EP2795332A2 - Séquences de marqueurs du cancer du sein et utilisation desdites séquences de marqueurs du cancer du sein - Google Patents

Séquences de marqueurs du cancer du sein et utilisation desdites séquences de marqueurs du cancer du sein

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Publication number
EP2795332A2
EP2795332A2 EP12818894.3A EP12818894A EP2795332A2 EP 2795332 A2 EP2795332 A2 EP 2795332A2 EP 12818894 A EP12818894 A EP 12818894A EP 2795332 A2 EP2795332 A2 EP 2795332A2
Authority
EP
European Patent Office
Prior art keywords
homo sapiens
breast cancer
protein
sequences
isoform
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.)
Withdrawn
Application number
EP12818894.3A
Other languages
German (de)
English (en)
Inventor
Angelika LÜKING
Axel Kowald
Annabel HÖPNER
Christian Scheer
Heidelinde Fiegl
Günter Daxenbichler
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Protagen GmbH
Original Assignee
Protagen GmbH
Priority date (The priority date 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 date listed.)
Filing date
Publication date
Application filed by Protagen GmbH filed Critical Protagen GmbH
Priority to EP12818894.3A priority Critical patent/EP2795332A2/fr
Publication of EP2795332A2 publication Critical patent/EP2795332A2/fr
Withdrawn legal-status Critical Current

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Classifications

    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/575—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57515—Immunoassay; Biospecific binding assay; Materials therefor for cancer of the breast
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00—Screening for compounds of potential therapeutic value
    • G01N2500/04—Screening involving studying the effect of compounds C directly on molecule A (e.g. C are potential ligands for a receptor A, or potential substrates for an enzyme A)
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00—Screening for compounds of potential therapeutic value
    • G01N2500/20—Screening for compounds of potential therapeutic value cell-free systems
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/56—Staging of a disease; Further complications associated with the disease

