Identification of specific biomarkers for breast cancer cells

• US 20030166026A1
• Filed: 01/08/2003
• Published: 09/04/2003
• Est. Priority Date: 01/09/2002
• Status: Abandoned Application

• Current Assignee: Lynx Therapeutics, Inc. (Illumina Incorporated)
• Original Assignee: Lynx Therapeutics, Inc. (Illumina Incorporated)
• Inventors: Goodman, Laurie J., Bowen, Benjamin A.
• Application Number:
  US10/339,782
• Publication Number:
  US 20030166026A1
• Time in Patent Office: Days
• US Class Current: 435/7.23
• CPC Class Codes: A61K 48/00 Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
• CPC Class Codes: C07K 14/47 from mammals
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/158 Expression markers

Abstract

Nucleic acids, proteins, antibodies, marker sets and arrays are provided for biomarkers for breast cancer. Methods for detecting breast cancer, modulating breast cancer phenotypes in cells, and for treating a subject with breast cancer are also provided.

Claims

1. A composition comprising at least one expression vector, wherein the at least one expression vector comprises a nucleic acid comprising:

(a) at least one polynucleotide sequence selected from the group consisting of;

SEQ ID NO;

1-SEQ ID NO;

491 or a polynucleotide sequence complementary thereto;

(b) at least one polynucleotide sequence comprising a conservative variation of a polynucleotide sequence of (a);

(c) at least one polynucleotide encoding a polypeptide sequence of SEQ ID NO;

492, or conservative variations thereof;

(d) at least one polynucleotide sequence that hybridizes under stringent conditions to a polynucleotide sequence of (a) or (b);

(e) at least one polynucleotide that is at least about 70% identical to a polynucleotide sequence of (a), or (b);

or,

(f) at least one polynucleotide sequence comprising at least about 10 contiguous nucleotides of a polynucleotide sequence selected from the group consisting of;

SEQ ID NO;

1-SEQ ID NO;

491, or a sequence complementary thereto.

2. The at least one expression vector of claim 1, wherein the at least one expression vector comprises a promoter operably linked to the nucleic acid comprising the polynucleotide of (a), (b), (c), (d), (e) or (f).

3. The at least one expression vector of claim 1, wherein the nucleic acid encodes a polypeptide.

4. The at least one expression vector of claim 1, wherein the nucleic acid encodes a sense or anti sense RNA.

5. A method of treating breast cancer in a patient, the method comprising administering to the patient an effective amount of the at least one expression vector of claim 1.

6. A composition comprising the at least one expression vector of claim 1 and an excipient.

7. The composition of claim 6, wherein the excipient is a pharmaceutically acceptable excipient.

8. A cell comprising the at least one expression vector of claim 1.

9. The cell of claim 8, which cell expresses a polypeptide of SEQ ID NO:

492.

10. An isolated or recombinant polypeptide comprising:

one or more amino acid sequences or subsequences encoded by a nucleic acid comprising;

(a) an amino acid sequence of SEQ ID NO;

492, and conservative variants thereof;

(b) an amino acid sequence encoded by a polynucleotide sequence selected from the group consisting of SEQ ID NO;

1 to SEQ ID NO;

491, and conservative variations thereof;

(c) an amino acid sequence encoded by a polynucleotide sequence that hybridizes under stringent conditions to a polynucleotide sequence selected from the group consisting of SEQ ID NO;

1 to SEQ ID NO;

491

(d) an amino acid sequence encoded by a polynucleotide sequence that is at least about 70% identical to a polynucleotide selected from the group consisting of SEQ ID NO;

1 to SEQ ID NO;

491;

or

(e) a polypeptide comprising an amino acid subsequence of (a), (b), (c) or (d).

11. The isolated or recombinant polypeptide of claim 10, comprising a fusion protein.

12. The isolated or recombinant polypeptide of claim 10, comprising a peptide or polypeptide tag.

13. The isolated or recombinant polypeptide of claim 12, wherein the peptide or polypeptide tag comprises a reporter peptide or polypeptide.

14. The isolated or recombinant polypeptide of claim 12, wherein the peptide or polypeptide tag comprises an epitope.

15. The isolated or recombinant polypeptide of claim 12, wherein the peptide or polypeptide tag comprises a localization signal or sequence.

16. A composition comprising the isolated or recombinant polypeptide of claim 10 and an excipient.

17. The composition of claim 16, wherein the excipient is a pharmaceutically acceptable excipient.

18. A method of treating breast cancer in a patient, the method comprising administering to the patient an effective amount of the isolated or recombinant polypeptide of claim 10.

