CA2307716A1 - Reagents and methods useful for detecting diseases of the breast - Google Patents

Reagents and methods useful for detecting diseases of the breast Download PDF

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Publication number
CA2307716A1
CA2307716A1 CA002307716A CA2307716A CA2307716A1 CA 2307716 A1 CA2307716 A1 CA 2307716A1 CA 002307716 A CA002307716 A CA 002307716A CA 2307716 A CA2307716 A CA 2307716A CA 2307716 A1 CA2307716 A1 CA 2307716A1
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Prior art keywords
sequence
polynucleotide
specific
group
polypeptide
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Abandoned
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CA002307716A
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French (fr)
Inventor
Patricia A. Billing-Medel
Maurice Cohen
Tracey L. Colpitts
Paula N. Friedman
Julian Gordon
Edward N. Granados
Steven C. Hodges
Michael R. Klass
Jon D. Kratochvil
John C. Russell
Stephen D. Stroupe
Hong Yu
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Abbott Laboratories
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Publication of CA2307716A1 publication Critical patent/CA2307716A1/en
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    • 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
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/48—Hydrolases (3) acting on peptide bonds (3.4)
    • C12N9/50—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25)
    • C12N9/64—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from animal tissue
    • C12N9/6421—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from animal tissue from mammals
    • C12N9/6424—Serine endopeptidases (3.4.21)
    • 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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • 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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/136—Screening for pharmacological compounds

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  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Molecular Biology (AREA)
  • Zoology (AREA)
  • Immunology (AREA)
  • Genetics & Genomics (AREA)
  • Wood Science & Technology (AREA)
  • Biomedical Technology (AREA)
  • Biochemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • General Health & Medical Sciences (AREA)
  • Microbiology (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Medicinal Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Pathology (AREA)
  • General Engineering & Computer Science (AREA)
  • Urology & Nephrology (AREA)
  • Biophysics (AREA)
  • Hematology (AREA)
  • Physics & Mathematics (AREA)
  • Oncology (AREA)
  • Food Science & Technology (AREA)
  • Cell Biology (AREA)
  • General Physics & Mathematics (AREA)
  • Hospice & Palliative Care (AREA)
  • Toxicology (AREA)
  • Gastroenterology & Hepatology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

A set of contiguous and partially overlapping cDNA sequences and polypeptides encoded thereby, designated as BS247 and transcribed from breast tissue, are described. These sequences are useful for the detecting, diagnosing, staging, monitoring, prognosticating, in vivo imaging, preventing or treating, or determining the predisposition of an individual to diseases and conditions of the breast, such as breast cancer. Also provided are antibodies which specifically bind to BS247-encoded polypeptide or protein, and agonists or inhibitors which prevent action of the tissue-specific BS247 polypeptides, which molecules are useful for the therapeutic treatment of breast diseases, tumors or metastases.

Description

REAGENTS

Claims (51)

We Claim:
1. A method of detecting the presence of a target BS247 polynucleotide in a test sample, said method comprising:
(a) contacting the test sample with at least one BS247-specific polynucleotide or complement thereof, wherein said BS247-specific polynucleotide has at least 65% identity with a polynucleotide selected from the group consisting of SEQUENCE ID NOS 1-8, and fragments or complements thereof; and (b) detecting the presence of target BS247 polynucleotides from the test sample which bind to said BS247-specific polynucleotide.
2. The method of claim 1, wherein said target BS247 polynucleotide is attached to a solid phase prior to performing step (a).
3. The method of claim 1, wherein said BS247-specific polynucleotide is attached to a solid phase prior to performing step (a).
4. A method for detecting BS247 mRNA in a test sample, said method comprising:
(a) performing reverse transcription on said sample using at least one primer in order to produce cDNA;
(b) amplifying the cDNA obtained from step (a) using oligonucleotides specific to BS247 as sense and antisense primers to obtain BS247 amplicon; and (c) detecting the presence of said BS247 amplicon, wherein the BS247 oligonucleotides utilized in steps (a) and (b) have at least 65% identity with a sequence selected from the group consisting of SEQUENCE ID NOS 1-8, and fragments or complements thereof.
5. The method of claim 4, wherein said test sample is reacted with a solid phase prior to performing one of steps (a), (b), or (c).
6. The method of claim 4, wherein said detection step comprises utilizing a detectable label capable of generating a measurable signal.
7. A method of detecting a target BS247 polynucleotide in a test sample suspected of containing said target polynucleotide, comprising:

