The salt gradient was established on Agilent AdvanceBio HIC column using Agilent Infinity II BioInert system from 0.8 M ammonium sulfate in 50 mM sodium phosphate at pH 7.0 to 50 mM sodium phosphate at pH 7.0 over 20 min at 0.5 mL/min flow rate. The column was washed with low salt and high salt to remove any remaining protein and re-equilibrated over 3 column volumes before each injection. id="p-350"
[0350]The samples were prepared by mixing equal parts of CG1-16, CGI-250, and CGI- 251 (in formulation buffer) and 2 M ammonium sulfate in 50 mM sodium phosphate at pH 7.0, resulting in the buffer with 1 M ammonium sulfate. The samples were cleared from the large particles (if present) by centrifugation at 14,000 x g for 5 min at room temperature and the supernatant was carefully collected. The concentration of each sample was measured after dilution using NanoDrop and calculated extinction coefficient, and percent of recovery was calculated. The concentration after dilution was used to calculate the amount of protein for each injection (typically, 20 micrograms of protein per injection). Peak retention times were monitored using protein absorbance at 280 nm. id="p-351"
[0351]A single mutation in CDR2 of CGI-16 was found to lower the hydrophobicity of the binder. It has been documented that more hydrophobic molecules have an increased tendency to aggregate non-specifically, interact with other surfaces or molecules, and can result in suboptimal developability properties (e.g., Mieczkowski et al. MAbs. 2023; 15(1):3185924).
EXAMPLE 5: ADDITIONAL SEQUENCES OF THE PRESENT DISCLOSURE For SEQ ID NOs.: 1-56 CDRs 1-3 are in bold and FRs 1-4 are underlined. >CG1-R-17 VH amino acid sequence (SEQ ID NO:1) EVOLVESGGGLVQPGGSLRLSCGASGFTFSSYWMSWVROAPGKGLEWVANIKOD GSEKYYVDSVKGRFTISRDNAKNSLYLOMNSLRAEDTAVYYCASALYYYYYYGM DVWGOGTTVTVS >CG1-R-18 VH amino acid sequence (SEQ ID NO:2) OVOLQESGPGLVKPSETLSLTCTVSGGSISSYYWSWIROPPGKGLEWIGYIYYSGSTN YNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARSLYYYYYYGMDVWGOG TTVTVS 117US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) >CGl-6 VH amino acid sequence (SEQ ID NO:3) OVHLQESGPGLVKPSETLSLTCTVSGGSVSSYYWNWIROPPGKGLEWIGYIYYSEST NYNTSLKSRVTISVDTSKNQFSLKLTSVTAADTAVYYCARSLYYYYYYGMDVWGO GTMVTVSS >CG1-1O VH amino acid sequence (SEQ ID NO:4) EVOLVESGGGLVOPGGSLRLSCAASGFTFNNYWMTWVROAPGKGLEWVANIKOD GNEKYYVDSVKGRFTISRDNAKNSLYLOMNSLRAEDTAVYYCAREGGWYWFDP WGQGTLVTVSS >CG1-12 VH amino acid sequence (SEQ ID NO:5) EVOLVESGGGLVQPGGSLRLSCAASGFTFSSYWMSWVROAPGKGLEWVANINOD GSEKNYVDSVKGRFTISRDNANNSLHLOMNSLRAEDTAVYYCTKSLYYYYYYGM DVWGOGTTVTVSS >CG1-15 VH amino acid sequence (SEQ ID NO:6) OVHLQESGPGLVKPSETLSLTCTVSGGSVSSYYWNWIROPPGKGLEWIGYIYYSEST NYNTSLKSRVTISVDTSKNQFSLKLTSVTAADTAVYYCARSLYYYYYYGMDVWGO GTMVTVSS >CG1-16 VH amino acid sequence (SEQ ID NO:7) EVQLVESGGGLVOPGGSLRLSCAASGFTFSDYWMTWVRQAPGKGLEWVANIKQD GSEKYYVDSVKGRFTISRDNAKNSLNLOMNSLRAEDTAVYYCAREGGWYWFDP WGQGTLVTVSS >CGl-23 VH amino acid