19. An array of polypeptides comprising two or more different polypeptides of claim 10.

20. An antibody specific for an isolated or recombinant polypeptide of claim 10.

21. The antibody of claim 20, wherein the antibody comprises a monoclonal antibody or polyclonal serum.

22. One or more isolated or recombinant polypeptides that bind to the antibody of claim 20.

23. The antibody of claim 20, which antibody is specific for an eptitope comprising a subsequence of a polypeptide of SEQ ID NO:

492.

24. A cell comprising at least one exogenous nucleic acid, which cell expresses a polypeptide of claim 10.

25. A labeled probe comprising a nucleic acid or polypeptide comprising:

(a) at least one polynucleotide sequence selected from the group consisting of;

SEQ ID NO;

1-SEQ ID NO;

491 or a polynucleotide sequence complementary thereto;

(b) at least one polynucleotide sequence comprising a conservative variation of a polynucleotide sequence of (a);

(c) at least one polynucleotide encoding a polypeptide sequence of SEQ ID NO;

492, or conservative variations thereof;

(d) at least one polynucleotide sequence that hybridizes under stringent conditions to a polynucleotide sequence of (a) or (b);

(e) at least one polynucleotide that is at least about 70% identical to a polynucleotide sequence of (a), or (b);

(f) at least one polynucleotide sequence comprising at least about 10 contiguous nucleotides of a polynucleotide sequence selected from the group consisting of;

SEQ ID NO;

1-SEQ ID NO;

491, or a sequence complementary thereto;

(g) at least one polypeptide or peptide comprising an amino acid sequence of SEQ ID NO;

492 or conservative variations thereof;

(h) at least one polypeptide or peptide comprising an amino acid subsequence of SEQ ID NO;

492, or conservative variants thereof comprising at least six amino acids;

or,

(i) at least one antibody specific for a polypeptide or peptide sequence of (g) or (h).

26. The labeled probe of claim 25, comprising a nucleic acid.

27. The labeled probe of claim 25, comprising an oligonucleotide.

28. The labeled probe of claim 25, the polynucleotide sequence of (f) comprises at least about 12 contiguous nucleotides.

29. The labeled probe of claim 25, the polynucleotide sequence of (f) comprises at least about 14 contiguous nucleotides.

30. The labeled probe of claim 25, the polynucleotide sequence of (f) comprises at least about 16 contiguous nucleotides.

31. The labeled probe of claim 25, the polynucleotide sequence of (f) comprises at least about 17 contiguous nucleotides.

32. The labeled probe of claim 25, comprising a peptide.

33. The labeled probe of claim 25, comprising an antigenic peptide.

34. The labeled probe of claim 25, comprising a fusion protein.

35. The labeled probe of claim 25, comprising an epitope tag.

36. The labeled probe of claim 25, comprising an isotopic, fluorescent, fluorogenic or colorimetric label.

37. The labeled probe of claim 25, comprising a DNA or RNA molecule.

38. A labeled probe of claim 25, comprising a cDNA, an amplification product, a transcript, a restriction fragment or an oligonucleotide.

39. A labeled probe of claim 25, comprising an array of probes comprising a plurality of nucleic acids comprising:

(a) two or more polynucleotide sequences selected from SEQ ID NO;

1 to SEQ ID NO;

491, or a subsequence thereof comprising at least about 10 contiguous nucleotides of any of SEQ ID NO;

1 to SEQ ID NO;

491;

(b) two or more polynucleotide sequences complementary to the polynucleotide sequence of (a);

or,

(c) two or more polynucleotide sequences that hybridize under stringent conditions to the polynucleotide sequences of (a) or (b).

40. An array of probes according to claim 39, wherein the nucleic acids are logically or physically arrayed.

41. A marker set for predicting at least one characteristic of a breast cancer cell, comprising a plurality of members, which members comprise:

(a) one or more polynucleotide sequence selected from the group consisting of;

SEQ ID NO;

1-SEQ ID NO;

491 or a polynucleotide sequence complementary thereto;

(b) one or more polynucleotide sequence comprising a conservative variation of a polynucleotide sequence of (a);

(c) one or more polynucleotide encoding a polypeptide sequence of SEQ ID NO;

492, or conservative variations thereof;

(d) one or more polynucleotide sequence that hybridizes under stringent conditions to a polynucleotide sequence of (a) or (b);

(e) one or more polynucleotide that is at least about 70% identical to a polynucleotide sequence of (a) or (b);

(f) one or more polynucleotide sequence comprising at least about 10 contiguous nucleotides of a polynucleotide sequence selected from the group consisting of;

SEQ ID NO;

1-SEQ ID NO;

491, or a sequence complementary thereto;

(g) one or more polypeptide comprising an amino acid sequence or subsequence of SEQ ID NO;

492 or conservative variants thereof comprising at least six amino acids; and

/or,

(h) one or more antibodies specific for a polypeptide or peptide sequence of (g) or encoded by (c).

