EP1100914A2 - Neue gene, die die hämatopoiese regulieren - Google Patents

Neue gene, die die hämatopoiese regulieren

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Publication number
EP1100914A2
EP1100914A2 EP99944319A EP99944319A EP1100914A2 EP 1100914 A2 EP1100914 A2 EP 1100914A2 EP 99944319 A EP99944319 A EP 99944319A EP 99944319 A EP99944319 A EP 99944319A EP 1100914 A2 EP1100914 A2 EP 1100914A2
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EP
European Patent Office
Prior art keywords
cells
amino acid
seq
sequence
polypeptide
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
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Application number
EP99944319A
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English (en)
French (fr)
Inventor
Michael Paul Cooke
Claire Louise Holness
Oksana Ivanivna Sirenko
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Novartis Pharma GmbH
Novartis AG
Original Assignee
Novartis Erfindungen Verwaltungs GmbH
Novartis AG
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Publication of EP1100914A2 publication Critical patent/EP1100914A2/de
Withdrawn legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4702—Regulators; Modulating activity
    • C07K14/4703—Inhibitors; Suppressors
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2799/00—Uses of viruses
    • C12N2799/02—Uses of viruses as vector
    • C12N2799/021—Uses of viruses as vector for the expression of a heterologous nucleic acid
    • C12N2799/027—Uses of viruses as vector for the expression of a heterologous nucleic acid where the vector is derived from a retrovirus

Definitions

  • the present invention relates to nucleic acid and amino acid sequences of three novel genes involved in the control of hematopoiesis.
  • Hematopoiesis (used interchangeably with hemopoiesis) is a process whereby multi-potent stem cells give rise to lineage-restricted progeny.
  • Hemopoietic stem cells (HSCs) are the only cells in the hematopoietic system that produce other stem cells and give rise to the entire range of blood and immune system cells.
  • CD34 + Thy-1 + Lin " cells from bone marrow and mobilized peripheral blood are highly enriched for HSCs (Murray et al., Blood Cells, 20:354 -370 (1995a); Murray et al., Blood, 85:368 - 378 (1995b)).
  • HSC This cell population is capable of self-renewal and long term multilineage differentiation and has been successfully used for autoiogous transplantation (Gazitt et al., Blood, 86:381 - 389 (1995)). Since HSCs self-renew and are multi-potent, they are ideal candidates for gene therapy. Gene therapy is a new treatment modality for a variety of genetic, neoplastic, or infectious diseases and has the potential to correct defects in all mature cells derived from HSC.
  • HSCs The molecular basis of hematopoiesis remains poorly understood. A greater understanding of the process whereby HSCs give rise to lineage-restricted progeny would facilitate the exploitation of HSCs for transplantation and gene therapy. To achieve this, the molecular pathways controlling hemopoietic cell growth and differentiation have been investigated. To this end, the present invention concerns the identification of candidate HSC regulatory genes and their impact on hematopoiesis.
  • a cDNA library is built and characterized from human CD34 " Thy-1 + stem cells. Sequence analysis of the cDNA library revealed a high degree of novel proteins which may play a role in hematopoiesis.
  • HSC hemopoietic stem cell
  • RNA expression profiling is performed and cDNAs whose expression is enriched in HSC are selected and compared to other differentiated blood cell types.
  • Candidate genes are fully sequenced.
  • the HSC-enriched genes which encode full length novel gene products are subcloned into a retroviral expression vector, which is used to overexpress the gene product in freshly isolated HSCs.
  • Three novel HSC regulatory genes and the proteins which they encode are identified. Each of the novel cDNAs are enriched in HSCs compared to their differentiated progeny, and when overexpressed in HSCs blocks the differentiation of stem cells.
  • the present invention discloses three novel genes involved in HSC regulation, hereinafter referred to as SCM 26, SCM 3, and SCM 113.
  • the invention concerns isolated polynucleotide sequences encoding a polypeptide comprising an amino acid sequence selected from the group consisting of the amino acid sequence of SEQ ID NO. 2; the amino acid sequence of SEQ ID NO. 4; the amino acid sequence of residues 1 - 239 of SEQ ID NO.4; the amino acid sequence of residues 240 - 543 of SEQ ID NO. 4; the amino acid sequence of SEQ ID NO. 6; and an amino acid sequence functionally equivalent to the above enumerated sequences.
  • the invention in a second embodiment, relates to an isolated DNA sequence comprising a nucleotide sequence selected from the group consisting of the polynucleotide sequence of SEQ ID NO 1 ; the polynucleotide sequence of SEQ ID NO. 3; the polynucleotide sequence of SEQ ID NO. 5; and a polynucleotide sequence at least 85% identical to a polynucleotide sequence as disclosed above.
  • the isolated polynucleotide sequence may consist of the complement of the polynucleotide sequences of those listed above.
  • the invention concerns, an isolated polypeptide comprising a member selected from the group consisting of, a polypeptide comprising the amino acid sequence of SEQ ID NO. 2; a polypeptide comprising the amino acid residues 26 - 40 of SEQ ID NO. 2; a polypeptide comprising the amino acid residues 25 - 82 of SEQ ID NO. 2; a polypeptide comprising the amino acid residues 147 - 157 of SEQ ID NO. 2; a polypeptide comprising the amino acid residues 266 - 275 of SEQ ID NO. 2; a polypeptide comprising the amino acid sequence of SEQ ID NO. 4; a polypeptide comprising the amino acid residues 1 - 239 of SEQ ID NO.
  • the isolated polypeptide comprises the amino acid sequence of SEQ ID Nos. 2, 4, 6, or a polypeptide having an amino acid sequence with 95% identity thereto.
  • the invention relates to an isolated polypeptide comprising a member selected from the group consisting of the amino acid residues 26 - 40 of SEQ ID NO. 2; the amino acid residues 25 - 82 of SEQ ID NO. 2; the amino acid residues 147 - 157 of SEQ ID NO.
  • the invention relates to a DNA sequence encoding one of the above enumerated polypeptides.
  • the invention concerns a vector which incorporates one of the claimed polynucleotide sequences of the invention.
  • the vector is a retroviral vector, adenoviral vector, or adeno-associated vector.
  • a host cell is claimed which includes the vector.
  • a preferred host cell is a hematopoietic cell, particularly a human CD34 + cell.
  • the invention concerns a method of increasing the effective dose of hematopoietic stem cells in a mammalian subject, comprising obtaining a population of CD34 + cells which includes a subpopulation of hematopoietic stem cells; introducing into the CD34 + cells a polynucleotide sequence of the invention encoding a disclosed polypeptide of the invention; obtaining a subpopulation of genetically modified stem cells which overexpress said polypeptide; and administering said subpopulation of genetically modified cells to a subject wherein the effective dose of the hematopoietic stem cells is increased.
  • the invention includes the step of selecting hematopoietic stem cells either prior to or after genetic modification.
  • the invention includes the step of culturing the population of hematopoietic CD34 + cells either prior to or after genetic modification.
  • the invention concerns, a method of increasing the effective dose of gene modified cells comprising obtaining a population of hematopoietic CD34 + cells which includes a subpopulation of hematopoietic stem cells; introducing into the population of CD34 + cells a polynucleotide sequence of the invention; introducing into the population of CD34 + cells a second polynucleotide sequence wherein said second polynucleotide sequence encodes a therapeutic gene; obtaining genetically modified cells wherein said cells are capable of expressing the polynucleotide sequence of the invention and the therapeutic gene wherein the effective dose of the cells capable of expressing the therapeutic gene is increased compared to wild-type cells; and administering the genetically modified cells to a mammalian subject.
  • the invention concerns a method of blocking the differentiation of mammalian hematopoietic stem cells in vitro comprising the steps of; isolating CD34 + cells from a source of hematopoietic cells; introducing a vector comprising the claimed polynucleotide sequences into the CD34 + cells, whereby a population of said cells are genetically modified by said vector; culturing the modified CD34 + cells in the presence of at least one cytokine in an amount sufficient to support growth of the modified cells; and selecting cells in which the polypeptide is overexpressed whereby differentiation is blocked.
  • the mammalian hematopoietic cells are human.
  • the CD34 + cells are further selected based on the following phenotypes Thy-1 + , CD34 + Thy-1 + , CD34 + Thy-1 + Lin ' , or CD34 + Thy-1 + CD38 ' , either prior to or after introduction of the vector.