sequence (SEQ ID NO:8) EVOVVESGGGLVOPGGSLRLSCAASGFTFSSYWMSWVROAPGKGLEWVANIKHD GSEKYYVDSVKGRFTISRDNAKNSLYLOMNSLRAEDRAVYYCVREGGWYWFDP WGQGTLVTVSS >CGl-27 VH amino acid sequence (SEQ ID NO:9) EVOLVESGGGLVQPGGSLRLSCAASGFTFSSYWMSWVROAPGKGLEWVANIKOD GSEKYYVDSVKGRFTISRDNAKNSOYLOMNSLRAEDTAVYYCAREGGWYWLDP WGQGTLVTVSS >CGl-33 VH amino acid sequence (SEQ ID NO: 10) OVOLVESGGGVVOPGGSLRLSCAASGFIFSSYWMSWVRQAPGKGLEWVANINODG SEKYYVDSVKGRFTISRDNANNSLFLOMNSLRAEDTAVYYCTKSLYYYYYYGMD VWGOGTTVTVSS >CG1-41 VH amino acid sequence (SEQ ID NO: 11) EVQLVECGGGLVOPGGSLRLSCAASGFTFSDYWMIWVRPAPGKGLEWVANIKOD GSEKYYVDSVKGRFTISRDNAKNSLNMOMNSLRAEDTAVYYCAREGGWYWFDP WGQGTLVTVSS >CGl-44 VH amino acid sequence (SEQ ID NO: 12) QVHLQESGPGLVKPSETLSLTCTVSGGSVSNYYWNWIROPPGKGLEWIGYIYYSEST NYNTSLKSRVTISLDTSKNEFSLKVTSVTAADTAVYYCARSLYYYYYYGMDVWGO GTTVTVSS 118US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) >CGl-46 VH amino acid sequence (SEQ ID NO: 13) OVHLQESGPGLVKPSETLSLTCTVSGGSVSNYYWNWIROPPGKGLEWIGYIYYSEST NYNTSLKSRVTISLDTSKNEFSLKVTSVTAADTAVYYCARSLYYYYYYGMDVWGO GTTVTVSS >CGl-55 VH amino acid sequence (SEQ ID NO: 14) EVOVVESGGGLVOPGGSLRLSCAASGFTFSSYWMSWVROAPGKGLEWVANIKHD GSEKYYVDSVKGRFTISRDNAKNSLYLOMNSLRAEDRAVYYCVREGGWYWFDP WGQGTLVTVSS >CG1-6O VH amino acid sequence (SEQ ID NO: 15) EVOLVESGGGLVOPGGSLRLSCAAAGFTFSNYWMSWVROAPGKGLEWVANIKOD GSEKYYVDSVKGRFTISRDNAKNSOYLOMNSLRVEDTAVYYCAREGGWYWLDP WGQGTLVTVSS >CG1-61 VH amino acid sequence (SEQ ID NO: 16) OVOLVESGGGVVOPGRSLRLSCAASGFTFSNYWMSWVRQAPGKGLEWVANIKOD GSEKYYVDSVKGRFTISRDNAKNSOYLOMNSLRVEDTAVYYCAREGGWYWLDP WGQGTLVTVSS >CGl-65 VH amino acid sequence (SEQ ID NO: 17) QVHLQESGPGLVKPSETLSLTCTVSGGSVSSYYWNWIROPPGKGLEWIGYIYYSEST NYNTSLKSRVTISVDTSKNQFSLKLTSVTAADTAVYYCARSLYYYYYYGMDVWGO GTTVTVSS >CGl-68 VH amino acid sequence (SEQ ID NO: 18) EVOLVESGGGLVQPGGSLRLSCAASGFTFSSYWMSWVROAPGKGLEWVANIKOD GSEKYYVDSVKGRFTISRDNAKNSOYLOMNSLRAEDTAVYYCAREGGWYWLDP WGQGTLVTVSS >CGl-74 VH amino acid sequence (SEQ ID NO: 19) EVOLVESGGGLVOPGGSLRLSCAAAGFTFSNYWMSWVROAPGKGLEWVANIKOD GSEKYYVDSVKGRFTISRDNAKNSOYLOMNSLRVEDTAVYYCAREGGWYWLDP WGQGTLVTVSS >CGl-78 VH amino acid sequence (SEQ ID NO:20) EVOLVESGGGLVQPGGSLRLSCAASGFTFNNYWMTWVROAPGKGLEWVANIKOD GNEKYYVDSVKGRFTISRDNAKNSLYLOMNSLRAEDTAVYYCAREGGWYWFDP WGQGTLVTVSS >CG1-1O4 VH amino acid sequence (SEQ ID NO:21) OVOLVESGGGVVHPGRSLRLSCAASGFTFSHYVMHWVRQAPGKGLEWVAVIWYD GSNINYAESLKGRFTISRDNSKNTLYLOLNSLRAEDTAVYYCARGPAPTIFWGOGT LVTVSS >CG1-11O VH amino acid sequence (SEQ ID NO:22) EVQLLESGGGLVOPGGSLRLSCAASGFTFSSNAMSWVROAPGKGLEWVSAISGRG GNTYYADSVKGRFTISRDNSKNTLYLQMLSLRAEDTAVYYCARDSYYDVLTAYYD FLTTGAREPWSPSR 119US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) >CG1-112 VH amino acid sequence (SEQ ID NO:23) EVQLVESGGGLVOPGGSLRLSCAASGFIFSSYWMSWVRQAPGKGLEWVANINQDG SEKYYVDSVKGRFTISRDNANDSLFLOMNSLRAEDTAVYYCTKSLYYYYYYGMD VWGOGTPVTVSS >CG1-176 VH amino acid sequence (SEQ ID NO:24) EVOLVESGGGLVOPGGSLRLSCAASGFTFSSYWMSWVRQAPGKGLEWVANIKOD GSEKYYVDSVKGRFTISRDNAKNSLFLOMNSLRAEDTAVYYCAREGGWYWFDPW