Definitions

  • the present invention relates to a method for
  • marker sequences for breast cancer Identification of marker sequences for breast cancer, the marker sequences identified by this method and their diagnostic use, diagnostic devices containing marker sequences for breast cancer, in particular an assembly and a protein array and their use.
  • the invention relates to methods for screening potential drugs for the treatment and prevention of breast cancer by means of these marker sequences.
  • Protein arrays are gaining increasing industrial importance in analytics and diagnostics as well as in pharmaceutical development. Protein arrays have become established as screening tools.
  • Protein arrays make it necessary to have the required proteins available.
  • protein expression libraries have been established for this purpose. High throughput z cloning of defined open reading frames is one
  • GATEWAY recombinational cloning application to the cloning of large numbers of open reading frames or ORFeems. Methods Enzymol, 328, 575-592).
  • ORFeems open reading frames
  • Methods Enzymol, 328, 575-592 are strongly related to the progress of the genome sequencing proce- dures and the annotation of these gene sequences.
  • determination of the expressed sequence is due
  • the cDNA of a particular tissue in a bacterial or a eukaryotic expression vector, such as yeast, is cloned.
  • the vectors used for the expression are generally characterized by the fact that they carry inducible promoters, with which the timing of protein expression can be controlled.
  • expression vectors have sequences for so-called
  • Affinity epitopes or proteins on the one hand for the specific detection of the recombinant fusion proteins by means of a directed against the affinity epitope
  • Antibody on the other hand becomes the specific one
  • antibody-presenting arrays are also described (Lal et al (2002) Antibody arrays: An embryonic but growing technology, DDT, 7, 143-149, Kusnezow et al., (2003) Antibody microarrays: An evaluation of production parameters, Proteomics, 3, 254-264).
  • Breast cancer is the most common malignant tumor of the human mammary gland. He occurs mainly in women; Only about one hundred of these cancers occur in men. Breast cancer is the most common cancer in women in the Western world and more women die from breast cancer than from another cancer. Most diseases occur sporadically (by chance), but there are both inherited and acquired risk factors. Numerous national and international programs for early detection and structured treatment aim to reduce mortality.
  • breast cancer early diagnosis is crucial for the further course of disease and prognosis. Although many tumor markers are associated with breast cancer, they are not suitable for early diagnosis because of their low specificity. They are mainly used to monitor disease progression or response to therapy.
  • US 2003/198972 Al discloses the identification and use of gene expression patterns associated with various stages of breast cancer.
  • the expression patterns are analyzed by comparative analysis of gene expression in healthy individuals or patients with benign changes and breast cancer
  • Microarrays which are equipped with polynucleotides, brought into contact. The intensity pattern is analyzed and allows assignment to different stages of breast cancer.
  • US 2012/021887 discloses the use of arrays and protein microarrays with marker sequences for breast cancer for the detection of breast cancer-specific autoantibodies. But there is still a need for
  • the invention relates to a method for identifying marker sequences for breast cancer, characterized in that a. Marker sequence candidates for breast cancer by
  • identifying a carrier on which at least 1,000 different proteins are immobilized being contacted with a serum sample from a breast cancer patient and identifying proteins that interact with the serum (marker sequence candidates), and b. the interaction of one or more marker sequence candidates from a. with the serum of patients with
  • Breast cancer is determined as compared to the interaction of the marker sequence candidate from a. with the serum of patients with benign alterations and the interaction of the marker sequence candidate from a. with serum from healthy controls, and c. Marker sequences are identified by being different with the serum from breast cancer patients
  • Control persons on the support according to a. simultaneously at least 5,000, preferably at least 10,000 different proteins immobilized simultaneously.
  • marker sequences for breast cancer are identified which are specific for breast cancer with a high risk of metastasis.
  • Marker sequences are identified for breast cancer that are highly specific. Marker sequences that are found with this method, on the one hand enable the early
  • breast cancer e.g. of its precursors and on the other hand, the distinction of breast cancer or its
  • marker sequences for breast cancer can be identified with the method according to the invention, which already at an early stage make it possible to predict the course and / or the risk of metastasis formation. Predicting the risk of metastasis also allows for improved therapy and targeted patient monitoring
  • the marker sequences of the invention are useful for the analysis of body fluids, e.g. Serum particularly suitable. This is a fast and easy way
  • the invention also relates to the
  • the invention provides marker sequences for breast cancer obtainable by an inventive
  • the invention also provides an arrangement comprising one or more marker sequences according to the invention.
  • the invention also provides a protein array comprising one or more marker sequences according to the invention.
  • the invention also provides a diagnostic agent comprising one or more marker sequences according to the invention and optionally further additives and / or auxiliaries.
  • the invention also provides a test kit comprising one or more marker sequences according to the invention and
  • the invention is also an inventive
  • the invention also provides an inventive
  • the subject of the invention is also a diagnostic agent according to the invention, characterized in that 2 or 3,
  • the invention also provides a test kit according to the invention characterized in that 2 or 3, preferably 4 or 5, more preferably 7 or 8 or more different
  • the invention also provides the use of one or more marker sequences according to the invention, one