  • the method of blocking differentiation of mammalian hematopoietic stem cells includes introducing a vector comprising a claimed polynucleotide sequence into CD34 + cells, genetically modifying a population of said cells with said sequence; allowing the expression of the polynucleotide sequence in said cells and blocking differentiation. The method may be in vitro or in vivo.
  • the invention concerns, a method of producing a polypeptide of the invention comprising the steps of: culturing a host cell comprising a polynucleotide sequence encoding the claimed polypeptides under conditions suitable for the expression of the polypeptide, and recovering said polypeptide from the host culture.
  • the invention relates to an antibody which binds to the claimed polypeptides. Additionally, the invention concerns a method of identifying mammalian hematopoietic stem cells or progeny thereof comprising, preparing an antibody to a claimed polypeptide; purifying the antibody; exposing a population of the mammalian hematopoietic cells to the antibody; allowing said cells to bind to the antibody; and selecting said bound cells.
  • Figure 1 illustrates the MIE vector.
  • cDNAs (large arrow) are inserted into the polylinker. Transcription is driven from the 5'LTR.
  • EGFP is included as a selective marker.
  • Figure 2 illustrates the nucleotide sequence and predicted amino acid sequence of SCM 26 and corresponds to SEQ ID NO. 1.
  • the cDNA insert in clone SCM 26 is 1316 nucleotides in length and includes a polyA + tail of 18 residues. There is a single long open reading frame of 345 amino acids starting from the first in frame methionine at position 51 and ending with a TGA stop codon at position 1086.
  • SCM 26 encodes a putative signal peptide sequence and seven transmembrane domains giving a cell surface location with an extracellular amino terminus and an intracellular COOH terminus as represented in Figure 3.
  • the northern blot analysis indicates two SCM 26 transcripts. One transcript is 1.5Kb, and the second transcript is 2.4Kb.
  • FIG. 3A illustrates a hydrophobicity plot of SCM 26 and the predicted signal peptide and 7 transmembrane regions.
  • Figure 3B shows the predicted topology of the SCM 26 protein in the membrane.
  • Figure 3C illustrates that the SCM 26 protein is enriched in CD34 + cells.
  • Figure 4 illustrates the nucleotide sequence of SCM 3 and corresponds to SEQ ID NO. 3.
  • the SCM 3 cDNA contains 2990 nucleotides and ends in a ploy A tail.
  • the predicted open reading frame begins at nucleotide 82 and ends at nucleotide 1710 and encodes a protein of 543 amino acids.
  • Figure 5 illustrates specific features of the SCM 3 protein.
  • the protein contains a region predicted to bind the myb factor at amino acid 72 and 9 predicted zinc-finger regions of the C2-H2 family.
  • Figure 6 illustrates the nucleotide and amino acid sequence of SCM 113 having 2027 nucleotides with an open reading frame from nucleotide 72 to 1889 and encoding a predicted protein of 607 amino acids (SEQ ID NO. 5).
  • Figure 7 illustrates sustained proliferation of genetically modified cells grown in liquid culture and incorporating a polynucleotide sequence encoding SCM 3.
  • HSCs hematopoietic stem cells
  • SCM 26 Three novel cDNAs are found to be enriched in hematopoietic stem cells (HSCs). These novel genes are disclosed as SCM 26, SCM 3 and SCM 116 and are illustrated in Figures 2, 4 and 6, respectively.
  • the term "gene” as used herein means the segment of DNA involved in producing a polypeptide chain; it includes regions preceding and following the coding region (leader and trailer) as well as intervening sequences (introns) between individual coding segments (exons).
  • the invention includes an isolated polynucleotide encoding a polypeptide having the amino acid sequence as depicted in SEQ ID NO. 2, SEQ ID NO. 4, SEQ ID NO. 6, the amino acid sequence of residues 1 - 239 of SEQ ID NO.4, the amino acid sequence of residues 240 543 of SEQ ID NO. 4, and amino acid sequences functionally equivalent thereto.
  • isolated refers to molecules, either nucleic acids or amino acid sequences, that are removed from or separated from their original environment and are at least 60% free, preferably 75% free, more preferably 90% free and most preferably 95% free from other components with which they are naturally associated.
  • polypeptides and polynucleotides of the invention are purified to homogeneity.
  • Nucleic acid sequence refers to an oligonucleotide, nucleotide or polynucleotide, and fragments or portions thereof, and to DNA or RNA of genomic or synthetic origin and include sense or antisense strands.
  • a DNA "coding sequence of” or a “nucleotide sequence encoding" a particular protein is a DNA sequence which is transcribed and translated into a protein when placed under the control of appropriate regulatory sequences.
  • polypeptide is used interchangeably herein with the term protein.
  • the term "functional equivalenf is used in connection with a protein, the sequence of which is dictated by at least a part of the DNA sequences depicted in Figures 2, 4 or 6.
  • the term means a protein having a like biological function and like or improved specific activity, and a similar amino acid sequence.
  • Similarity or “identity” between two polypeptides or polynucleotides is determined by comparing the amino acid sequence and conserved amino acid substitutes of one polypeptide to the sequence of a second polypeptide. Similarity may be determined by procedures well known in the art, for example a BLAST program (Basic Local Alignment Search Tool at the National Center for Biological Information).
  • the present invention includes polypeptides having an amino acid sequence which is at least 75% identical to the polypeptides of SEQ ID NOs. 2, 4, 6 or fragments thereof. It is preferred that the degree of identity is at least 85%, even more preferably at least 90%, most preferably is least 95%, still more preferably at least 97%, and most preferably at least 99% identical to a protein depicted in SEQ ID NOs. 2, 4, 6 or fragments thereof. "Identity" as the term is used herein, refers to a polynucleotide or polypeptide sequence comprising a percentage of the same bases as a reference polynucleotide or polypeptide.
  • a polynucleotide or polypeptide which is at least 90% identical to a reference polynucleotide or polypeptide, has polynucleotide bases or amino acid residues which are identical in 90% of the bases or residues which make up the reference polynucleotide or polypeptide and may have different bases or residues in 10% of the bases or residues which comprise that polynucleotide or polypeptide sequence.
  • One way of calculating the percentage of sequence identity is by comparing two optimally aligned sequences over the window of comparison, determining the number of positions at which the identical nucleic acid base (e.g., A, T, C, G, U, or I) occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison (i.e., the window size), and multiplying the result by 100 to yield the percentage of sequence identity.
  • the identical nucleic acid base e.g., A, T, C, G, U, or I
  • ragmenf when used in connection with an amino acid sequence means a part of the sequence depicted in Figures 2, 5 or 6 and having at least 10 amino acid residues, preferably 50 amino acids residues, even more preferably 100 amino acid residues and most preferably 200 amino acid residues which are similar to the amino acid sequences of Figures 2, 5 or 6.
  • a variant i.e. a fragment polypeptide and reference polypeptide may differ in amino acid sequence by one or more substitutions, additions, deletions, truncations which may be present in any combination.
  • preferred variants are those that vary from a reference polypeptide by conservative amino acid substitutions. Such substitutions are those that substitute a given amino acid by another amino acid of like characters.
  • amino acids are considered conservative replacements (similar): a) alanine, serine, and threonine; b) glutamic acid and asparatic acid; c) asparagine and glutamine d) arginine and lysine; e) isoleucine, leucine, methionine and valine and f) phenylalaine, tyrosine and tryptophan. Most highly preferred are variants which retain the same biological function and activity as the reference polypeptide from which it varies.
  • Bio function within the meaning of this application is to be understood in a broad sense. It includes, but is not limited to, the particular functions disclosed in this application. Further, biological functions are not only those, which a polypeptide displays in its physiological context, i.e. as part of a living organism, but includes functions which it may perform in a non-physiological setting, e.g. in an in vitro test system.
  • a biological function of the SCM 3 gene product within the meaning of this application is the capability to improve the expansion of cells as measured in liquid culture assays as essentially described in example 5.
  • Another example of a biological function of SCM 3 gene product within the meaning of this application is the capability to inhibit myeloid differentiation of hematopoietic progenitor cells as essentially described in example 8.
  • the invention includes degenerate polynucleotides, DNA sequences which encode the polypeptides of the invention and particularly the amino acid sequence of SEQ ID NOs. 2, 4, 6 and fragments thereof, but having variations in the nucleotide coding sequences.