(a) contacting the test sample with at least one BS247-specific oligonucleotide as a sense primer and with at least one BS247 oligonucleotide as an anti-sense primer and amplifying to obtain a first stage reaction product;
(b) contacting said first stage reaction product with at least one other BS247-specific oligonucleotide to obtain a second stage reaction product, with the proviso that the other BS247 oligonucleotide is located 3' to the BS247 oligonucleotides utilized in step (a) and is complementary to said first stage reaction product; and (c) detecting said second stage reaction product as an indication of the presence of the target BS247 polynucleotide, wherein the BS247 oligonucleotides utilized in steps (a) and (b) have at least 65% identity with a sequence selected from the group consisting SEQUENCE B7 NOS 1-8, and fragments or complements thereof.
8. The method of claim 7, wherein said test sample is reacted with a solid phase prior to performing one of steps (a), (b), or (c).
9. The method of claim 7, wherein said detection step comprises utilizing a detectable label capable of generating a measurable signal.
10. The method of claim 9, wherein said detectable label is reacted to a solid phase.
11. A test kit useful for detecting BS247 polynucleotide in a test sample, said test kit comprising a container containing at least one BS247 polynucleotide having at least 65% identity with a sequence selected from the group consisting of SEQUENCE ID NOS 1-8, and fragments or complements thereof.
12. A purified polynucleotide derived from a BS247 nucleic acid molecule, wherein said polynucleotide has at least 75% identity with a sequence selected from the group consisting of SEQUENCE ID NO 1, SEQUENCE m NO 2, SEQUENCE ID
NO 3, SEQUENCE ID NO 8, SEQUENCE ID NO 6, SEQUENCE ID NO 7, SEQUENCE ID NO 8, a fragment of SEQUENCE ID NO 4, a fragment of the polynucleotide occurring at positions 1-568 of SEQUENCE ID NO 7 or SEQUENCE
ID NO 8, and complements thereof.
13. The polynucleotide of claim 12, wherein said polynucleotide hybridizes selectively to a BS247 nucleic acid sequence.
14, The polynucleotide of claim 12, wherein said polynucleotide has an overall length of about 20 to about 50 nucleotides.
15. The polynucleotide of claim 12, wherein said polynucleotide has an overall length of about 10 to about 25 nucleotides.
16. The polynucleotide of claim 12, wherein said polynucleotide is produced by recombinant techniques.
17. The polynucleotide of claim 12, wherein said polynucleotide is produced by synthetic techniques.
18. The polynucleotide of claim 12, wherein said polynucleotide comprises a sequence encoding at least one BS247 epitope.
19. The polynucleotide of claim 12, wherein said polynucleotide is attached to a solid phase.
20. The polynucleotide of claim 19, wherein said solid phase comprises an array of polynucleotide molecules attached thereto.
21. A recombinant expression system comprising a nucleic acid sequence that includes an open reading frame derived from a BS247 polynucleotide, wherein said open reading frame is operably linked to a control sequence compatible with a desired host, and said nucleic acid sequence has at least 75.% identity with a sequence selected from the group consisting of SEQUENCE ID NOS 1-8, and fragments or complements thereof.
22. A cell transfected with the recombinant expression system of claim 21.
23. A BS247 polypeptide having at least 75% identity with an amino acid sequence selected from the group consisting of SEQUENCE ID NO 21, SEQUENCE
ID NO 22, SEQUENCE ID NO 23, SEQUENCE ID NO 24, SEQUENCE ID NO 25, SEQUENCE ID NO 26, and fragments thereof.
24. The polypeptide of claim 23, wherein said polypeptide is produced by recombinant techniques.
25. The polypeptide of claim 23, wherein said polypeptide is produced by synthetic techniques.