GOGTLVTVS S >CG1-177 VH amino acid sequence (SEQ ID NO:25) EVQLVESGGGLVOPGGSLRLSCAASGFTFSDYWMTWVRQAPGKGLEWVANIKQD GSEKYYVDSVKGRFTISRDNAKNSLNLOMNSLRAEDTAVYYCAREGGWYWFDP WGQGTMVTVSS >CG1-179 VH amino acid sequence (SEQ ID NO:26) EVOVVESGGGLVOPGGSLRLSCAASGFTFSSYWMTWVROAPGKGLEWVANIKOD GSEKYYVDSVKGRFTISRDNAKNSLYLOMNSLRAEDTAVYYCAREGGWYWFDP WGQGTLVTVSS >CG1-189 VH amino acid sequence (SEQ ID NO:27) EVOVVESGGGLVOPGGSLRLSCAASGFTFSSYWMTWVROAPGKGLEWVANIKOD GSEKYYVDSVKGRFTISRDNAKNSOYLOMNSLRAEDTAVYYCAREGGWYWFDP WGQGTLVTVSS >CG1-R-17 VL amino acid sequence (SEQ ID NO:28) DIVMTOSPLSLPVTPGEPASISCRSSOSLLHSNGYNYLDWYLOKPGOSPQLLIYLGSI RASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMOALOTPYTFGOGTRLEIKRT >CG1-R-18 VL amino acid sequence (SEQ ID NO:29) DIVMTOSPLSLPVTPGEPASISCRSSOSLLYSHGYNYLDWYLOKPGOSPQLLIYLGSI RASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMOALOTPWTFGOGTKVEIKRT >CGl-6 VL amino acid sequence (SEQ ID NO:30) DIVMTOSPLSLPVTPGEPASISCMSSOSLLOSHGYNHLDWYLOKPGOSPOLLIYLGS NRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMOALOTPWTFGOGTKVDIK RT >CG1-1O VL amino acid sequence (SEQ ID NO:31) DIOMTOSPSSLSASVGDRVTITCRASOSISSFLNWYOOKPGKAPKLLIYTASSLOSGV PSRFSGSGSGTDFTLTISSLOPEDFATYYCOOSYSTPYTFGOGTKVEIKRT >CG1-12 VL amino acid sequence (SEQ ID NO:32) DIVMTOSPLSLPVTPGEPASISCRSSOSLLLSHGYNYLDWYLOKPGOSPOLLIYLGSS RASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMOGLOTPWTFGOGTKVDIKRT >CG1-15 VL amino acid sequence (SEQ ID NO:33) DIVMTOSPLSLPVTPGEPASISCMSSOSLLOSHGYNHLDWYLOKPGOSPOLLIYLGS NRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMOALOTPWTFGOGTKVDIK RT 120US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) >CG1-16 VL amino acid sequence (SEQ ID NO:34) DIOMTOSPSSLSASVGDRVTITCRASOSISSFLNWYOOKPGKAPKLLLYAASSFLSGV PSRFSGSGSGTDFTLTISSLOPEDFATYYCOOSYSTPYTFGOGTKVDIKRT >CGl-23 VL amino acid sequence (SEQ ID NO:35) DIOMTOSPSSLSASVGDRVTITCRASOIISSFLNWYHOKPGKAPKLLIYAASSLOSGV PSRFSGSGSGTDFTLTISSLOPEDFATYYCOOSYSTPYTFGOGTRLEIKRT >CGl-27 VL amino acid sequence (SEQ ID NO:36) DIOMTOSPSSLSASVGDRVTITCRASOSIASFLNWYOOKPGKAPKLLIYTASSLOGG VPSRFSGSGSGTDFTLTISSLOPEDFATYYCOOSYSTPYTFGOGTRLEIKRT >CGl-33 VL amino acid sequence (SEQ ID NO:37) DIVMTOSPLSLPVTPGEPASISCRSSOSLLLSHGYNYLDWYLOKPGOSPOLLIYLGSS RASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMOGLOTPWTFGOGTKVDIKRT >CG1-41 VL amino acid sequence (SEQ ID NO:38) DIOMTOSPSSLSASVGDRVTITCRASOSISSFLNWYOOKPGKAPKLLLYAASSFLSGV PSRFSGSGSGTDFTLTISSLOPEDFATYYCOOSYSTPYTFGOGTKVEIKRT >CGl-44 VL amino acid sequence (SEQ ID NO:39) DIVMTOSPLSLPVTPGEPASISCRSSOSLLOSHGFNHLDWYLOKPGOSPQLLIYLVSN RASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMOALOTPWTFGOGTKVDIKRT >CGl-46 VL amino acid sequence (SEQ ID NO:40) DIVMTOSPLSLPVTPGEPASISCRSSOSLLOSHGFNHLDWYLOKPGOSPQLLIYLVSN RASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMOALOTPWTFGOGTKVEIKRT >CGl-55 VL amino acid sequence (SEQ ID NO:41) DIOMTOSPSSLSASVGDRVTITCRASOIISSFLNWYHOKPGKAPKLLIYAASSLOSGV