  • the degeneracy of the genetic code allows for various nucleic acid sequences, DNA's and RNA's, to encode the same protein.
  • an amino acid is encoded by two or more synonymous codons, for example the amino acid alanine is encoded by GCU, GCC and GCA.
  • the invention includes polynucleotides encoding a variant of the polypeptide as shown in Figure 2, Figure 5 or Figure 6.
  • nucleotide variants are alternate forms of the polynucleotide sequence which may have a deletion, substitution, or addition of one or more nucleotides and which are functionally equivalent to the encoded protein.
  • encoding refers to the inherent property of specific sequences of nucleotides in a nucleic acid, such as e.g. a gene in a chromosome or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having a defined sequence of nucleotides (e.g., rRNA, tRNA, other RNA molecules) or amino acids and the biological properties resulting therefrom.
  • a gene encodes a protein, if transcription and translation of mRNA produced by that gene produces the protein in a cell or other biological system.
  • Both the coding strand, the nucleotide sequence of which is identical to the mRNA sequence and is usually provided in sequence listings, and non-coding strand, used as the template for transcription, of a gene or cDNA can be referred to as encoding the protein or other product of that gene or cDNA.
  • a nucleic acid that encodes a protein includes any nucleic acids that have different nucleotide sequences but encode the same amino acid sequence of the protein due to the degeneracy of the genetic code. Nucleic acids and nucleotide sequences that encode proteins may include introns.
  • SCM gene refers to the amino acid sequence of substantially purified SCM peptides obtained from any species, particularly preferred are mammalian, including human, mouse, and chicken, and most particularly human, and from any source whether natural, synthetic or recombinant.
  • SCM expression is broadly used in this disclosure to mean the expression of a polynucleotide sequence of the invention.
  • the polypeptides so expressed are referred to as SCM proteins.
  • the invention further includes an isolated DNA sequence including the polynucleotide sequence of SEQ ID NO. 1 , SEQ ID NO. 3, SEQ ID NO. 5, a fragment thereof and a sequence having at least 85% identity thereto.
  • Isolated nucleic acid sequences are substantially similar if they are capable of hybridizing under stringent conditions to the sequence of Figures 2, 4 or 6.
  • Isolated nucleic acid sequences are also considered substantially similar if they are polynucleotides which are at least 85%, preferably at least 90%, more preferably at least 95%, even more preferably 97%, and most preferably 99% identical to the sequences of SEQ ID NOs. 1 , 3, 5 or a fragment thereof.
  • the fragment includes the polynucleotide encoding the amino acid sequence of residue 1 - 239 of SEQ ID NO. 4, variants and complementary sequences thereto. In another preferred embodiment the fragment includes the polynucleotide encoding the amino acid sequence of residue 240 - 543 of SEQ ID NO. 4., variants and complementary sequences thereto.
  • fragment means a nucleotide sequence including part of the sequence depicted in Figures 2, 4 or 6 and comprising as few as at least 30, 50, 75, 80, 100 or more nucleotides, preferably at least 200, 300, 400, 500, 600, or more nucleotides, even more preferably at least 800, 1000, 1500, 2000 or more nucleotides.
  • the fragment will have at least 100 nucleotides, preferably 500 nucleotides, even more preferably 800 nucleotides and most preferably at least 1000 nucleotides.
  • the fragment will have at least 1500 nucleotides, preferably 2000 nucleotides, and most preferably at least 2500 nucleotides.
  • the fragment will have at least 1000 nucleotides, preferably 1500 nucleotides, and most preferably at least 2000 nucleotides.
  • the invention further provides an isolated polynucleotide consisting of the complement of the above disclosed polynucleotides.
  • complement refers to the binding of polynucleotides under permissive conditions by base pairing, for example the sequence of "AGT” binds to the complementary sequence TCA".
  • a polynucleotide sequence will hybridize with the reference sequence i.e. SEQ ID NOs. 1, 3, or 6 or a part thereof under stringent conditions.
  • Stringent hybridization conditions are those in which hybridization is effected between 50° and 60°C in saline buffer solution.
  • the DNA to be used for hybridization may be prepared in a conventional manner and be targeted to form an identifiable probe by procedures well known in the art.
  • conditions may be selected that are about 5 to 20 degrees C lower than the thermal melting point (T m ) for the specific sequence at a defined ionic strength and pH.
  • T m is the temperature (under defined ionic strength and pH) at which 50 % of a target sequence hybridizes to a complementary probe.
  • the DNA to be used for hybridization may be prepared in a conventional manner and be targeted to form an identifiable probe by procedures well known in the art.
  • antisense means nucleotide sequences that are complementary to a specific DNA or RNA sequence (sense strand). This invention further includes complementary or antisense polynucleotides.
  • the invention concerns isolated polypeptides which have the deduced the amino acid sequence selected from the group of SEQ ID NO. 2, SEQ ID NO. 4, SEQ ID NO. 6, fragments thereof, functionally equivalent polypeptides thereto.
  • a polypeptide fragment may have a sequence which is at least 10 amino acids, preferably at least 50 amino acid, even more preferably at least 100 amino acids, and most preferably at least 200 amino acids which are identical to the polypeptide sequence of Figure 2, 5, or 6.
  • polypeptide including amino acid residues 26 - 40 of SEQ ID NO. 2; the polypeptide including amino acid residues 25 - 82 of SEQ ID NO. 2; the polypeptide including amino acid residues 147 - 157 of SEQ ID NO. 2; and the polypeptide including amino acid residues 266 - 275 of SEQ ID NO. 2.
  • a functionally equivalent polypeptide of Figure 2, 5 or 6 is a variant wherein one in which one or more amino acid residues are substituted with conserved or non-conserved amino acid residues, or one in which one or more amino acid residues includes a substituent group.
  • Conservative substitutions are the replacements, one for another, among the aliphatic amino acids Ala, Val, Leu and He; interchange of the hydroxl residues Ser and Thr; exchange of the acidic residues Asp and Glu; substitution between amide residues Asn and Gin; exchange of the basic residues Lys and Arg; and replacements among aromatic residues Phe and Tyr.
  • the invention features polypeptide sequences having at least 75% identity with the polypeptide sequences illustrated in Figures 2, 5, 6, or fragments and functionally equivalent polypeptides thereof.
  • the polypeptides have at least 85% identity, more preferably at least 90% identity, even more preferably at least 95% identity, still more preferably at least 97% identity, and most preferably at least 99% identity with the amino acid sequences illustrated in Figures 2, 5, 6, or the fragments including amino acid residue 1 -239 or 240 - 543 of Figure 5.
  • the SCM encoding sequence may be introduced as a construct into a host cell, in a preferred embodiment the SCM encoding sequence will be placed into a vector.
  • the term "vector” means an agent used to carry new genes or DNA segments into cells. Vectors include the necessary elements for the transcription and translation of the inserted coding sequence. Preferred polynucleotides included in the construct or the vector are the sequences encoding for SCM 3, SCM 26, SCM 113 and functionally equivalent sequences having at least 85% identity thereto, and preferably having at least 90% identity thereto. Methods used to construct vectors are known and described in various publications. In particular techniques for constructing suitable vectors are reviewed in considerable detail in Sambrook et al., Molecular Cloning: A Laboratory Manual, 2 nd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989).
  • Vectors may include but are not limited to viral vectors, such as baculovirus, retroviruses, adenoviruses, adeno-associated viruses, and herpes simplex viruses; bacteriophages; cosmids; plasmid vectors; synthetic vectors; and other recombination vehicles typically used in the art.
  • the vector comprises a polynucleotide operatively linked to a regulatory sequence. Regulatory sequences include promoters, enhancers, polyadenylation signals, and other expression control elements.
  • the promoter may be either a prokaryotic or eukaryotic promoter.
  • the vector may further comprise a polyadenylation signal that is positioned 3' of the carboxy-terminal amino acid.
  • Vectors containing both a promoter and a cloning site into which a polynucleotide can be operatively linked are well known in the art. Such vectors are capable of transcribing RNA in vitro or in vivo, and are commercially available from sources such as Stratagene (La Jolla, CA) and Promega Biotech (Madison, WI). Specific examples include, pSG, pSV2CAT, pXtl from Stratagene and pMSG, pSVL, pBPV and pSVK3 from Pharmacia.