26. A specific binding molecule which binds to at least one BS247-specific epitope, wherein said B5247 epitope is derived from an amino acid sequence having at least 65% identity with an amino acid sequence selected from the group consisting of SEQUENCE ID NO 21, SEQUENCE ID NO 22, SEQUENCE ID NO 23, SEQUENCE ID NO 24, SEQUENCE ID NO 25, SEQUENCE ID NO 26, and fragments thereof.
27. The specific binding molecule of claim 26, wherein said molecule is an antibody molecule.
28. An test kit for determining the presence of BS247-specific antigen or anti-BS247-specific antibody in a test sample, said kit comprising a container containing a 85247 polypeptide having at least 65% identity with an amino acid sequence selected from the group consisting of SEQUENCE ID NO 21, SEQUENCE
ID NO 22, SEQUENCE ID NO 23, SEQUENCE ID NO 24, SEQUENCE ID NO 25, SEQUENCE ID NO 26, and fragments thereof.
29. The test kit of claim 28, wherein said BS247 polypeptide is attached to a solid phase.
30. An test kit for determining the presence of BS247 antigen in a test sample, said kit comprising a container containing a specific binding molecule which binds to a BS247 antigen having at least one BS247 epitope.
31. The kit of claim 30, wherein said specific binding molecule is attached to a solid phase.
32. A method for producing a polypeptide comprising at least one BS247-specific epitope, said method comprising incubating host cells that have been transfected with an expression vector containing a polynucleotide sequence encoding a polypeptide, wherein said polypeptide comprises an amino acid sequence having at least 65% identity with an amino acid sequence selected from the group consisting of SEQUENCE ID NO 21, SEQUENCE ID NO 22, SEQUENCE ID NO 23, SEQUENCE ID NO 24, SEQUENCE ID NO 25, SEQUENCE ID NO 26, and fragments thereof.
33. A method for detecting BS247-specific antigen in a test sample suspected of containing said BS247-specific antigen, comprising:
(a) contacting the test sample with a specific binding molecule which binds to at least one epitope of a BS247-specific antigen selected from the group consisting of SEQUENCE ID NO 21, SEQUENCE ID NO 22, SEQUENCE ID NO 23, SEQUENCE ID NO 24, SEQUENCE ID NO 25, SEQUENCE ID NO 26, and fragments thereof, wherein said contacting is performed for a time and under conditions sufficient for the formation of binding molecule/antigen complexes; and (b) detecting the presence of said complexes as an indication of the presence of said BS247 antigen.
34. The method of claim 33, wherein said specific binding molecule is an antibody molecule or a fragment thereof.
35. The method of claim 33, wherein said specific binding molecule is attached to a solid phase.
36. A method for detecting the presence of antibodies specific for a BS247-specific antigen in a test sample suspected of containing such antibodies, said method comprising:
(a) contacting the test sample with a BS247 polypeptide, wherein said BS247 polypeptide contains at least one BS247-specific epitope derived from an amino acid sequence having at least 65% identity with an amino acid sequence selected from the group consisting of SEQUENCE ID NO 21, SEQUENCE ID NO 22, SEQUENCE
ID NO 23, SEQUENCE ID NO 24, SEQUENCE ID NO 25, SEQUENCE ID NO 26, and fragments thereof, and further wherein said contacting is performed for a time and under conditions sufficient to allow antigen/antibody complexes to form; and (b) detecting the presence of said complexes as an indication of the presence of antibodies specific for a BS247 antigen.
37. The method of claim 36, wherein said BS247 polypeptide is attached to a solid phase.
38. A cell transfected with a nucleic acid sequence encoding at least one BS247-specific epitope, wherein said nucleic acid sequence is selected from the group consisting of SEQUENCE ID NOS 1-8, and fragments or complements thereof.
39. A method for producing antibodies which specifically bind to BS247 antigen, comprising administering to an individual an isolated immunogenic polypeptide or fragment thereof in an amount sufficient to elicit an immune response, wherein said immunogenic polypeptide comprises at least one BS247-specific epitope and has at least 65% identity with a sequence selected from the group consisting of SEQUENCE