PSRFSGSGSGTDFTLTISSLOPEDFATYYCOOSYSTPYTFGOGTKVDIKRT >CG1-6O VL amino acid sequence (SEQ ID NO:42) DLOMTOSPSSLSASVGDRVTITCRASOSIASFLNWYOOKPGKAPKLLIYTASSFOGG VPSRFSGSGSGTDFTLTISSLOPEDFATYYCOOSYSTPYTFGOGTKVDIKRT >CG1-61 VL amino acid sequence (SEQ ID NO:43) DLOMTOSPSSLSASVGDRVTITCRASOSIASFLNWYOOKPGKAPKLLIYTASSFOGG VPSRFSGSGSGTDFTLTISSLOPEDFATYYCOOSYSTPYTFGOGTKVDIKRT >CGl-65 VL amino acid sequence (SEQ ID NO:44) DIVMTOSPLSLPVTPGEPASISCRSSOSLLOSHGYNHLDWYLQKPGOSPOLLIYLGS NRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMOALOTPWTFGOGTKVDIK RT >CGl-68 VL amino acid sequence (SEQ ID NO:45) DIOMTOSPSSLSASVGDRVTITCRASOSIASFLNWYOOKPGKAPKLLIYTASSLOGG VPSRFSGSGSGTDFTLTISSLOPEDFATYYCOOSYSTPYTFGOGTKLEIKRTVAAP 121US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) >CGl-74 VL amino acid sequence (SEQ ID NO:46) EIOMTOSPSSLSASVGDRVTITCRASOSIASFLNWYOOKPGKAPKLLIYTASSFOGGV PSRFSGSGSGTDFTLTISSLOPEDFATYYCOOSYSTPYTFGOGTKVEIKRTVAAP >CGl-78 VL amino acid sequence (SEQ ID NO:47) DIOMTOSPSSLSASVGDRVTITCRASOSISSFLNWYOOKPGKAPKLLIYTASSLOSGV PSRFSGSGSGTDFTLTISSLOPEDFATYYCOOSYSTPYTFGOGTKVDIKRT >CG1-1O4 VL amino acid sequence (SEQ ID NO:48) DIOMTOSPSTPSASVGDRVTITCRASOSISSWLAWYOOKPGKAPKLLIYKASSLESG VPSRFSGSGSGTEFTLTISSLOPDDFATYYCOOYNSYSYTFGOGTKLESNVR >CG1-11O VL amino acid sequence (SEQ ID NO:49) DVLMTOSPSSLSASLGERVSLTCOASODISNNLNWYOOTPGKAPRLLIYDTSKLEDG VPSRFSGTGYRTDFIFTISSLEEEDVATYFCLOHRYLPWTFGGGTKLEIKRT >CG1-112 VL amino acid sequence (SEQ ID NO:50) DIVMTOSPLSLPVTPGEPASISCRSSOSLLLSHGYNYLDWYLOKPGOSPOLLIYLGSS RASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMOGLOTPWTFGOGTKVEIKRT >CG1-176 VL amino acid sequence (SEQ ID NO:51) DIOMTOSPSSLSASVGDRVTITCRASOSISSFLNWYOOKPGKAPKLLIYAASSFOSGV PSRFSGSGSGTDFTLTISSLOPEDFATYYCOOSYSTPYTFGOGTKVDIKRT >CG1-177 VL amino acid sequence (SEQ ID NO:52) DIOMTOSPSSLSASVGDRVTITCRASOSISSFLNWYOOKPGKAPKLLLYAASSLLSGV PSRFSGSGSGTDFTLTISSLOPEDFATYYCOOSYSTPYTFGOGTRLEIKRT >CG1-179 VL amino acid sequence (SEQ ID NO:53) DIOMTOSPSSLSASVGDRVTITCRASOSISSFLNWYOOKPGKAPKLLIYAASSFOSGV PSRFSGSGSGTDFTLTISSLOPEDFATYYCOOSYSTPYTFGOGTRLEIKRT >CG1-189 VL amino acid sequence (SEQ ID NO:54) EIOMTOSPSSLSASVGDRVTITCRASOSIASFLNWYOQKPGKAPKLLIYAASSLOSGV PSRFSGSGSGTDFTLTISSLOPEDFATYYCOOSYSTPYTFGOGTRLEIKRT CGI-16 x CD3 bispecific Ab which contains three chains: >CG1-16 bispecific He (SEQ ID NO:55) EVQLVESGGGLVQPGGSLRLSCAASGFTFSDYWMTWVRQAPGKGLEWVANIKQDG SEKYYVDSVKGRFTISRDNAKNSLNLQMNSLRAEDTAVYYCAREGGWYWFDPWG QGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSDTKVDKKVEPKSCDK THTCPPCPAPPVAGPSVFLFPPKPKDTLMISRTPEVTCVVVDVKHEDPEVKFNWYVD GVEVHNAI 122US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) ▻CGI-16 Lc (SEQ ID NO:56) DIQMTQSPSSLSASVGDRVTITCRASQSISSFLNWYQQKPGKAPKLLLYAASSFLSGV PSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPYTFGQGTKVDIKRTVAAPSVFI FPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTY SLSS TLTL SK AD YEKHK V Y ACE VTHQGL S SP VTK SFNRGEC >CD3 bispecific (SEQ ID NO:57) evqlvesggglvqpggslrlscaasgftfstyamnwvrqapgkglewvgrirsky