  • Protein arrays a diagnostic agent according to the invention or a test kit according to the invention for early detection, diagnosis, prognosis, therapy control and / or aftercare in breast cancer.
  • the invention also provides the use of one or more marker sequences according to the invention, one
  • Protein arrays Protein arrays, a diagnostic agent according to the invention or a test kit according to the invention for distinguishing
  • the invention also provides the use of one or more marker sequences according to the invention, one
  • Protein arrays Protein arrays, a diagnostic agent of the invention or a test kit according to the invention for individualized
  • Patient groups cohorts, populations, breast cancer variants, stages of breast cancer.
  • the invention also provides the use of one or more marker sequences according to the invention, one A device according to the invention, a protein array according to the invention, a diagnostic agent of the invention or a test kit according to the invention for detecting and / or determining the amount of one or more autoantibodies associated with breast cancer, for example in
  • Body fluids such as serum, tissue or tissue extracts of the patient.
  • the invention also provides the use of one or more marker sequences according to the invention, one
  • Protein arrays Protein arrays, a diagnostic agent of the invention or a test kit according to the invention for the analysis of
  • Autoantibodies and / or for monitoring changes in autoantibody profiles for example in body fluids such as serum, tissue or tissue extracts of the patient.
  • the invention also provides the use of one or more marker sequences according to the invention, one
  • Protein arrays a diagnostic agent of the invention or a test kit according to the invention for the screening of substances (drugs) for breast cancer.
  • the invention also provides a target for the treatment and / or therapy of breast cancer, wherein the target of the marker sequences of the invention SEQ ID No. 1-1473 and
  • Protein sequences and sequences encoded by SEQ ID no. 1 - 491, partial sequences thereof and their homologues are selected.
  • the invention also provides a method for
  • one or more marker sequence (s) selected from the group comprising the sequences SEQ ID NO. 1 - 1473 and
  • Protein sequences and sequences encoded by SEQ ID no. 1 - 491, partial sequences thereof and their homologues are applied to a carrier,
  • the breast cancer-specific marker sequences SEQ ID No. 1 - 491 has been described here for the first time. All of these sequences have in common that they have been identified by means of a protein array and the method described in the examples. The invention therefore relates in particular breast cancer-specific markers ⁇ sequence selected from the sequences
  • SEQ ID no. 1-491 comprising SEQ ID no. 1-491 and partial sequences of SEQ ID No. 1-491 with at least 90%, preferably 95% of the length of the sequences SEQ ID NO. 1-491 and homologs of SEQ ID No. 1-
  • the invention thus provides marker sequences and arrangements of marker sequences for breast cancer which can be used as part of individualized diagnostics and therapy, for example in the case of different patients, patient groups, cohorts, population groups,
  • breast cancer variants targeted and customized to diagnose breast cancer and to monitor the therapy.
  • Marker sequence (s) is / are selected from the sequences SEQ ID NO. 1 - 1473 and partial sequences of SEQ ID No. 1-1473 with at least 90%, preferably at least 95% of the length of SEQ ID NO. 1 - 1473 and homologs of SEQ ID No. 1 - 1473 and their partial sequences with an identity of at least 95%, preferably at least 98% or more, to the corresponding ones Sequences and proteins / peptides encoded by the sequences SEQ ID no. 1 - 491, encoded by their partial sequences and homologues for breast cancer diagnosis and therapy, in particular for the early detection of breast cancer, for the diagnosis of breast cancer, for the prognosis, for example of the risk of
  • the invention also relates to the detection and determination of the amount of at least two different autoantibodies in a patient, correspondingly at least two
  • the invention is also an inventive
  • SEQ ID no. 1 to 1473 is / are selected from group SEQ ID no. 1 to 1473 and partial sequences of SEQ ID No. 1-1473 with at least 90%, preferably at least 95% of the length of SEQ ID NO. 1 - 1473 and
  • the invention is also an inventive
  • breast cancer-specific marker sequence wherein at least 2, for example 3 to 5 or 10, preferably 30 to 50 or 50 to 100 or more breast cancer-specific
  • Marker sequences are determined on or to a patient to be examined.
  • the invention is also an inventive
  • breast cancer specific marker sequence (s) are / are applied to a solid support, in particular a filter, membrane, bead or small platelet or bead, for example a magnetic or
  • Fluorophore-labeled beads a silicon wafer, glass, metal, plastic, a chip, a mass spectrometric target or a matrix.
  • a particular embodiment relates to the use of a filter as a solid support.
  • a filter As a filter, PVDF, nitrocellulose or nylon is further preferred (e.g., Immobilon P
  • Breast cancer specific marker sequence present as clone (s). Therefore, the invention relates to the use of breast cancer-specific marker sequences for the diagnosis of
  • Breast cancer being at least one breast cancer-specific
  • Marker sequence of a DNA, in particular cDNA selected from the group SEQ ID No. 1-491 or RNA selected from the group 492-982 or a partial sequence or a fragment or a homologous sequence thereof is determined on or to a patient to be examined.
  • breast cancer-specific marker sequences also called marker sequences according to the invention
  • the breast cancer-specific marker sequences according to the invention were able to be detected by differential screening of samples, namely healthy subjects, with patient samples containing breast cancer
  • these marker sequences according to the invention could be detected for the first time by means of protein arrays (see
  • the invention also provides a method for
  • Identification of marker sequences for breast cancer comprising the steps of a) providing sequences on an array, b) identifying marker sequence candidates for
  • breast cancer-specific marker sequences include a group of diseases that may be precursors to breast cancer and their establishment as breast cancer, breast cancer (as defined, for example, in US Pat
  • the marker sequences according to the invention can also be combined, supplemented or extended with known biomarkers for this indication. However, at least 50%,