ID NO 21, SEQUENCE ID NO 22, SEQUENCE ID NO 23, SEQUENCE ID NO 24, SEQUENCE ID NO 25, SEQUENCE ID NO 26, and fragments thereof.
40. A method for producing antibodies which specifically bind to BS247 antigen, comprising administering to an individual a plasmid comprising a sequence which encodes at least one BS247-specific epitope derived from a polypeptide having an amino acid sequence selected from the group consisting of SEQUENCE ID NO
21, SEQUENCE ID NO 22, SEQUENCE ID NO 23, SEQUENCE ID NO 24, SEQUENCE ID NO 25, SEQUENCE ID NO 26, and fragments thereof.
41. The test kit of claim 11 further comprising a container with tools useful for collection of said sample, wherein the tools are selected from the group consisting of lancets, absorbent paper, cloth, swabs and cups.
42. The test kit of claim 28 further comprising a container with tools useful for collection of said sample, wherein the tools are selected from the group consisting of lancets, absorbent paper, cloth, swabs and cups.
43. The test kit of claim 30 further comprising a container with tools useful for collection of said sample, wherein the tools are selected from the group consisting of lancets, absorbent paper, cloth, swabs and cups.
44. The test kit of claim 30, wherein said specific binding molecule is an antibody or fragment thereof.
45. The polynucleotide of claim 12, wherein said polynucleotide codes for a BS247 protein which comprises an amino acid sequence having at least 75%
identity to SEQUENCE ID NO 21.
46. The polynucleotide of claim 12, wherein said polynucleotide comprises DNA having at least 85% identity with SEQUENCE ID NO 7 or SEQUENCE ID NO
47. The method of claim 1, wherein the presence of said target BS247 polynucleotide in the test sample is indicative of breast disease.
48. The method of claim 4, wherein the presence of said amplicon is indicative of breast disease.
49. The method of claim 7, wherein the presence of said second stage reaction product is indicative of breast disease.
50. The method of claim 33, wherein detection of said complexes is indicative of breast disease.
51. The method of claim 36, wherein detection of said complexes is indicative of breast disease.
CA002307716A 1997-10-28 1998-10-28 Reagents and methods useful for detecting diseases of the breast Abandoned CA2307716A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US96883897A 1997-10-28 1997-10-28
US6343197P 1997-10-28 1997-10-28
US60/063,431 1997-10-28
US08/968,838 1997-10-28
PCT/US1998/022906 WO1999022027A1 (en) 1997-10-28 1998-10-28 Reagents and methods useful for detecting diseases of the breast

Publications (1)

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CA2307716A1 true CA2307716A1 (en) 1999-05-06

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CA002307716A Abandoned CA2307716A1 (en) 1997-10-28 1998-10-28 Reagents and methods useful for detecting diseases of the breast

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EP (1) EP1027457A1 (en)
CA (1) CA2307716A1 (en)
WO (1) WO1999022027A1 (en)

Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1999046391A2 (en) * 1998-03-12 1999-09-16 Millennium Biotherapeutics, Inc. Prostate derived serine protease (pdsp) protein and nucleic acid molecules and uses therefor
WO2002036616A2 (en) * 2000-10-30 2002-05-10 Diadexus, Inc. Compositions and methods relating to breast specific genes and proteins
US6855517B2 (en) 2000-11-20 2005-02-15 Diadexus, Inc. Compositions and methods relating to breast specific genes and proteins

Family Cites Families (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6103237A (en) * 1993-07-22 2000-08-15 Hybritech Incorporated Stable variant hK2 polypeptide
US5962300A (en) * 1997-03-26 1999-10-05 Incyte Pharmaceuticals, Inc. Human kallikrein

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WO1999022027A1 (en) 1999-05-06

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