  • Preferred vectors include retroviral vectors (See, Coffin et al., "Retroviruses", (1997) Chapter 9 pp; 437-473 Cold Springs Harbor Laboratory Press). Vectors useful in the invention are produced recombinantly by procedures already taught in the art. WO94/29438, WO97/21824 and WO97/21825 describe the construction of retroviral packaging plasmids and packing cell lines. Exemplary vectors include the pCMV mammalian expression vectors, such as pCMV6b and pCMV6c (Chiron Corp.), pSFFV-Neo, and pBluescript-Sk+.
  • Non-limiting examples of useful retroviral vectors are those derived from murine, avian or primate retroviruses. Common retroviruses are those based on the Moloney murine leukemia virus (MoMLV-vector). Other MoMLV derived vectors include, Lmily, LINGFER, MINGFR and MINT (Chang et al., Blood 92:1 - 11 (1998)). Further vectors include those based on Gibbon ape leukemia virus (GALV) and Moloney murine sacroma virus (MoMSV) and spleen focus forming virus (SFFV). Vectors derived from the murine stem cell virus (MESV) include MESV-MiLy (Agarwal et al., J.
  • Retroviral vectors also include vectors based on lentiviruses, and non-limiting examples include vectors based on human immunodeficiency virus (HIV-1 and HIV-2). New vector systems are continually being developed to take advantage of particular properties of parent retroviruses such as host range, usage of alternative cell surface receptors and the like.
  • the present invention is not limited to particular retroviral vectors, but may include any retroviral vector.
  • Particularly preferred vectors include DNA from a murine virus corresponding to two long terminal repeats, and a package signal.
  • the murine viral vector is derived from a MoMLV or a MSCV.
  • the viral gag, pol and env sequence will generally be removed from the virus, creating room for insertion of foreign DNA sequences.
  • Genes encoded by foreign DNA are usually expressed under the control a strong viral promoter in the long terminal repeat (LTR). Selection of appropriate control regulatory sequences is dependent on the host cell used and selection is within the skill of one in the art. Numerous promoters are known in addition to the promoter of the LTR.
  • Non-limiting examples include the phage lambda PL promoter, the human cytomegalovirus (CMV) immediate early promoter; the U3 region promoter of the Moloney Murine Sarcoma Virus (MMSV), Rous Sacroma Virus (RSV), or Spleen Focus Forming Virus (SFFV); Granzyme A promoter; Granzyme B promoter, CD34 promoter; and the CD8 promoter. Additionally inducible or multiple control elements may be used.
  • CMV human cytomegalovirus
  • MMSV Moloney Murine Sarcoma Virus
  • RSV Rous Sacroma Virus
  • SFFV Spleen Focus Forming Virus
  • Granzyme A promoter Granzyme A promoter
  • Granzyme B promoter CD34 promoter
  • CD8 promoter the CD8 promoter. Additionally inducible or multiple control elements may be used.
  • Such a construct can be packed into viral particles efficiently if the gag, pol and env functions are provided in trans by a packing cell line. Therefore when the vector construct is introduced into the packaging cell, the gag-pol and env proteins produced by the cell, assemble with the vector RNA to produce infectious virons that are secreted into the culture medium. The virus thus produced can infect and integrate into the DNA of the target cell, but does not produce infectious viral particles since it is lacking essential packaging sequences. Most of the packing cell lines currently in use have been transfected with separate plasmids, each containing one of the necessary coding sequences, so that multiple recombination events are necessary before a replication competent virus can be produced. Alternatively the packaging cell line harbors a provirus.
  • RNA produced from the recombinant virus is packaged instead. Therefore, the virus stock released from the packaging cells contains only recombinant virus.
  • retroviral packaging lines include PA12, PA317, PE501, PG13, ⁇ CRIP, RD114, GP7C-tTA-G10, ProPak-A (PPA-6), and PT67. Reference is made to Miller et al., Mol. Cell Biol.
  • vectors include adenoviral vectors (See, Frey, B.M. et al., Blood, 91 :2781 , (1998); and W 095/27071 ) and adeno-associated viral vectors (See, Chatterjee et al., Current Topics in Microbiol. And Immunol., 218:61 - 73, 1996). Also reference is made to Shenk, Chapter 6, 161 - 178, Breakefield et al., Chapter 8 201-235; Kroner-Lux et al., Chapter 9 235 - 256 in Stem cell Biology and Gene Therapy, eds. Quesenberry et al., John Wiley & Sons, 1998 and U.S. Pat Nos.
  • adenovirus- derived vectors may be advantageous under certain situation because they are not capable of infecting non-dividing cells, and unlike retroviral DNA, the adenoviral DNA is not integrated into the genome of the target cell. Further, the capacity to carry foreign DNA is much larger in adenoviral vectors than retroviral vectors.
  • the adeno-associated viral vectors are another useful delivery system. The DNA of this virus may be integrated into non- dividing cells, and a number of polynucleotides have been successful introduced into different cell types using adeno-associated viral vectors.
  • the construct or vector will include two or more heterologous nucleic acid sequences; a) the nucleic acid sequence encoding a polypeptide of the invention and b) one or more additional nucleic acid sequence.
  • the additional nucleic acid sequence is a polynucleotide which encodes a selective marker, a structural gene, a therapeutic gene, a ribozyme, or an antisense sequence.
  • a selective marker may be included in the construct or vector for the purposes of monitoring successful genetic modification and for selection of cells into which DNA has been integrated. Non-limiting examples include drug resistance markers, such as G148 or hygromycin. Additionally negative selection may be used, for example wherein the marker is the HSV-tk gene.
  • This gene will make the cells sensitive to agents such as acyclovir and gancyclovir. Selection may also be made by using a cell surface marker, for example, to select overexpression of SCM by fluorescence activated cell sorting (FACS).
  • FACS fluorescence activated cell sorting
  • the NeoR (neomycin/G148 resistance) gene is commonly used but any convenient marker gene may be used whose gene sequences are not already present in the target cell can be used.
  • NGFR low-affinity Nerve Growth Factor
  • EFGP enhanced fluorescent green protein
  • DHFR dihydrofolate reductase gene
  • HSA murine CD24
  • HSA murine CD8a(lyt)
  • bacterial genes which confer resistance to puromycin or phleomycin and ⁇ -glactosidase.
  • gene therapy cells which express heterologous genetic material in vivo.
  • the genetic material is suitably a gene for the normal protein.
  • the gene may be for a protective protein or the gene may encode a protective RNA such as a ribozyme or antisense sequence.
  • Gene Therapy may be in vivo, administering the vector to the subject so that host target cells are transformed in situ or ex vivo wherein the target cells are transformed in vitro and then introduced into the subject.
  • the structural gene may be the entire gene or only the functionally active fragment of the gene.
  • the structural gene may include for example a gene that regulates cell differentiation or a therapeutic gene capable of compensating for a deficiency in a patient that arises from a defective endogenous gene.
  • a therapeutic gene may be one that antagonizes production or function of an infectious agent, antagonizes pathological processes, improves a host's genetic makeup, or facilitates engraftment.
  • a therapeutic gene or gene sequences are ones effective in the treatment of adenosine deaminase deficiency (ADA); sickle cell anemia; recombinase deficiency; recombinase regulatory gene deficiency; HIV such as an antisense or trans-dominant REV gene or a gene carrying a herpes simplex virus thymidine kinase (HSV-tk)).
  • HSV-tk herpes simplex virus thymidine kinase
  • the therapeutic gene will generally be of human origin although genes of closely related species that exhibit high homology and biologically identical or equivalent function in humans may be used if the gene does not produce an adverse immune reaction in the recipient.
  • the second polynucleotide sequence may encode new antigens or drug resistant genes or may encode a toxin or an apoptosis inducer effective to specifically kill cancerous cells, or a specific suicide gene to cancerous hematopoietic cells may be included.
  • a therapeutic active amount of a nucleic acid sequence or a therapeutic gene is an amount effective at dosages and for a period of time necessary to achieve the desired result. This amount may vary according to various factors including but not limited to sex, age, weight of a subject, and the like.
  • the additional polynucleotide sequence(s) may be introduced into the host cell on the same vector as the polynucleotide sequence encoding the polypeptides of the invention or the additional polynucleotide sequence may be introduced into the host cells on a second vector.
  • a selective marker will be included on the same vector as the SCM encoding nucleic acid sequence.
  • the vector will include at least three polynucleotide encoding sequences comprising the SCM encoding polynucleotide, a selectable marker and a therapeutic gene.