  • Protein array the diagnostic agent according to the invention or the test kit according to the invention.
  • test kit the test kit according to the invention.
  • the arrangement according to the invention, the assay and protein array according to the invention and the use according to the invention represent at least 75%, preferably 80% or 85%, particularly preferably 90% or 95% of marker sequences according to the invention.
  • the determination of the breast cancer-specific marker sequences takes place outside the human body and the determination takes place in an ex vivo / in vitro diagnosis.
  • the invention also relates to an assay or protein array comprising an arrangement / use according to the invention.
  • the invention relates to a diagnostic device and / or an assay, in particular a protein array for
  • the invention also relates to the use of a
  • inventive arrangement or an assay or protein array according to the invention for the analysis of Autoantibody profiles of patients, in particular for
  • the invention also provides a diagnostic (test kit) for the early detection and / or diagnosis of breast cancer and / or
  • Prognosis and / or prediction of the risk of metastasis formation in breast cancer comprising an arrangement according to the invention, preferably on a carrier or an assay or protein array according to the invention and, if appropriate, further additives and auxiliaries.
  • the invention also provides a diagnostic (test kit) for monitoring therapy and / or aftercare in breast cancer comprising an arrangement according to the invention or a
  • inventive assay or protein array and optionally other additives and excipients.
  • the invention relates to the use of breast cancer-specific
  • Marker sequence of a cDNA selected from the group SEQ ID No. 1-491 (clone sequences) or SEQ ID No. 492-982 (RNA) or one each by SEQ ID No. 1-982 is a coded protein or each a partial sequence or fragment thereof.
  • the invention also provides a method for
  • one or more breast cancer-specific marker sequences selected from the group of the sequences SEQ ID NO. 1 - 1473 and partial sequences of SEQ ID No. 1-1473 with at least 90%, preferably at least 95% of the length of SEQ ID NO. 1 - 1473 and homologues of SEQ ID no. 1 - 1473 and their partial sequences with an identity of at least 95%, preferably at least 98% or more of the corresponding sequences and proteins / peptides encoded by the sequences SEQ ID NO. 1-491, encoded by their partial sequences and homologues are applied to a support and
  • One or more breast cancer specific marker sequences are used in a method of diagnosis and / or in a diagnostic and / or a test kit.
  • Marker sequences used together or in combination, for example, directly in series or in parallel.
  • a particular embodiment of the invention relates to the method, wherein stratification or therapy control Decisions for treatment and therapy of the patient, in particular hospitalization of the patient, use, effect and / or dosage of one or more drugs, a therapeutic measure or the monitoring of a patient
  • Classification of a disease including prognosis includes. Furthermore, the invention relates to a method for stratifying, in particular for risk stratification and / or
  • therapy control also includes the classification of patients into responders and non-responders with regard to a therapy or its course of therapy.
  • Diagnosis in the sense of this invention means the positive detection of breast cancer by means of the breast cancer-specific marker sequences according to the invention and the assignment of the patients to breast cancer.
  • diagnosis includes medical diagnosis and investigations in this regard, in particular in vitro diagnostics and laboratory diagnostics Proteomics and nucleic acid blots
  • diagnosis also includes the differential diagnosis of breast cancer by means of the breast cancer-specific invention
  • Stratification also: stratification or therapy control
  • stratification means that, for example, the methods according to the invention allow decisions for the treatment and therapy of the patient, be it hospitalization of the patient, use, effect and / or dosage of one or more drugs, a therapeutic one Measure or the monitoring of a course of disease as well as course of therapy or etiology or classification of a disease, eg in a new or existing subtype or the differentiation of diseases and their patients.
  • the term "stratification" includes in particular the
  • Prognosis means the prediction of disease progression, for example the prediction of recurrence-free survival, overall survival, the risk of metastasis formation.
  • patient is understood to mean any test person - human or mammal - with the proviso that the subject is examined for breast cancer.
  • breast cancer-specific marker sequence in the sense of this invention means that the nucleic acid, for example DNA, in particular cDNA or RNA or the encoded amino acid sequence or the respective polypeptide or protein obtainable therefrom is significantly (specifically) for
  • Breast cancer-specific marker sequences may be nucleic acid sequences and amino acid sequences, including modifications.
  • Breast cancer-specific and “for breast cancer” means that, for example, the cDNA or the respectively obtainable polypeptide or protein interact with substances from the body fluid or tissue extract of a patient with breast cancer (eg antigen (epitope) / antibody
  • Body fluid or tissue excision occur either only or at least increased in breast cancer or are expressed, whereas these substances are not present in patients without breast cancer, or at least to a lesser extent (smaller amount, lower concentration).
  • ⁇ breast cancer-specific marker sequences may also be characterized on the other hand that they interact with
  • Breast cancer-specific marker sequences may also be present in healthy volunteers, but their amount (concentration) changes, for example, in the development, establishment and therapy of breast cancer.
  • the breast cancer-specific marker sequences are therefore biomarkers for breast cancer.
  • the breast cancer ⁇ specific marker sequences can in this way a profile of substances from body fluid and tissue extract
  • Autoantibody profile includes the amount of one or more
  • Breast cancer-associated autoantibody profiles thus include on the one hand the composition (one or more
  • the breast cancer-specific marker sequence is an antigen or a part of an antigen or encodes an antigen or a part of an antigen.