NNYATYYADSVKGRFTISRDDSKNTLYLQMNSLRAEDTAVYYCVRHGNFGDSYVS WFAYWGQGTLVTVSSGKPGSGKPGSGKPGSGKPGSQAWTQEPSLTVSPGGTVTLT CGSSTGAVTTSNYANWVQQKPGKSPRGLIGGTNKRAPGVPARFSGSLLGGKAALTIS GAQPEDEADYYCALWYSNHWVFGGGTKLTVLEPKSSDKTHTCPPCPAPPVAGPSVF lfppkpkdtlmisrtpevtcvvvdvkhedpevkfnwyvdgvevhnaktkpreeqyn STYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAP1EKTISKAKGQPREPQVYTLPPS REQMTKNQA'KLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLT VDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK > FLAG (SEQ ID NO:58) DYKDDDDK ▻polyhistidine (6-His; (SEQ ID NO:59)) HHHHHH ▻hemagglutinin (HA; (SEQ ID NO:60)) YPYDVPDYA ▻CGI (SEQ ID NO:61) FLEPTGAEA ▻CMAl (SEQ ID NO:62) FLLCSRAEA >PI3 (SEQ ID NO:63) FLLPTGVYL ▻MIF (SEQ ID NO:64) FLLPTGLSSL ▻CMV (SEQ ID NO:65) NLVPMVATV ▻PAP135 (SEQ ID NO:66) ILLWQPIPV ▻Signal Peptide (SEQ ID NO: 124) MQPLLLLAFLLPTGAEA >C-peptide (SEQ ID NO: 125) FKLLDQMETPL 123US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) >4-lBB CAR Endodomain Sequence (SEQ ID NO: 126;according to the embodiment: the underlined sequence is the CDS hinge domain; the bold domain is the CDS transmembrane domain; the Italic sequence is 4-1BB signaling domain; and the remainder (N-RVK... PPR-C) is the CD3(؛ costimulatory domain)rtf ؛ ، gr^//yz^،7p^7rpv ؛ tlvcAT ؛ waplagtcgvlllslv ؛ v ؛ tttpaprpptpaptiasqplslrpeacrpaaggavhtrgldfacd^et/gcscr^eeeeggceZRVKFSRSADAPAYQQGQNQLYNELNLGRREEYDVLDKRRGRD PEMGGKPRRKNPQEGLYNELQKDKMAEAYSEIGMKGERRRGKGHDGLYQGLSTAT KDTYDALHMQALPPR >CD28 CAR Endodomain Sequence (SEQ ID NO: 127;according to the embodiment: the underlined sequence is the CD28 hinge domain; the bold domain is the CD28 transmembrane domain; the Italic sequence is CD28 signaling domain; and the remainder (N-RVK... PPR-C) is the CD3(؛ costimulatory domain) AAALDNEKSNGTIIHVKGKHLCPSPLFPGPSKPFWVLVVVGGVLACYSLLVTVAFII ^NRSKRSRLLHSDYMNMTPRRPGPTRKHYQPYAPPRDFAAYRSKVKY^SNDNPNXQ QGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPRRKNPQEGLYNELQKDKMA EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPR >Fc-CD28 CAR Endodomain Sequence (SEQ ID NO:128;according to the embodiment: the underlined sequence is the Fc hinge domain; the bold domain is the CD28 transmembrane domain; the Italic sequence is CD28 signaling domain; and the remainder (N-RVK... PPR-C) is the CD3(؛ costimulatory domain)SDPAEPKSPDKTHTCPPCPAPPVAGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDP EVKFNWYVDGVEVHNAKTKPREEQYOSTYRVVSVLTVLHODWLNGKEYKCKVSN KALPAPIEKTISKAKGQPREPOVYTLPPSRDELTKNOVSLTCLVKGFYPSDIAVEWES NGOPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWOOGNVFSCSVMHEALHNHYTO KSLSLSPGKKDPKFWVLVVVGGVLACYSLLVTVAFIIFWVF5AF5FLZF5DEWVMZ PF7?FGPZRA7Zy()PE4PPFZ)F4v4yF5RVKFSRSADAPAYQQGQNQLYNELNLGRREEY DVLDKRRGRDPEMGGKPRRKNPQEGLYNELQKDKMAEAYSEIGMKGERRRGKGH DGLYQGLSTATKDTYDALHMQALPPR >CG1-16 heavy chain CDR2 region fragment (SEQ ID NO:129) IKODGSEK >Variant CGI-250 heavy chain CDR2 region fragment (SEQ ID NO: 130) IKQSGSEK >Variant CGI-251 heavy chain CDR2 region fragment (SEQ ID NO: 131) IKQDASEK >Variant CGI-250 and CGI-251 light chain variable region (SEQ ID NO: 132) DIQMTQSPSSLSASVGDRVTITCRASQSISSFLNWYQQKPGKAPKLLLYAASSFLSGV PSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPYTFGQGTKVDIK 124US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) >Variant CGI-250 heavy chain variable region (SEQ ID NO: 133) EVQLVESGGGLVQPGGSLRLSCAASGFTFSDYWMTWVRQAPGKGLEWVANIKQSG SEKYYVDSVKGRFTISRDNAKNSLNLQMNSLRAEDTAVYYCAREGGWYWFDPWG QGTLVTVSS >Variant CGI-251 heavy chain variable region (SEQ ID NO: 134) EVQLVESGGGLVQPGGSLRLSCAASGFTFSDYWMTWVRQAPGKGLEWVANIKQDA SEKYYVDSVKGRFTISRDNAKNSLNLQMNSLRAEDTAVYYCAREGGWYWFDPWG QGTLVTVSS EXAMPLE 6: ADDITIONAL ASPECTS OF THE PRESENT DISCLOSURE [0352]Disclosed are materials, compositions, and ingredients that can be used for, can be used in conjunction with or can be used in preparation for the disclosed embodiments. These and other materials are disclosed herein, and it is understood that when combinations, subsets, interactions, groups, etc. of these materials are disclosed that while specific reference of each various individual and collective combinations and permutations of these compositions may not be explicitly disclosed, each is specifically contemplated and described herein. For example, if a method is disclosed and discussed, and a number of modifications that can be made to a number of molecules included in the method are discussed, each and every combination and permutation of the method, and the modifications that are possible are specifically contemplated unless specifically indicated to the contrary. Likewise, any subset or combination of these is also specifically contemplated and disclosed. This concept applies to all aspects of this disclosure including, but not limited to, steps in methods using the disclosed compositions. Thus, if there are a variety of additional steps that can be performed, it is understood that each of these additional steps can be performed with any specific method steps or combination of method steps of the disclosed methods, and that each such combination or subset of combinations is specifically contemplated and should be considered disclosed. id="p-353"
[0353]Publications cited herein and the material for which they are cited are hereby specifically incorporated by reference in their entireties. The following description provides further non-limiting examples of the disclosed compositions and methods. 125US2008 29831787 1

Claims (49)

Attorney Docket No. 090723-1438905(MDA21-122PCT) WHAT IS CLAIMED IS:
1. An isolated antibody or antigen binding portion thereof comprising:a heavy chain (HC) variable region sequence, wherein the HC variable region comprises a CDRI sequence comprising one of SEQ ID NOs:67-78; anda light chain (EC) variable region sequence, wherein the EC variable region comprises a CDR1 sequence comprising one of SEQ ID NOs:96-105.