42. The marker set of claim 41, wherein the plurality of members comprise one or more of oligonucleotides, expression products, and amplification products.

43. The marker set of claim 42, wherein the oligonucleotides are synthetic oligonucleotides.

44. The marker set of claim 41, wherein the plurality of members comprise labeled nucleic acid probes.

45. The marker set of claim 41, wherein the plurality of members comprise a plurality of polypeptides or peptides.

46. The marker set of claim 41, wherein the plurality of members comprise a plurality of antibodies.

47. The marker set of claim 41, wherein the plurality of members, comprise nucleic acids and polypeptides.

48. The marker set of claim 41, wherein the plurality of members are logically or physically arrayed.

49. The marker set of claim 48, wherein the array comprises a bead array.

50. The marker set of claim 41, wherein each member of the marker set comprises at least about 10 contiguous nucleotides from at least one of SEQ ID NO:

1-SEQ ID NO;

491.

51. The marker set of claim 41, wherein the plurality of members together comprise a plurality of sequences or subsequences selected from a plurality of nucleic acids represented by SEQ ID NO:

1-SEQ ID NO;

491.

52. The marker set of claim 41, comprising a majority of members that together comprise a majority of subsequences from a majority of SEQ ID NO:

1-SEQ ID NO;

491.

53. The marker set of claim 41, wherein breast cancer is predicted by hybridizing the nucleic acids of the marker set to a DNA or RNA sample from a cell or a tissue, and detecting at least one expressed expression product.

54. An array comprising the marker set of claim 41.

55. The marker set of claim 41, wherein the at least one characteristic of a breast cancer cell is selected from the group consisting of transformation state, invasiveness, stage, a protein expressed, and a protein expressed on the surface of the breast cancer cell.

56. A method for modulating at least one characteristic of a breast cell, the method comprising:

modulating expression or activity of at least one polypeptide encoded by a nucleic acid, the nucleic acid comprising;

(a) at least one polynucleotide sequence selected from the group consisting of;

SEQ ID NO;

1-SEQ ID NO;

491 or a sequence complementary thereto;

(b) at least one polynucleotide sequence comprising a conservative variation of a polynucleotide sequence of (a);

(c) at least one polynucleotide encoding a polypeptide sequence of SEQ ID NO;

492, or conservative variations thereof;

(d) at least one polynucleotide sequence that hybridizes under stringent conditions to a polynucleotide sequence of (a) or (b);

(e) at least one polynucleotide that is at least about 70% identical to a polynucleotide sequence of (a), or (b);

or,

(f) at least one polynucleotide sequence comprising at least about 10 contiguous nucleotides of a polynucleotide sequence selected from the group consisting of;

SEQ ID NO;

1-SEQ ID NO;

491, or a sequence complementary thereto.

57. The method of claim 56, comprising modulating expression by expressing an exogenous nucleic acid comprising a polynucleotide sequence selected from SEQ ID NO:

1 to SEQ ID NO;

491.

58. The method of claim 56, comprising modulating expression in a cell line or non-human mammal.

59. The method of claim 58, wherein the non-human mammal comprises a mouse, a rat, a dog, a rabbit, a pig, a sheep or a non-human primate.

60. The method of claim 56, comprising modulating expression by expressing an antisense RNA or a ribozyme.

61. The method of claim 56, wherein expression is modulated in response to a carcinogenic signal.

62. The method of claim 61, wherein a plurality of expression products are detected.

63. The method of claim 62, wherein the plurality of expression products are detected in an array.

64. The method of claim 63, wherein the array comprises a bead array.

65. The method of claim 63, wherein the array comprises a tissue array.

66. The method of claim 56, further comprising detecting altered expression or activity of an expression product encoded by a nucleic acid comprising a polynucleotide sequence selected from SEQ ID NO:

1 to SEQ ID NO;

491.

67. The method of claim 66, comprising detecting altered expression or activity in response to a carcinogenic signal.

68. The method of claim 66, wherein a data record comprising the altered expression or activity is recorded in a database.

69. The method of claim 68, wherein the database comprises a plurality of character strings recorded on a computer or in a computer readable medium.

70. The method of claim 56, wherein the at least one characteristic of a breast cell is selected from the group consisting of transformation state, invasiveness, stage, a protein expressed, and a protein expressed on the surface of the breast cell.