  • the breast cancer-specific marker sequence recognizes / binds to autoantibodies present (enhanced), or to a lesser extent (or no longer), in the course of genesis, establishment and therapy of breast cancer (hereinafter "breast cancer-associated autoantibodies Autoantibodies are formed by the body against the body's own antigens, which are produced, for example, in breast cancer.Autoantibodies are formed by the body against different substances and pathogens. [Vor Treatment Im] In the context of the present invention, in particular the breast cancer-associated autoantibodies which are detected on the occurrence and in the course of time the formation of breast cancer are formed
  • Breast cancer-associated autoantibodies can be detected using the methods of the invention and
  • Breast cancer-specific marker sequences are detected and thus serve as an indication for breast cancer.
  • the detection and monitoring of the amount of breast cancer-associated marker sequences are detected and thus serve as an indication for breast cancer.
  • Autoantibodies in the patient can be used for early detection, diagnosis and / or therapy monitoring / therapy control and for
  • breast cancer-associated autoantibody profile In other cases, two or more breast cancer-specific marker sequences will be necessary to map a breast cancer-associated autoantibody profile.
  • the breast cancer-associated autoantibodies can be detected with breast cancer specific marker sequences derived from another individual, for example, from a commercial cDNA library.
  • Embodiments of the invention relate to the breast cancer-associated marker sequences SEQ ID No. 1-491, SEQ ID. No. 492-982 and / or partial sequences of SEQ ID No. 1 - 982, and sequences coding for the proteins SEQ ID No. 983 to 1473 and / or partial sequences of these proteins.
  • the breast cancer-associated autoantibodies can be detected with breast cancer specific marker sequences derived from the same individual (autoantigen), for example, from a patient specific or a group of patients (e.g.
  • Autoantibodies can be formed by the patient many years before the onset of the first disease symptoms. This would be an early detection, diagnosis and also prognosis and
  • the invention Devices and means (array, array, protein array, diagnostic, test kit) and methods thus allow very early intervention compared to known methods, which significantly improves prognosis and survival rates.
  • the invention also makes it possible to detect and monitor breast cancer at any stage of its development and treatment, as well as under surveillance
  • the agents of the invention also allow for easy home handling by the patient and cost-effective routine screening for early detection.
  • Each patient may have one or more different autoantibodies associated with breast cancer in the course of breast cancer and the progression of breast cancer
  • composition and / or the amount of breast cancer-specific autoantibodies formed in the course of breast cancer development and progression of the disease change so that a quantitative evaluation is necessary.
  • Therapy / treatment of breast cancer leads to changes in the composition and / or amount of breast cancer-associated autoantibodies.
  • breast cancer-specific marker sequences according to the invention enable the individual compilation of breast cancer-specific marker sequences in an arrangement for individual patients, groups of patients, specific cohorts,
  • breast cancer-associated autoantibodies can be detected using the corresponding antigens / autoantigens in
  • Such an interaction is for example a bond, in particular a binding substance at least one breast cancer specific marker sequence or in case the breast cancer specific marker sequence has one
  • Nucleic acid for example a cDNA
  • a suitable substance under chosen conditions, in particular stringent conditions (for example as usual
  • Hybridization conditions is hybridization in 4 x SSC at 37 ° C followed by several washing steps in 1 x SSC
  • Tissue extraction of a patient and the breast cancer specific marker sequences is preferably a protein-protein
  • Such substances for example antigens, autoantigens, breast cancer-associated autoantibodies, are part of a body fluid, in particular blood, according to the invention.
  • Cerebrospinal fluid, synovial fluid or a tissue extract for example from tumor tissue of the patient.
  • the invention relates to the use of these body fluids and tissue extracts for early detection, diagnosis, prognosis, therapy control and aftercare.
  • the breast cancer-specific marker sequences or the substances recognized by these marker sequences for example breast cancer-associated autoantibodies, may be present at a significantly higher or lower expression rate or concentration, which indicates breast cancer.
  • proteomics or nucleic acid blots the relative
  • Marker sequences detected substances determined.
  • the protein is preferred for a protein
  • RNA breast cancer-specific marker sequences according to the invention are the subject of Table A (RNA) and can be clearly identified by the respectively cited database entry (also by means of the Internet: http://www.ncbi.nlm.nih.gov/) (by means of accession no.). , see also the corresponding
  • the invention also encompasses the full-length sequences of the breast cancer-specific marker sequences according to the invention, namely as defined by the known database entry according to Table A, SEQ ID NO. 1 - 1473 called. Furthermore, therefore, also include analog
  • SEQ 1 -1473 again represent partial sequences, at least with high homology.
  • the breast cancer-specific marker sequences SEQ 1-1473 are preferred according to the invention.
  • the marker sequences also include such
  • nucleic acid sequence in particular cDNA sequence and the corresponding amino acid sequence, such as
  • the invention also relates to homologs of breast cancer-specific marker sequences and partial sequences, for example fragments of breast cancer-specific marker sequences.
  • Homologs are, for example, nucleic acid and / or nucleic acid
  • Protein sequences for example homologs of SEQ ID no. 1 - 1473, in particular homologs of SEQ ID No. 1-491 and SEQ ID No. 492-982 having an identity with the breast cancer ⁇ specific marker sequences of at least 70% or 80%, preferably 90% or 95%, more preferably 96% or 97% or more, for example 98% or 99%.
  • the homology in the event that the breast cancer-specific marker sequences are antigens the homology in the event that the breast cancer-specific marker sequences are antigens, the homology in the event that the breast cancer-specific marker sequences are antigens, the homology in the event that the breast cancer-specific marker sequences are antigens, the homology in the event that the breast cancer-specific marker sequences are antigens, the homology in