2. The isolated antibody or antibody fragment of claim 1, wherein the HC variable region further comprises a CDR2 sequence comprising one of SEQ ID NOs:79-87, or 129-131.
3. The isolated antibody or antibody fragment of claim 1 or claim 2, wherein the EC variable region further comprises a CDR2 sequence comprising one of SEQ ID NOs: 106-117.
4. The isolated antibody or antibody fragment of any one of claims 1-3, wherein the HC variable region further comprises a CDR3 sequence comprising one of SEQ ID NOs: 88-95.
5. The isolated antibody or antibody fragment of any one of claims 1-4, wherein the EC variable region further comprises a CDR3 sequence comprising one of SEQ ID NOs: 118-123.
6. The isolated antibody or antibody fragment of any one of claims 1-5, wherein the antibody or antibody fragment is a human antibody or human antibody fragment.
7. An isolated antibody or antigen binding portion thereof comprising:(a) a heavy chain variable region (VH) having at least 90% identity to any one of SEQ IDNOs:7, 8, 9, 15, 16, 55, 133, or 134; and(b) a light chain variable region (VL) having at least 90% identity to any one of SEQ ID NOs:24, 35, 36, 42, 43, 56, or 132.
8. The isolated antibody or antibody fragment of any one of claims 1-7, wherein the antibody fragment is a monovalent scFv (single chain fragment variable) antibody, divalent scFv, Fab fragment, F(ab’)2 fragment, F(ab’)3 fragment, Fv fragment, or single chain antibody.
9. The isolated antibody or antibody fragment of any one of claims 1-8, wherein said antibody is a chimeric antibody, bispecific antibody, trispecific or other multi-specific antibody, or BiTE. 126US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT)
10. The isolated antibody or antibody fragment of any one of claims 1-9, wherein said antibody is an IgG antibody or a recombinant IgG antibody or antibody fragment.
11. The isolated antibody or antibody fragment of any one of claims 1-10, wherein the antibody or antibody fragment hasa) increased binding affinity for CGI presented by HLA-A*0201 compared to sample from a wild-type subject or subject not having a cancer.
12. The isolated antibody or antibody fragment of any one of claims 1-11, wherein the antibody is conjugated or fused to an imaging agent, a cytotoxic agent, a metal, or a radioactive moiety.
13. The isolated antibody or antibody fragment of claim 12, wherein the imaging agent is a fluorophore.
14. The isolated antibody or antibody fragment of claim 12, wherein the radioactive moiety comprises at least one 0fZr-89, Cu-64, F-18, Y-90, Lu-177, At-211, Ac-225, orPb-212.
15. The isolated antibody or antibody fragment of any one of claims 1-14, wherein the antibody is an immune conjugate or a radio-immune conjugate.
16. The isolated antibody or antibody fragment of any one of claims 1-15, wherein the antibody is an antibody-drug conjugate.
17. The isolated antibody or antibody fragment of any one of claims 1-16, wherein the isolated antibody or antibody fragment further comprises an amino acid having at least 90% identity with SEQ ID NO:57.
18. The isolated antibody or antibody fragment of any one of claims 1-17, comprising amino acid sequences having at least 90% similarity with any one of SEQ ID NOs: 55, 56, and 57. 127US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT)
19. The isolated antibody or antibody fragment of any one of claims 1-18, comprising any one of SEQ ID NOs. 55-57.
20. The isolated antibody or antibody fragment of any one of claims 1-19, consisting essentially of any one of SEQ ID NOs. 55-57.
21. The isolated antibody or antibody fragment of any one of claims 1-20, consisting essentially of:(a) a heavy chain variable region (VH) having at least 90% identity to any one of SEQ IDNOs:7, 8, 9, 15, 16, 55, 133, or 134; and(b) a light chain variable region (VL) having at least 90% identity to any one of SEQ ID NOs: 34, 35, 36, 42, 43, 56, or 132.
22. The isolated antibody or antibody fragment of any one of claims 1-20, consisting essentially of:(a) any one of SEQ ID NOs: 7, 8, 9, 15, 16, 55, 133, or 134; and(b) any one of SEQ ID NOs: 34, 35, 36, 42, 43, 56, or 132.