  • the host target cells of the present invention are mammalian cells and these include but are not limited to humans, mice, monkeys, farm animals, sport animals, pets, and other laboratory rodents and animals. Particularly preferred mammals are human, mice and rabbit.
  • Preferred cells include stem cells of various cell types, such as, hematopoietic, muscle, epithelial, neural, liver, embryo and bone stem cells, particularly HSCs. Stem cells are capable of self-renewal divisions and give rise to differentiated progeny. They or their progeny contain the engrafting potential for in vivo therapeutic application.
  • Hematopoietic stem cells are pluripotent and may also be defined in vitro by the presence of CAFC activity. General reference is made to Potten OS.
  • Particularly preferred host cells include hematopoietic cells. These cells encompass hematopoietic stem cells, erythrocytes, neutrophils, monocytes, platelets, mast cells, eosinophils and basophils, B and T lymphocytes and NK cells as well as the respective lineage progenitor cells. T-cells are defined as a type of lymphocyte and are thought to develop from hematopoietic stem cells.
  • T-cells There are many types of T-cells including thymocytes, helper T-cells, inducer T-cells, suppressor T cells, or any other subset of T- cells.
  • progenitor or progenitor cell indicates a cell population which no longer is a stem cell but also which has not yet become a terminally differentiated cell.
  • lymphoid, myeloid, or erythroid in conjunction with the term progenitor indicates the potential cell population into which the progenitor is capable of maturing.
  • Human hematopoietic stem cells, T-cells and lymphoid, myeloid, or erythroid progenitor cells are especially preferred host cells.
  • Methods of obtaining hematopoietic cells and stem cells are well known in the art and not repeated herein in any detail.
  • methods of isolating stem cells and progenitor cells include isolation from other cells in hematopoietic tissue of the body and particularly bone marrow.
  • Stem cells and progenitor cells from bone marrow constitute only a small percentage of the total number of hematopoietic cells.
  • Stem cells appear to be in the range of about 0.01 to about 0.1% of the bone marrow cells.
  • Bone marrow cells may be obtained from ilium, sternum, tibiae, femora spine and other bone cavities.
  • hematopoietic stem cells include embryonic yolk sac, fetal liver fetal and adult spleen, blood including adult peripheral blood and umbilical cord blood (To et al., Blood 89:2233 - 2258 (1997)).
  • an appropriate solution may be used to flush the bone, including but not limited to salt solution, supplemented with fetal calf serum or other naturally occurring factors in conjunction with an acceptable buffer at low concentration, generally about 5 to 25 mM.
  • Buffers include but are not limited to HEPES, phosphate and lactate buffers. Bone marrow can also be aspirated from the bone in accordance with conventional techniques.
  • hematopoietic cells may be separated from other cells.
  • Various procedures may be employed and include physical separation, magnetic separation using antibody-coated magnetic beads, affinity chromatography, and cytotoxic agents joined to a monoclonal antibody or used in conjunction with a monoclonal antibody.
  • FACS fluorescence activated cell sorters
  • cell separation or selection is not critical to the invention, and specific cell types may be separated either prior to genetic modification or after genetic modification. Preferably cells are initially separated by a coarse separation followed by using positive and/or negative selection.
  • the surface antigen expression profile of an enriched hematopoietic stem cell population may be identified by CD34 + Thy-1 + Lin ' .
  • enriched phenotypes may include: CD2 ⁇ CD3 " , CD4 ' , CD8 ' , CD10 ' , CD14 ' , CD15 “ , CD19 ' , CD20 ' , CD33 ' , CD34 " , CD38 ,0 " , CD45RA ' , CD59 +/” , CD71 " , CDW109 + , glycophorin ' , AC133 + , HLA-DR + ⁇ c-kit + and EM + .
  • Lin ' refers to a cell population selected on the basis of lack of expression of at least one lineage specific marker, for example CD2, CD3, CD14, and CD56.
  • the combination of expression markers used to isolate and define an enriched HSC population may vary depending on various factors and may vary as other expression markers become available.
  • Murine HSCs with similar properties to the human CD34 + Thy-1 + Lin ' may be identified by I ⁇ * Thy-1.1 to Lir ⁇ ⁇ o Sca-1 + (KTLS). Other phenotypes are well known.
  • KTLS Lir ⁇ ⁇ o Sca-1 +
  • Other phenotypes are well known.
  • CD34 expression is combined with selection for Thy-1 , a composition comprising approximately fewer than 5% lineage committed cells can be isolated (U.S. Patent No. 5,061 ,620).
  • T-cell antigen receptor TCR
  • TCR-2 consististing of ⁇ and ⁇ polypeptides
  • TCR-1 consististing of ⁇ and ⁇ polypeptides
  • B cells may be selected, for example, by expression of CD19 and CD20.
  • Myeloid cells may be selected, for example, by expression of CD14, CD15, and CD16.
  • NK cells may be selected based on expression of CD56 and CD16. Erythrocytes may be identified by expression of glycophorin A. Compositions enriched for progenitor cells capable of differentiation into myeloid cells, dendritic cells, or lymphoid cells also include the phenotypes CD45RA + CD34 + Thy-1 + and CD45RA + CD10 + Lin ' CD34 + . One skilled in the art is aware of other useful markers for various cell types.
  • the cells are cultured in a suitable medium comprising a combination of growth factors that are sufficient to maintain growth.
  • the term culturing refers to the propagation of cells on or in media of various kinds. It is understood that the descendants of a cell grown in culture may not be completely identical (either morphologically, genetically or phenotypically) to the parent cell. Methods for culturing stem cells and hematopoietic cells are well known to those skilled in the art, and some of these methods are briefly mentioned herein. Any suitable culture container may be used, and these are readily available from commercial vendors.
  • the seeding level is not critical, and it will depend on the type of cells used. In general, the seeding level will be at least 10 cells per ml, more usually at least about 100 cells per ml and generally not more than 10 6 cells per ml.
  • Various culture media can be used and non-limiting examples include Iscove's modified Dulbecco's medium (IMDM), X-vivo 15 and RPMI-1640. These are commercially available from various vendors.
  • IMDM Iscove's modified Dulbecco's medium
  • X-vivo 15 and RPMI-1640 are commercially available from various vendors.
  • the formulations may be supplemented with a variety of different nutrients, growth factors, such as cytokines and the like.
  • cytokine refers to any one of the numerous factors that exert a variety of effects on cells, such as inducing growth and proliferation.
  • the cytokines may be human in origin or may be derived from other species when active on the cells of interest.
  • molecules having similar biological activity to wild type or purified cytokines for example produced by recombinant means, and molecules which bind to a cytokine factor receptor and which elicit a similar cellular response as the native cytokine factor.
  • the medium can be serum free or supplemented with suitable amounts of serum such as fetal calf serum, autologous serum or plasma. If cells or cellular products are to be used in humans, the medium will preferably be serum free or supplemented with autologous serum or plasma. (Lansdorp et al., J. Exp. Med. 175:1501 (1992) and Petzer et al., PNAS 93:1470 (1996)).
  • Non-limiting examples of compounds which may be used to supplement the culture medium are thrombopoietin (TPO), Flt3 ligand (FL), c-kit ligand (KL, also known as stem cell factor (SCF) or Stl), Interleukin (IL) such as, IL-1 , IL-2, IL-3, IL-6, (soluble IL-6 receptor), IL-11, and IL-12, granulocyte-colony stimulating factor (G-CSF), granulocyte macrophage -colony stimulating factor (GM-CSF), leukemia inhibitory factor (LIF), MIP-1 ⁇ , and erythropoietin (EPO). These compounds may be used alone or in any combination, and preferred concentration ranges may be readily determined from the published art.
  • a preferred non-limiting medium includes mlL-3, mlL-6 and mSCF.
  • a general preferred range of TPO is from about 0.1ng/mL to about 500 ⁇ g/mL, more preferred is from about 1.Ong/mL to about 1000ng/mL even more preferred is from about 5.0ng/mL to about 300ng/mL.
  • a preferred concentration range for each of FL and KL is from about 0.1ng/mL to about 1000ng/mL, more preferred is from about 1.Ong/mL to about 500ng/mL.
  • IL-6 is a preferred factor to be included in the culture, and a preferred concentration range is from about 0.1ng/mL to about 500ng/mL and more preferred in from about 1.Ong/mL to about 100ng/mL.