  • Sequence area in which the antigen-antibody or antigen-autoantibody interaction takes place at least 95%, preferably at least 97%, particularly preferably at least 99%.
  • Mutations such as base-exchange mutations, raster mutations, base insertion mutations, base-loss mutations,
  • the invention also subsequences of
  • fragments of the marker sequences according to the invention are those nucleic acids or proteins / peptides which are opposite to the complete nucleic acid or the
  • the deletion may be at or near the end and / or within the sequence.
  • partial sequences and / or fragments comprising 50 to 100 nucleotides, 70-120 nucleotides of a complete sequence, for example of SEQ ID 1473, are included. Homologs of partial sequences and fragments are also included according to the invention.
  • the breast cancer-specific marker sequences compared to the sequences 1-1473 are shortened so that they consist only of the / the binding sites for the relevant breast cancer associated autoantibodies.
  • Breast cancer-specific marker sequences which differ from the sequences SEQ ID no. 1 - 1473 in that they contain one or more insertions, the
  • Insertions for example, 1 to 100 or more
  • Nucleotides / amino acids preferably 5 to 50, more preferably 10 to 20 nucleotides / amino acids in length and the sequences otherwise identical or homologous to the
  • Sequences 1 - 1473 are. Particularly preferred
  • Partial sequences which are at least 90%, preferably at least 95%, particularly preferably at least 97% or 98%, of the length of the breast cancer-specific marker sequences according to the invention, SEQ ID no. 1 -491, SEQ ID. No. 492-982, SEQ ID No. 983 - 1473 exhibit. Also included according to the invention are homologs of the partial sequences.
  • Breast cancer-specific marker sequence may be represented in varying amounts in one or more regions in the array or on the carrier. This allows a variation of the sensitivity.
  • the regions may each comprise a total of breast cancer-specific marker sequences, i. a sufficient number of different breast cancer-specific marker sequences, in particular 2, 3, 4, 5, 6, 7, 8, 9 or 10 or more different and optionally further
  • Nucleic acids and / or proteins in particular biomarkers.
  • Marker sequences and optionally further nucleic acids and / or proteins in particular biomarkers represented on the carrier. Also preferred are more than 2,500, more preferably 10,000 or more different or identical breast cancer-specific marker sequences and optionally further nucleic acids and / or proteins, in particular
  • Biomarker on the carrier represents.
  • the arrangement is such
  • breast cancer-specific marker sequences represented on the array in the form of a grid on present to a carrier are designed that the breast cancer-specific marker sequences represented on the array in the form of a grid on present to a carrier. Further, such arrangements
  • the breast cancer-specific marker sequences are spotted.
  • Such high density spotted assemblies are disclosed, for example, in WO 99/57311 and WO 99/57312, and may be advantageously used in a robotic automated high throughput method.
  • the term "assay" or diagnostic device also includes such
  • Embodiments of a device such as ELISA, bead-based assay, line assay, Western blot, immunochromatographic
  • Methods e.g., so-called lateral flow immunoassays or similar immunological single or multiplex detection methods.
  • a "protein array” in the sense of this invention is the
  • Solid support carrier sequences wherein the breast cancer specific marker sequences are proteins or peptides or portions thereof and wherein the carrier may be of any shape and / or size and wherein the carrier is preferably a solid carrier.
  • the breast cancer specific marker sequences of the assembly are fixed to a support, but preferably spotted or immobilized even printed, i. reproducible
  • One or more breast cancer-specific proliferative hormones are applied.
  • One or more breast cancer-specific proliferative hormones are applied.
  • One or more breast cancer-specific proliferative hormones are applied.
  • breast cancer-specific marker sequences be present and available in different amounts based on a spot. Furthermore, the breast cancer-specific marker sequences may be standardized on the carrier (eg by serial
  • a standard e.g., a gold standard
  • a standard may also be applied to the carrier.
  • the breast cancer specific marker sequences are present as clones.
  • Such clones can be obtained, for example, by means of a cDNA expression library according to the invention (Büssow et al., 1998
  • Expression vectors obtained from an expressing cDNA library consisting of the cDNA marker sequences.
  • Expression vectors preferably contain inducible
  • Promoters Induction of expression may be e.g. by means of an inductor, such as IPTG.
  • an inductor such as IPTG.
  • Expression vectors are described in Terpe et al. (Terpe T Appl Microbiol Biotechnol 2003 Jan; 60 (5): 523-33).
  • Expression libraries are known to the person skilled in the art, these can be prepared according to standard works, such as Sambrook et al., Molecular Cloning, Laboratory Laboratory, 2nd edition (1989), CSH press, Cold Spring Harbor, New York Further preferred are such expression libraries
  • tissue-specific eg human tissue, in particular human organs, for example from breast tissue or tissue from breast cancer
  • expression libraries are also included according to the invention, which can be obtained by exon trapping. Instead of expression library can be spoken synonymously from an expression bank.
  • protein arrays or corresponding expression libraries which have no redundancy (so-called: Uniclone® library) and can be prepared, for example, according to the teachings of WO 99/57311 and WO 99/57312. These preferred Uniclone libraries have a high content of non-defective, fully expressed proteins of a cDNA expression library.
  • the clones may not be such as transformed bacteria, recombinant phage or transformed cells of mammals, insects, fungi, yeasts or plants.
  • the clones are fixed on a solid support, spotted or immobilized. Therefore, the invention relates to a
  • Marker sequences are present as clones.
  • breast cancer-specific marker sequences may be in the form of a fusion protein
  • the day can be one such as c-myc, His-tag, Arg-tag, FLAG, alkaline