23. A chimeric antigen receptor (CAR) comprising:(a) an extracellular target-binding domain comprising an antibody or antigen binding portion thereof of any of claims 1-22;(b) a transmembrane domain; and(c) a signaling domain.
24. The CAR of claim 23, wherein the antibody or antigen binding portion thereof is a single chain antibody fragment, a single chain Fv (scFv), a single chain Fab, a single chain Fab’, a single domain antibody fragment, a single domain multispecific antibody, an intrabody, a nanobody, or a single chain immunokine.
25. 25 The CAR of claim 23 or 24, wherein the antibody or antigen binding portion thereof is a scFv comprising an amino acid sequence that is at least 90% identical to SEQ ID NO: 1- 27, 133, or 134.
26. The CAR of any of claims 23-25, wherein the hinge and transmembrane domains comprise CD8a or CD28 hinge and transmembrane domains. 128US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT)
27. The CAR of any of claims 23-26, wherein the signaling domain comprises a 4-1BB signaling domain, a CD28 signaling domain, an OX-40 signaling domain, and/or a CD3(؛ signaling domain.
28. The CAR of any of claims 23-27, wherein the CAR further comprises a leader sequence and/or a hinge domain.
29. The CAR of any of claims 23-28, wherein the CAR comprises an amino acid sequence that is at least 90% identical to SEQ ID NOs: 1-27, 133, or 134.
30. The CAR of any of claims 23-29, wherein the extracellular target-binding domain further comprises one or more additional antigen-binding domains.
31. The CAR of claim 30, wherein the one or more additional antigen-binding domains specifically bind to CD3.
32. A recombinant nucleic acid molecule encoding an antibody or antigen binding portion thereof of any of claims 1-22 or a CAR of any of claims 23-31.
33. An isolated nucleic acid encoding the antibody heavy and/or light chain variable region of the antibody or antibody fragment or other amino acid of any one of claims 1-32.
34. An expression vector comprising the nucleic acid of claim 33.
35. A hybridoma or engineered cell comprising a nucleic acid encoding the antibody or antibody fragment of any one of claims 1-22 or CAR of any one of claims 1-32.
36. A hybridoma or engineered cell comprising a nucleic acid of claim 35.
37. A pharmaceutical preparation comprising:(a) a pharmaceutically acceptable carrier; and(b) an isolated antibody or antigen binding portion thereof of any one of claims 1-or a cell comprising a CAR of any one of claims 23-31.
38. A diagnostic preparation comprising:(a) a pharmaceutically acceptable carrier; and 129US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT) (b) an isolated antibody or antigen binding portion thereof of any one of claims 1-22.
39. A method for treating a subject having a cancer, comprising administering to a subject in need thereof a therapeutically effective amount of the pharmaceutical preparation of claim 37.
40. A method for treating a subject having a cancer, comprising administering to a subject in need thereof a therapeutically effective amount of an isolated antibody or antibody fragment of any one of claims 1-22 or a cell comprising a CAR of any one of claims 23-31.
41. A method for the diagnosis of a cancer, comprising:(a) administering to a subject in need thereof an effective amount of the diagnostic preparation of claim 28, and(b) detecting binding of the isolated antibody or antigen binding portion thereof as a determination of the presence of the cancer.
42. A method of detecting the presence of a cancer or malignant cell in a biological sample, comprising:(a) contacting said sample with the diagnostic preparation of claim 38, and(b) detecting an amount of binding of the isolated antibody or antigen binding portion thereof as a determination of the presence of said cancer or malignant cell.
43. The method of any one of claims 39-42, wherein the cancer is a myeloid malignancy.
44. The method of claim 43, wherein the myeloid malignancy is acute myeloid leukemia(AML), chronic myeloid leukemia (CML) or myelodysplastic syndrome (MDS).
45. The method of any one of claims 39-42, wherein the cancer is a non-myeloid leukemia.
46. The method of claim 45, wherein the non-myeloid leukemia is acute lymphoblastic leukemia (ALL) or chronic lymphocytic leukemia (CLL). 130US2008 29831787 1 Attorney Docket No. 090723-1438905(MDA21-122PCT)
47. The method of any one of claims 39-42, wherein the cancer is a solid tumor malignancy.
48. The method of claim 47, wherein the solid tumor malignancy is lung cancer.
49. A method of making the isolated antibody or antibody fragment of any one of claims 1-22, the method comprising culturing the hybridoma or engineered cell of claim 35 or under conditions that allow expression of the antibody and, optionally, isolating the antibody from the culture. 131US2008 29831787 1
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