  • Hyper IL-6, a covalent complex of IL-6 and IL-6 receptor may also be used in the culture.
  • fibronectin refers to a glycoprotein that is found throughout the body, and its concentration is particularly high in connective tissues where it forms a complex with collagen.
  • polypeptides of the invention may be produced by culturing the host cell comprising a polynucleotide of the invention under conditions suitable for the expression of the polypeptide and recovering said polypeptide from the host culture.
  • Methods of obtaining polypeptides from host cells grown in culture are well known in the art. ln the present invention, the methods of genetic modification are intended to encompass any genetic modification method of exogenous or foreign gene transfer or nucleic acid transfer into mammalian cells (particularly human stem cell and hematopoietic cells).
  • transduction viral mediated transfer of host DNA from a host or donor to a recipient, either in vitro or in vivo
  • transfection transformation of cells with isolated viral DNA genomes
  • liposome mediated transfer electroporation, calcium phosphate transfection or coprecipitation and others.
  • Methods of transduction include direct co-culture of cells with producer cells (Bregni et al., Blood 80:1418 - 1422 (1992)) or culturing with viral supernatant alone with or without appropriate growth factors and polycations (Xu et al., Exp. Hemat. 22:223 - 230 (1994)).
  • the host cells are transduced with a retroviral vector as previously described.
  • the host cell range that may be infected is determined by the viral envelope protein.
  • the recombinant virus can be used to infect virtually any other cell type recognized by the env protein provided by the packaging cell, resulting in the integration of the viral genome in the transduced cell and the stable incorporation of the foreign gene product.
  • murine ecotropic env of MoMLV allows infection of rodents cells
  • amphotropic env allows infection of rodent, avian and some primate cells including human cells.
  • Amphotropic packaging of cell lines for use with MoMLV systems are known in the art and are commercially available.
  • Xenotropic vector systems also exist which allow infection of human cells.
  • the genetically modified cells obtained as described above may be used immediately, expanded or frozen at for example liquid nitrogen temperatures and stored for long periods of time, being thawed and capable of being used.
  • the cells may be stored by methods well known in the art. Once the genetically modified cells are thawed they may be further expanded. Methods of expansion of HSCs by use of growth factors and/or stromal cells associated with stem cell proliferation and differentiation are well known to those skilled in the art (US Pat. No. 5,744,361). Methods of using the genetically modified cells include in vitro and in vivo applications.
  • the invention further concerns, a method for increasing the effective dose of hematopoietic cells, particularly stem cells in a subject which includes obtaining a population of CD34 + cells, including a subpopulation hematopoietic stem cells; introducing into the population of CD34 + cells a polynucleotide sequence of the invention; obtaining a subpopulation of genetically modified stem cells which overexpress the polypeptide encoded by said polynucleotide; and administering said subpopulation of genetically modified cells to a mammalian subject wherein the effective dose of the hematopoietic stem cells is increased.
  • Method of obtaining hematopoietic cells has previously been disclosed.
  • the HSC may be selected using various known and previously mentioned techniques either prior to or after genetic modification.
  • the hematopoietic cells may be isolated based on phenotype expression as disclosed hereinabove.
  • the polynucleotide is introduced on a vector. While any method of genetic modification may be used to introduce a polynucleotide of the invention into the host cells, transduction is the preferred method of genetic modification.
  • an "effective amount or dose” is an amount sufficient to effect beneficial or desired results.
  • An effective amount may be administrated in one or more administrations. Determination of an effective amount is within the capability of those skilled in the art. Particularly preferred subjects of the invention in general include living mammals such as human, mice and rabbit, most preferred are humans.
  • the administration of a genetically modified cell comprising a polynucleotide sequence of the invention may be by conventional means, for example, injection, oral administration, inhalation and others. Appropriate carries and diluents may be included in the administration of the modified cells. Samples including the modified cells and progeny thereof may be taken and tested to determine transduction efficiency.
  • the population of CD34 + cells may be cultured either prior to or after genetic modification of the host cells.
  • overexpression refers to expression of a polypeptide of the invention brought about by genetic modification of a host cell with a nucleic acid sequence encoding the polypeptide.
  • Particularly preferred are polynucleotides that encode SCM 3, SCM 26, SCM 113 and functionally equivalent polypeptides having 85% identity thereto. Overexpression may take place in cells normally lacking expression of polypeptides functionally equivalent or identical to the SCM proteins claimed herein or overexpression may take place in cells with endogenous expression of polypeptides functionally equivalent or identical to the SCM protein claimed herein. While overexpression may take place in any cell type particularly preferred host cells include hematopoietic cells, particularly HSCs and T-cells.
  • a HSC may have an endogenous level of expression of functionally equivalent or identical polypeptide to a SCM protein, but the host cell would not be genetically modified to include a nucleic acid sequence of the invention encoding a SCM polypeptide and capable of expression thereof.
  • a wild type cell is a cell type of the host cell but not genetically modified to include a polynucleotide sequence encoding a SCM polypeptide of the invention and would not result in overexpression.
  • the overexpression of SCM proteins can be measured by various methods well known in the art. A preferred method includes the measurement of a marker gene particularly EGFP by FACS.
  • the method may also provide the introduction of a second polynucleotide sequence encoding a therapeutic gene, an antisense gene or a ribozyme into the population of CD34 + cells as described herein above.
  • the invention concerns a method of increasing the effective dose of gene modified cells. Host cells and particularly hematopoietic stem cells overexpressing the polynucleotides of the invention are useful therapeutically. Differentiation of the cells is blocked resulting in expansion of non- differentiated stem cells. Expansion of non-differentiated stem cells gives an increase in stem cell dose either ex vivo or in vivo, thereby potentially allowing more rapid engraftment. This may result in increased representation of genetically modified cells in a subject.
  • the genetically modified host cells are maintained for a period of time sufficient for overexpression of SCM proteins.
  • a suitable time period will depend inter alia upon cell type used and is readily determined by one skilled in the art.
  • genetically modified cells of the invention may overexpress SCM proteins for the lifetime of the host cell.
  • the time period will be in the range of 1 to 45 days, more preferably in the range of 1 to 30 days, even more preferably in the range of 1 to 20 days, still more preferably in the range of 1 to 10 days, and most preferably in the range of 1 to 5 days.
  • a further application of the invention concerns a method of blocking the differentiation of mammalian hematopoietic stem cells including introducing a polynucleotide sequence of the invention into CD34 + cells; genetically modifying a population of the CD34 + cells; allowing expression of the polynucleotide sequence in the cells; and blocking differentiation of said genetically modified cells.
  • the polynucleotide will encode SCM 3, SCM 26, SCM 113 or functionally equivalent polypeptides thereto.
  • stem cells are pluripotent and capable of self-renewal. Differentiation is defined as the restriction of the potential of a cell to self renew with a change in the functional capacity of the cell.
  • blocking differentiation is used broadly in the context of this invention and includes not only the prevention of differentiation but also means the altering of differentiation. Differentiation may be determined by methods well known in the art and these include analysis for surface markers associated with cells of a defined differentiated state. While not meant to limit the invention, generally differentiation will be slowed to about at least 10%, preferably to about 15%, more preferably to about 20%, and most preferably to about 30% or greater fewer cells expressing a specific differentiation marker.
  • Such markers include, for example, CD4, CD8, CD13, CD14, CD19, CD36, CD40, CD41 and CD94.
  • differentiation will be slowed to about at least greater than 15% and preferably greater than 20%, fewer cells expressing the marker CD14.
  • the method of blocking the differentiation of mammalian hematopoietic stem cells may also include isolating hematopoietic cells, particularly CD34 + cells from a source of such cells and introducing a polynucleotide of the invention into the cells whereby the cells are genetically modified. Additionally it is preferred that the polynucleotide be introduced on a vector, preferably a retroviral vector wherein the host cells are genetically modified by transduced.
  • a vector preferably a retroviral vector wherein the host cells are genetically modified by transduced.
  • the invention still further includes an antibody which binds to the polypeptides of the invention.
  • SCM antibody encompasses any antibody or fragment thereof either native or recombinant, synthetic or naturally derived, which retains sufficient specificity to bind specifically to the SCM protein.
  • the SCM antibody may be monoclonal or polyclonal that binds to SCM protein. In this regard the antibody recognizes, preferentially hematopoietic cells, particularly stem cells.