  • Phosphatase V5 tag, T7 tag or strep tag, HAT tag, NusA, S tag, SBP tag, thioredoxin, DsbA, a fusion protein,
  • this invention corresponds to a grid that the order of a microtiter plate (8-12 wells strips, 96 wells, 384 wells or more), one Has silicon wafers, a chip, a mass spectrometric target or a matrix.
  • the invention relates to an assay or protein array for identification and
  • Characterizing a substance for example, hit, conductive substance, candidate, active ingredient for breast cancer, characterized in that an arrangement or assay according to the invention with a. ) is brought into contact with at least one substance to be examined and b. ) a binding success is detected.
  • a substance for example, hit, conductive substance, candidate, active ingredient
  • the substance to be investigated may be any native or non-native biomolecule, a (synthetic) chemical molecule, a natural product, a mixture or a
  • Binding results interactions such as protein-protein interactions (e.g., breast cancer specific protein
  • Marker sequence such as antigen / antibody
  • reporter enzymes such as alkaline phosphatase
  • a readout is e.g. by means of a
  • Microarray laser scanner a CCD camera or visually.
  • the invention relates to a drug / prodrug or prodrug for breast cancer
  • the invention is also the use of a
  • Breast cancer-specific marker sequence selected from sequences SEQ ID No. 1 - 1473 and partial sequences from SEQ ID No. 1-1473 with at least 90%, preferably at least 95% of the length of SEQ ID No. 1 - 1473 and homologs of SEQ ID No. 1 - 1473 and their partial sequences with an identity of at least 95%, preferably at least 98% or more to the
  • the invention thus relates to the use of the marker sequences according to the invention, preferably in the form of an arrangement, as an affinity material for carrying out a
  • Body fluids of a patient with breast cancer such as blood or plasma, bind to the marker sequences according to the invention and consequently can be selectively removed from the body fluid.
  • the examples are performed using the UNIarray technology platform based on quantitative analysis of autoantibody profiles in breast cancer patients' serum. This is intended to systematically breast cancer-associated antigens and breast cancer-associated autoantigens (biomarkers)
  • these candidates will be selected for breast cancer-specific marker sequences on serum samples from 100 breast cancer patients and 100 benign women
  • Example 3 The selection of particularly significant biomarkers (breast cancer-specific marker sequences) is carried out by means of
  • the candidates for breast cancer specific marker sequences are evaluated as discriminating between different subjects (e.g., healthy / unhealthy) / patient groups (e.g., low / high risk of metastasis) / cohorts (e.g., particular history).
  • the marker sequence candidates are applied to a protein array and validated.
  • the data analysis is carried out via statistical analyzes, such as threshold value analysis, Support Vector Machine Alogrithm (SVM).
  • SVM Support Vector Machine Alogrithm
  • the sample consumption for validation is only 50 ⁇ / sample.
  • cohorts of category I and II will be selected in this way.
  • the resulting protein array is specific for breast cancer.
  • This protein array includes one or more breast cancer-specific marker sequences and detects breast cancer-associated
  • Anti-estrogen therapy adjuvant chemotherapy or adjuvant aromatase inhibitor therapy.
  • Corresponding protein arrays are being developed for diagnosis, predicting the course of therapy, and predicting metastasis.
  • results of the autoantibody analysis are compared with the golden standard of diagnosis and the identified marker sequences are validated (breast cancer specific marker sequences, marker sequences for breast cancer). The results will then be compared with other clinical
  • a particular autoantibody profile or signal of the protein array is correlated with the response of breast cancer to a particular therapy.
  • changes in the autoantibody profile are validated, including with regard to various treatment options (continuous-time modeling).
  • Example 6 In the development of a protein array for the prediction of metastasis formation, breast cancer specific
  • Metastasis are suitable. By comparing
  • Bioinformatic analyzes can be performed as part of the identification and validation of breast cancer specific marker sequences. For each serum can do so by means of
  • Antigens are measured. These data are used to rank the spotted antigens for their ability to differentiate between healthy and diseased sera.
  • Evaluation can be performed on normalized intensity data using the non-parametric Mann-Whitney test.
  • an internal standard is used that is spotted on each protein array. Since a p-value is calculated for each antigen, methods for correcting the multiple testing are used. As a very conservative approach a Bonferroni correction is performed and in addition the less restrictive False Discovery Rate (FDR) according to Benjamini & Hochberg is calculated.
  • FDR False Discovery Rate
  • the data are used to classify the sera.
  • different multivariate methods are used. These are methods from the statistical
  • Threshold method which is suitable for both classification and visual representation of the data.
  • the erfindungsgermä call sequences are listed in the attached sequence listing.
  • the clone sequences (cDNA) SEQ ID no. 1-491, the RNA sequences SEQ ID. No. 492-982 and the protein sequences SEQ ID No. 983 - 1473).
  • RNA breast cancer specific marker sequences
  • mitochondrial isoform 2 precursor [Homo sapiens]
  • ID-1 isoform b [Homo sapiens]
  • histone deacetylase 7 isoform a [Homo sapiens]
  • Phosphodiesterase 4 isoform 1 [Homo sapiens]
  • modulator 2 isoform 2 [Homo sapiens] 612 gi 140018634 NM_015440.3 monofunctional C-tetrahydrofolate synthase, mitochondrial isoform 2 precursor [Homo sapiens]
  • RNA-binding protein 14 isoform
  • Chemotaxis regulator precursor [Homo sapiens]
  • mitochondrial isoform Ib precursor [Homo sapiens]
  • GIPC1 isoform 2 [Homo sapiens]
  • adenosylhomocysteinase 2 isoform a [Homo sapiens]
  • subunit 5 isoform b [Homo sapiens]
  • initiation factor 2 subunit 2 [Homo sapiens] 719 gi 1237649014 NM_006824.2 probable rRNA processing
  • RNA-binding protein 10 isoform
  • initiation factor 3 subunit M [Homo sapiens] 732 gi 1197100772 NM_020320.3 probable arginyl tRNA
  • member 39 isoform a [Homo sapiens]
  • beta isoform 1 [Homo sapiens]
  • subfamily D member 3 isoform 1 [Homo sapiens]