71. A method for identifying a breast cancer gene, the method comprising:

(i) providing at least one nucleic acid comprising;

(a) at least one polynucleotide sequence selected from the group consisting of;

SEQ ID NO;

1-SEQ ID NO;

491, or a polynucleotide sequence complementary thereto;

(b) at least one polynucleotide encoding a polypeptide sequence of SEQ ID NO;

492, or conservative variations thereof;

(c) at least one polynucleotide sequence that hybridizes under stringent conditions to a polynucleotide sequence of (a) or (b);

(d) at least one polynucleotide that is at least about 70% identical to a polynucleotide sequence of (a), or (b);

(e) at least one polynucleotide sequence that hybridizes to a nucleic acid that is physically linked in the human genome to a nucleic acid comprising a polynucleotide sequence of (a), (b), (c) or (d);

or,

(f) at least one polynucleotide sequence comprising at least about 10 contiguous nucleotides of a polynucleotide sequence selected from the group consisting of;

SEQ ID NO;

1-SEQ ID NO;

491, or a sequence complementary thereto; and

,

(ii) identifying at least one nucleic acid corresponding to a breast cancer gene.

72. The method of claim 71, wherein the polynucleotide sequence in (i) is selected from the group consisting of:

SEQ ID NO;

1-SEQ ID NO;

491, or a conservative variation thereof.

73. The method of claim 72, wherein the breast cancer gene comprises a locus on human chromosome 11.

74. The method of claim 72, wherein the breast cancer gene comprises a locus that maps to human chromosome 11q13-q14.

75. The method of claim 71, comprising providing at least one expression vector comprising a polynucleotide sequence selected from among the polynucleotide sequences of (a), (b), (c), (d), (e) or (f).

76. The method of claim 71, comprising providing at least one probe comprising a polynucleotide sequence selected from among the polynucleotide sequences of (a), (b), (c), (d), (e) or (f);

and,

hybridizing the at least one probe to an expression product of a breast cancer gene.

77. The method of claim 71, wherein providing the at least one nucleic acid comprises amplifying a target sequence comprising a polynucleotide sequence selected from among the polynucleotide sequences of (a), (b), (c), (d), (e) or (f).

78. The method of claim 77, wherein the amplifying comprises a quantitative reverse transcriptase-polymerase chain reaction (RT-PCR).

79. The method of claim 77, comprising identifying a target sequence that is differentially expressed in a transformed breast cell compared to a non-transformed breast cell.

80. The method of claim 79, wherein the transformed breast cell comprises a positive estrogen receptor (ER+) cell.

81. The method of claim 71, further comprising detecting altered expression or activity of a product encoded by the at least one nucleic acid comprising a polynucleotide sequence selected from among the polynucleotide sequences of (a), (b), (c), (d), (e) or (f).

82. The method of claim 81, wherein the altered expression or activity of the product is determined by analysis of massively parallel signature sequence data.

83. The method of claim 81, wherein the altered expression or activity is determined to be differentially expressed to a p<

0.01 level of confidence.

84. The method of claim 81, wherein the altered expression or activity is determined to be differentially expressed to a p<

0.001 level of confidence.

85. The method of claim 81, comprising detecting altered expression in a transformed cell.

86. The method of claim 81, comprising detecting altered expression in response to a carcinogenic signal.

87. The method of claim 81, comprising detecting altered expression in response to tamoxifen.

91. The method of claim 85, wherein the detecting step comprises qualitative detection.

88. A method of detecting breast cancer in a subject, the method comprising:

(i) providing a subject cell or tissue sample of nucleic acids; and

,

(ii) detecting at least one polymorphic nucleic acid or at least one expression product corresponding to a polynucleotide sequence comprising;

(a) at least one polynucleotide sequence selected from the group consisting of;

SEQ ID NO;

1-SEQ ID NO;

491 or a polynucleotide sequence complementary thereto;

(b) at least one polynucleotide sequence comprising a conservative variation of a polynucleotide sequence of (a);

(c) at least one polynucleotide encoding a polypeptide sequence of SEQ ID NO;

492, or conservative variations thereof;

(d) at least one polynucleotide sequence that hybridizes under stringent conditions to a polynucleotide sequence of (a) or (b);

(e) at least one polynucleotide that is at least about 70% identical to a polynucleotide sequence of (a), or (b);

or,

(f) at least one polynucleotide sequence comprising at least about 10 contiguous nucleotides of a polynucleotide sequence selected from the group consisting of;

SEQ ID NO;

1-SEQ ID NO;

491, or a sequence complementary thereto,

wherein the polymorphic nucleic acid or expression or activity of the expression product is correlatable to breast cancer.

89. The method of claim 88, wherein the expression product comprises an RNA.

90. The method of claim 88, wherein the expression product comprises a protein or polypeptide.

92. The method of claim 88, wherein the detecting step comprises quantitative detection.