  • SCM 3, 26 or 113 protein, or a fragment or variant thereof For the production of antibodies, various host subjects, may be immunized by injection with SCM 3, 26 or 113 protein, or a fragment or variant thereof.
  • General techniques for the production of antibodies are known and various protocols for measuring protein are also known including enzyme linked immunosorbant assay and fluorescent activated cell sorting. While the protein as illustrated in Figures 2, 4 or 6 may be used to raise antibodies.
  • the protein sequence of SCM 26 is most preferred.
  • a polyclonal antiserum against SCM 26 amino acid residues 26 - 40 is raised in rabbits using well known techniques.
  • Peptide specific antibodies are purified by affinity chromatography and used for immunoblots or wildtype f ibroblast or fibroblasts transfected with a retroviral vector expressing SCM 26, Figure 3.
  • the invention encompasses not only antibodies which bind to a polypeptide of the invention but also a method of identifying stem cells, particularly hematopoietic stem cells or the progeny thereof. This includes preparing an antibody to a polypeptide of the invention, purifying the antibody, exposing a population of hematopoietic cells to the antibody allowing the exposed cells to bind with the antibody and then selecting bound cells. Techniques including antibody preparation and purification are well known in the art and these techniques are preformed on a routine basis.
  • the long term culture-initiating cell (LTCIC) assay involves culturing a cell population on stromal cell monolayers for approximately 5 weeks and then testing in a 2 week semisolid media culture for the frequency of clonogenic cells retained (Sutherland et al., Blood 74:1563 (1989)).
  • the Colony-Forming Unit Culture (CFU-C) assay involves use of cell count as the number of colony-forming units per unit volume or area of a sample The assay is used to measure clonal growth of quickly maturing progenitors in semi-solid media supplemented with serum and growth factors. Depending on the growth factors used to stimulate growth mature and/or primitive progenitors may be determined.
  • Cobblestone area forming colony (CAFC) assays measure clonal proliferation of long-lived progenitors supported by stromal cell monolayers and growth factor/serum supplemented media. On the appropriate stromal monolayers, cells pluripotent for myeloid and lymphoid lineages may be determined. (Young et al., Blood 88:1619, (1996)).
  • SCID-hu bone assays measure the proliferation and multilineage differentiation of cells with bone marrow repopulating activity. These cells are likely to contribute to durable engraftment in clinical transplantation.
  • SCID-hu thymus assays measure the proliferation and differentiation in thymocytes. Both bone marrow repopulating and more mature T-lineage progenitors may be measured.
  • GM-CSF granulocyte-macrophage colony stimulating factor
  • HSCs Thy-1 + hematopoietic stem cells
  • CD34 + Thy-1 + HSC stem cells are purified by flow sorting as described by Gazitt et al., Blood, 86:381-389 (1995).
  • Total RNA is purified from >10 7 HSC using RNA-Stat (Tel-Test B inc, Friendswood, Texas).
  • PolyA + RNA is purified from total RNA on oligo dT (Pharmacia Biotech) and used to synthesize cDNA (Stratagene unidirectional cDNA synthesis kit). Each cDNA molecule generated using this kit has an EcoR1 sticky end at the 5' end and a Xhol sticky end at the 3' end.
  • the cDNA is directionally cloned into lambda ZAP express that had been digested with EcoR1 and Xhol restriction enzymes (Stratagene).
  • the ligated cDNA lambda ZAP is packaged using Gigapack III gold (Stratagene) and transfected into XL1-Blue MRF's cells (Stratagene).
  • a total of 0.5 x 10 6 independent clones are produced.
  • the lambda phage are harvested and in vivo excised to pBlueScript (pBS) using ExAssist helper phage and SOLR strain E. coli according to recommended Stratagene protocol.
  • Random clones are mini prepped by Qiagen 96 well system, restriction digestion with EcoR1 plus Xhol and electrophoresed to show inserts in the size range 0.5-5.0 Kb with an average size of 2.3 Kb.
  • 10,000 mini prep clones are sequenced using T3 primed (i.e. 5' end) dye terminator sequencing reactions and processed on an ABI377 automated sequencer (PE Applied Biosystems). Sequence data is analyzed by BLASTX and BLASTN (Basic Local Alignment Search Tool) searches against GenBank. A number of clones are identified as being either completely novel or having homology only with ESTs.
  • Expression profiling is used to identify cDNA sequences which are preferentially expressed in HSCs.
  • the cDNA inserts of clones identified as being either completely novel or having homology only with expressed sequence tags (ESTs) are amplified by PCR using T3 and T7 primers and then sent to Synteni are the microdot arrays are generated.
  • Microdot array probes are synthesized from RNA purified from mobilized peripheral blood CD34 + cells and labeled with Cy3 and from either peripheral blood cells (PBL) RNA or CD11b RNA or CD4 RNA or CD19 RNA and labeled with Cy5 using standard protocols as recommended by Synteni.
  • the CD34 probe and the PBL probe are mixed and allowed to hybridize to a microdot array.
  • the microarray After hybridization and washing, the microarray is scanned to determine the intensity of probe binding to each cDNA. Hybridizations, washing and scanning are performed by Synteni. Probe binding is proportional to gene expression level. The raw binding data is balanced by monitoring probe binding to Synteni control elements on the microarray; this accounts for differences in the fluorescent labeling of the two probes. The ratio of the two binding intensities, the balanced differential expression (BDE) gives a quantitative measurement of relative gene expression level. Table 1 shows the differential expression of SCM3 in 3 independent experiments. Similar results are observed for SCM26 and SCM113 (data not shown).
  • cDNAs that are expressed more in stem cells than in peripheral blood cells (PBL)
  • these cDNAs are designated selected cDNAs.
  • the selected cDNAs are defined as being expressed at least two fold higher in stem cells (BDE>2.0) and have a low expression in PBL cells.
  • the control cDNAs, CD34, flk2 (fetal liver kinase) and KIT (stem cell factor or alternatively steel factor, or c-Kit ligand) are known to be preferentially expressed in HSC and this is confirmed using transcript imaging.
  • cDNA inserts are subcloned from pBS and into an MSCV based retroviral vector (Hawley et al., Gene Therapy, 1 :136 - 138 (1994).
  • the cDNA inserts are subcloned into vector MIE. (See Figure 1).
  • MIE is constructed from MINGFR (Cheng et al., Blood 92:83-92 (1998) by removing the nerve growth factor receptor (NGFR) gene and replacing it with enhanced green fluorescent protein (EGFP) gene on a 707bp Nco1 - blunted Bsp1 fragment.
  • the NGFR gene is replaced by restriction digestion with Clal, filling in the sticky end and then digestion with Nco1.
  • the EGFP is isolated from pEGFP-1 (Clontech) and has GenBank Accession No. U55761.
  • MIE vector has the essential components LTR-IRES-EGFP.
  • the cDNA inserts are cloned into MIE at the EcoR1 site by PCR of the coding region of either SCM3, SCM26 and SCM113 and cloning to PCR2, removal from PCR2 by EcoR1 digestion and ligation into MIE. This gives gene expression mediated by the LTR and the ribosome entry site (IRES) allows for simultaneous translation of both the gene of interest and EGFP proteins from one primary transcript. Expression of EGFP allows selection of transduced cells by FACS.
  • the SCM3 cDNA fragment containing the entire coding region of SEQ ID NO. 3 is amplified by PCR and the 3' primer included an in fame hemaglutining (HA) tag (5' TAC CCC TAC GAC GTG CCC GAC TAC GCC - SEQ ID NO. 7) followed by a stop codon, is subcloned into the MIE vector at the EcoR1 site. Additionally 3' and 5' truncations of the SCM 3 gene are made.
  • the 5' fragment lacks the DNA binding region.
  • the fragment is illustrated in Figure 2 from nucleotide residue 81 to nucleotide residue 783.
  • the 3' fragment is the zinc finger domain from nucleotide residue 784 to nucleotide residue 1710.
  • Vectors including the 5' and 3' fragments are constructed as described above for the full length SCM 3 except that for the 3' fragment the 5' PCR primer included an in frame ATG start codon.
  • the HA tag and anti-HA antibodies are used to follow protein expression by western blots.
  • the SCM 26 cDNA fragment containing the entire coding region of SEQ ID NO.1 is cloned out of pBS by digestion with Sma1 and Xhol .