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  • Immunology (AREA)
  • Engineering & Computer Science (AREA)
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  • Biomedical Technology (AREA)
  • Chemical & Material Sciences (AREA)
  • Hematology (AREA)
  • Urology & Nephrology (AREA)
  • Biotechnology (AREA)
  • Biochemistry (AREA)
  • Cell Biology (AREA)
  • Food Science & Technology (AREA)
  • Medicinal Chemistry (AREA)
  • Physics & Mathematics (AREA)
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  • Microbiology (AREA)
  • General Health & Medical Sciences (AREA)
  • General Physics & Mathematics (AREA)
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  • Peptides Or Proteins (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)

Abstract

L'invention concerne un procédé servant à identifier des séquences de marqueurs du cancer du sein, les séquences de marqueurs identifiées à l'aide de ce procédé et leur utilisation diagnostique, des dispositifs diagnostiques contenant les séquences marqueurs du cancer du sein, en particulier un système et une puce à protéines ainsi que leur utilisation. L'invention concerne en outre un procédé servant à détecter des principes actifs potentiels afin de traiter et de prévenir le cancer du sein au moyen desdites séquences de marqueurs.
EP12818894.3A 2011-12-22 2012-12-24 Séquences de marqueurs du cancer du sein et utilisation desdites séquences de marqueurs du cancer du sein Withdrawn EP2795332A2 (fr)

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EP12818894.3A EP2795332A2 (fr) 2011-12-22 2012-12-24 Séquences de marqueurs du cancer du sein et utilisation desdites séquences de marqueurs du cancer du sein

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EP11195459.0A EP2607900A1 (fr) 2011-12-22 2011-12-22 Séquences de marqueurs pour cancer du sein et leur utilisation
EP12818894.3A EP2795332A2 (fr) 2011-12-22 2012-12-24 Séquences de marqueurs du cancer du sein et utilisation desdites séquences de marqueurs du cancer du sein
PCT/EP2012/076875 WO2013093115A2 (fr) 2011-12-22 2012-12-24 Séquences de marqueurs du cancer du sein et utilisation desdites séquences de marqueurs du cancer du sein

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Families Citing this family (11)

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WO2015153838A1 (fr) * 2014-04-02 2015-10-08 Rogne Bioscience Inc. Méthodes et compositions pour le traitement de troubles inflammatoires
US10677795B2 (en) * 2014-05-09 2020-06-09 Protagen Ag Marker sequences for the diagnosis and stratification of systemic sclerosis patients
WO2017013214A1 (fr) * 2015-07-23 2017-01-26 INSERM (Institut National de la Santé et de la Recherche Médicale) Procédés pour prédire le temps de survie et la faculté de réponse au traitement d'un patient atteint d'un cancer solide
WO2019099732A1 (fr) * 2017-11-16 2019-05-23 Brainbox Solutions, Inc. Indicateurs de biomarqueurs protéiques de lésions et/ou de maladies neurologiques et leurs procédés d'utilisation
AU2020395327A1 (en) * 2019-12-05 2022-07-21 Cornell University Stabilization of retromer for the treatment of Alzheimer's disease and other neurodegenerative disorders
CN111812325A (zh) * 2020-07-11 2020-10-23 成都益安博生物技术有限公司 一种乳腺癌的外周血tcr标志物及其检测试剂盒和应用
WO2022192697A1 (fr) * 2021-03-11 2022-09-15 The Children's Hospital Of Philadelphia Compositions et méthodes utiles pour le traitement de maladies d'insuffisance médullaire associées à des ribosomopathies
WO2023006348A1 (fr) * 2021-07-02 2023-02-02 Katholieke Universiteit Leuven Protéines symétriques
EP4112632A1 (fr) * 2021-07-02 2023-01-04 Katholieke Universiteit Leuven Protéines symétriques
WO2023230570A2 (fr) * 2022-05-25 2023-11-30 Flagship Pioneering Innovations Vii, Llc Compositions et procédés de modulation de pilotes génétiques
CN121186360B (zh) * 2025-11-25 2026-04-14 长兴固容生物科技有限公司 一种用于乳腺癌筛查、诊断的标志物组及其用途

Family Cites Families (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP1073771B1 (fr) 1998-04-30 2004-12-01 Max-Planck-Gesellschaft Zur Förderung Der Wissenschaften E.V. Nouveau procede permettant la selection de clones dans une banque d'expression et comprenant un rearrangement
ATE282717T1 (de) 1998-04-30 2004-12-15 Max Planck Gesellschaft Neuartiges verfahren zur identifizierung von klonen mit einer gewünschten biologischen eigenschaft, ausgehend von einer expressionsgenbank
US20030198972A1 (en) * 2001-12-21 2003-10-23 Erlander Mark G. Grading of breast cancer
IT1392885B1 (it) 2009-02-13 2012-04-02 Perini Fabio Spa Dispositivo separatore di pacchi di prodotti laminari e macchina impiegante detto dispositivo
WO2012021887A2 (fr) * 2010-08-13 2012-02-16 Arizona Borad Of Regents, A Body Corporate Acting For And On Behalf Of Arizona State University Biomarqueurs pour la détection précoce du cancer du sein

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
See references of WO2013093115A2 *

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US20140371098A1 (en) 2014-12-18
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EP2607900A1 (fr) 2013-06-26

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