  • MIE is digested with EcoR1 , the sticky ends filled in, and then digested with Xhol .
  • the SCM26 fragment is ligated into the blunt/Xhol cut MIE.
  • the SCM 113 cDNA fragment containing the entire coding region of SEQ ID NO. 5. is cloned into MIE as described above for SCM3.
  • the retrovirus is produced by transfecting retroviral vector into the RV packaging cell line phoenix (Kinsella et al., Human Gene Therapy, 7(12):1405-1413, 1996) obtained from Nolan Laboratories using standard transfection protocols (Promega). Viral supernatant is collected after 48 hours.
  • leukaphersis samples are obtained from normal adult donors mobilized with 7.5 or 10.0 ⁇ g/kg/day of granulocycte-colony stimulating factor (G-CSF) for 5 - 6 days.
  • CD34 + cells are enriched from leukaphersis samples at SyStemix (Palo Alto, CA) using Isolex 300SA or 300I (Baxter Healthcare Corp., Deerfield III.) as described in Young et al., Blood, 88:1619 -1631 , (1996), and by methods well-known in the art.
  • the CD34 + cells are cultured at 2x10 6 cells per ml in 10mL cultures in serum free ex-vivo 15 medium (BioWhittaker, Walkerville, MD) for 48 hours at 37°C and 5% CO 2 .
  • the cultures are supplemented with TPO, 100 ng/mL (R & D Systems, Minneapolis, MN); SCF, 100 ng/mL (SyStemix, Palo Alto CA); Flt3-L, 100 ng/mL (SyStemix, Palo Alto CA); and IL-6, 20 ng/mL as described in Luens et al., Blood, 91(4):1206 - 1215 (1998).
  • the cells are centrifuged for 5 minutes at 4000 rpm at 37 °C and resuspended in the same medium described directly above.
  • the cells are added to fibronectin fragment CH-296 (FN) (BioWhittaker, Walkerville, MD) coated plates (10 ⁇ g/mL) containing an equal volume of retroviral supernatant for 20 hour culture at 37°C in 5% CO 2 without polybrene or protamine sulphate. (Hanenburg et al., Human Gene Therapy, 8:2193 - 2206, 1997).
  • Cells are stained with anti-CD34-APC MoAb or isotype control. (Becton Dickinson).
  • the staining buffer is HBSS/2% fetal calf serum (FCS) and 10 mmol/L HEPES for 20 minutes on ice together with anti-Thy-1 (GM201 ) PE-conjugated MoAb at 5 ⁇ g/mL.
  • FCS fetal calf serum
  • GM201 anti-Thy-1
  • Cells are washed twice in SB and then resuspended in SB with propidium iodide (10 ⁇ g/mL.
  • Cells are sorted on the FACSTAR Plus cell sorter (Becton Dickinson, San Jose, CA). EGFP fluorescence is detected in the FITC channel.
  • CD34 + and CD34 ' regions as well as Thy-1 + and Thy-1 " are set using the isotype controls.
  • Cell populations from the EGFP + region are selected after removal of cells of high propidium iodide uptake and electronically gating on CD34 + cells (or Thy-1 + subset of CD34 + cells). Reanalysis of the sorted cells indicates a purity greater than 90% for EGFP CD34 + , and ranging from 60% to 95% for Thy-1 + after sorting for EGFP + Thy- 1 + cells.
  • cells are counted using a hemocytometer and 40,000 or 60,000 cells are incubated in ex-vivo media with TPO (100 ng/mL), SCF (100 ng/mL), FL (100 ng/mL), IL-6 (20 ng/mL) at a cell concentration of 0.2 x 10 6 /mL.
  • TPO 100 ng/mL
  • SCF 100 ng/mL
  • FL 100 ng/mL
  • IL-6 (20 ng/mL
  • SCM 3 has a positive effect on cell expansion after 2 weeks of culture. While overexpression of SCM 3 has little effect during the first 7 days of culture, by 14 days, cultures of SCM 3 expressing cells show enhanced viability and proliferation. This effect continues for 2 months. SCM 3 expressing cells continue to grow while control cells stopped proliferation ( Figure 7). After 6 weeks of liquid culture, the number of clonogenic cells (CFU- C) is determined (See Example 6). Cells overexpressing SCM3 are 20 fold enriched in CFU- C frequency in comparison with control cells.
  • CFU-C clonogenic cells
  • CFU-C assays use MethoCult H4230 methylcellulose (Stem Cell Technologoies Inc., Vancouver, Canada V5Z4J7) supplemented with IL-3 (1 Ong/mL); IL-6 (1 Ong/mL); SCF (100ng/mL); and EPO (2U/mL). Sorted cells are plated in 35mm dishes, in triplicate at 500 cells/dish. Colonies ( >50 cells) are counted 14 days after plating and an average from 3 dishes are taken for each experimental condition. The colonies are classified as CFU-M (myeloid like), CFU-E (erythoid like), or CFU-Mix (mixed).
  • SCM 113 results in 40% decrease in the total CFU-C, significantly for both erythroid and myeloid lineages.
  • Overexpression of SCM 26 results in a 25% decrease in the total number of CFU-C.
  • Overexpression of SCM 26 also results in a decrease in number of single lineage colonies: 30% decrease in erythroid colonies, 2-fold decrease in myeloid colonies.
  • SCM 26 overexpression gives 2-fold increase in the number of mixed type colonies in CFU-C assays (difference significant). Data not shown.
  • Example 7 Replatin ⁇ of CFUC to secondary colonies
  • cells from methylcellulose are harvested and plated into secondary cultures with IL-3 (1 Ong/mL); IL-6 (1 Ong/mL); SCF (100ng/mL); and EPO (2U/mL).
  • IL-3 1 Ong/mL
  • IL-6 1 Ong/mL
  • SCF 100ng/mL
  • EPO 2U/mL
  • cells are harvested from methylcellulose by washing dishes 2x with Phosphate Buffered Saline (Dubecco), and replated at 10000 cells /dish into methylcellulose culture, as described above.
  • Overexpression of SCM3 increases the number of secondary colonies 4.7 fold compared to control cells. Similar results are seen with SCM 26 and SCM 113. Expression of SCM 113 increases the number of secondary colonies after replating 4.6 fold. Overexpression of SCM 26 increased replating efficiency, on average by 4.5 fold.
  • Example 8 Phenotvpic analysis of cells after methylcellulose or liquid culture
  • SCM 3 gene results in inhibition of myeloid differentiation of hematopoietic progenitor cells (Table 2).
  • overexpression of SCM 3 results in a 2-fold decrease in percentage and absolute number of cells expressing myeloid markers (CD14, Table 2 and CD13, data not shown). This is observed after 2 or 3 weeks culturing in methylcellulose in the presence of GM-CSF, IL-6, IL-3, SCF, EPO or in liquid culture in the presence of TPO, Flt3, CSF, IL-6 (difference significant).
  • the absolute level of expression (mean of fluorescence) is also decreased (data not shown). Similar results are seen for SCM26 and SCM113. Table 2 CD14 expression following culture.
  • Table 2 shows data on CD14 + expression on cells with overexpression of SCM3, SCM113, SCM26 and amino acid residues 240 - 543 of SCM3. The fold reduction in CD14 expression level is shown relative to cells transduced with control MIE vector alone.
  • Transduced cells as described above are injected into irradiated SCID-hu mice.
  • the SCID bone assay is preformed as described by Murray et al., Blood, 85:368, 1995.
  • C.B.-17 scid/scid mice are used as recipients of human fetal bone grafts.
  • Limiting dilution analysis is performed to determine the dose SCM3, SCM26 or SCM113 expressing cells or control cells that will give donor reconstitution in the SCID-hu bone model.
  • Fetal bone grafts are injected with cell doses of 5,000, 10,000, and 30,000 cells per graft into mice that receive whole body irradiation (350 rads) shortly before cell injection. Cells are not sorted for EGFP expression.
  • the bone grafts are recovered, and the bone marrow cells are harvested and analyzed for donor cell engraftment using EGFP fluorescence and by methods well known in the art.
  • Example 10 Production of SCM Antibodies.
  • a polyclonal antibody to a SCM 26 fragment corresponding to amino acid residues 25 - 82 of SEQ ID No. 2. is generated and used to immunize rabbits by methods well known in the art. (Antibodies: A Laboratory Manual, Harlow et al. eds., (1987).

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