Methods for identifying risk of melanoma and treatments thereof

• US 20050118117A1
• Filed: 11/06/2003
• Published: 06/02/2005
• Est. Priority Date: 11/06/2002
• Status: Abandoned Application

• Current Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Original Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Inventors: Braun, Andreas, Roth, Richard B., Nelson, Matthew Roberts, Kammerer, Stefan M.
• Application Number:
  US10/703,817
• Publication Number:
  US 20050118117A1
• Time in Patent Office: Days
• US Class Current: 424/59
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: C07K 14/4748 Tumour specific antigens; Tumour rejection antigen precursors [TRAP], e.g. MAGE
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism

Abstract

Provided herein are methods for identifying risk of melanoma in a subject and/or subjects at risk of melanoma, reagents and kits for carrying out the methods, methods for identifying candidate therapeutics for treating melanoma, therapeutic methods for treating melanoma in a subject and compositions comprising one or more melanoma cells and one or more NRP1, NID2 or ENDO180 directed agents. These embodiments are based upon an analysis of polymorphic variations in a NRP1, NID2 or ENDO180 nucleic acid, exemplified by nucleotide sequences of SEQ ID NO: 1, 2 or 3.

Claims

1. A method for identifying a subject at risk of melanoma, which comprises detecting the presence or absence of one or more polymorphic variations associated with melanoma in a nucleic acid sample from a subject, wherein the polymorphic variation is detected in a nucleotide sequence selected from the group consisting of

(a) the nucleotide sequence of SEQ ID NO:

1, 2 or 3;

(b) a nucleotide sequence which encodes a polypeptide consisting of the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO;

1, 2 or 3;

(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO;

1, 2 or 3; and

(d) a fragment of a nucleotide sequence of (a), (b), or (c);

whereby the presence of the polymorphic variation is indicative of the subject being at risk of melanoma.

2. The method of claim 1, which further comprises obtaining the nucleic acid sample from the subject.

3. The method of claim 1, wherein the one or more polymorphic variations are detected at chromosome positions selected from the group consisting of 33767168, 50495413 and 61089738.

4. The method of claim 1, wherein a polymorphic variation is detected at chromosome position 50497467.

5. The method of claim 1, wherein a polymorphic variation is detected at one or more positions in SEQ ID NO:

1 selected from the group consisting of 12008, 32137, 32720, 43721, 44339, 45640, 48768, 74247, 75828, 76381, and 84909.

6. The method of claim 5, wherein a polymorphic variation is detected at position 32137 in SEQ ID NO:

1.

7. The method of claim 5, wherein a polymorphic variation is detected at position 32720 in SEQ ID NO:

1.

8. The method of claim 5, wherein a polymorphic variation is detected at position 43721 in SEQ ID NO:

1.

9. The method of claim 5, wherein a polymorphic variation is detected at position 45640 in SEQ ID NO:

1.

10. The method of claim 3, wherein one or more polymorphic variations are detected at one or more positions in linkage disequilibrium with one or more chromosome positions selected from the group consisting of 33767168, 50495413 and 61089738.

11. The method of claim 4, wherein the one or more polymorphic variations are detected at one or more positions in linkage disequilibrium with chromosome position 50497467.

12. The method of claim 5, wherein one or more polymorphic variations are detected at one or more positions in linkage disequilibrium with one or more positions in SEQ ID NO:

1 selected from the group consisting of 12008, 32137, 32720, 43721, 44339, 45640, 48768, 74247, 75828, 76381, and 84909.

13. The method of claim 1, wherein detecting the presence or absence of the one or more polymorphic variations comprises:

hybridizing an oligonucleotide to the nucleic acid sample, wherein the oligonucleotide is complementary to a nucleotide sequence in the nucleic acid and hybridizes to a region adjacent to the polymorphic variation;

extending the oligonucleotide in the presence of one or more nucleotides, yielding extension products; and

detecting the presence or absence of a polymorphic variation in the extension products.

14. The method of claim 1, wherein the subject is a human.

15. A method for identifying a polymorphic variation associated with melanoma proximal to an incident polymorphic variation associated with melanoma, which comprises:

identifying a polymorphic variation proximal to the incident polymorphic variation associated with melanoma, wherein the polymorphic variation is detected in a nucleotide sequence selected from the group consisting of;

(a) the nucleotide sequence of SEQ ID NO;

1, 2 or 3;

(b) a nucleotide sequence which encodes a polypeptide consisting of the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO;

1, 2 or 3;

(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO;

1, 2 or 3; and

(d) a fragment of a nucleotide sequence of (a), (b), or (c) comprising the polymorphic variation;

determining the presence or absence of an association of the proximal polymorphic variant with melanoma.

16. The method of claim 15, wherein the incident polymorphic variation is at a chromosome position selected from the group consisting of 33767168, 50495413 and 61089738.

17. The method of claim 15, wherein the incident polymorphic variation is at chromosome position 50497467.

18. The method of claim 15, wherein the incident polymorphic variation is at a position in SEQ ID NO:

1 selected from the group consisting of 12008, 32137, 32720, 43721, 44339, 45640, 48768, 74247, 75828, 76381, and 84909.

19. The method of claim 15, wherein the proximal polymorphic variation is within a region between about 5 kb 5′

of the incident polymorphic variation and about 5 kb 3′

of the incident polymorphic variation.

20. The method of claim 15, which further comprises determining whether the proximal polymorphic variation is in linkage disequilibrium with the incident polymorphic variation.

21. The method of claim 15, which further comprises identifying a second polymorphic variation proximal to the identified proximal polymorphic variation associated with melanoma and determining if the second proximal polymorphic variation is associated with melanoma.

22. The method of claim 21, wherein the second proximal polymorphic variant is within a region between about 5 kb 5′

of the incident polymorphic variation and about 5 kb 3′

of the proximal polymorphic variation associated with melanoma.

23. An isolated nucleic acid comprising a nucleotide sequence selected from the group consisting of:

(a) the nucleotide sequence of SEQ ID NO;

1, 2 or 3;

(b) a nucleotide sequence which encodes a polypeptide consisting of the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO;

1, 2 or 3;

(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO;

1, 2 or 3; and

(d) a fragment of a nucleotide sequence of (a), (b), or (c); and

(e) a nucleotide sequence complementary to the nucleotide sequences of (a), (b), (c), or (d);

wherein the nucleotide sequence comprises one or more nucleotides selected from the group consisting of a thymine at chromosome position 33767168, an adenine at chromosome position 50495413, a guanine at chromosome position 61089738, a thymine at chromosome position 50497467, an adenine at position 12008 in SEQ ID NO;

1, a guanine at position 32137 in SEQ ID NO;

1, a cytosine at position 32720 in SEQ ID NO;

1, a thymine at position 43721 in SEQ ID NO;

1, a guanine at position 44339 in SEQ ID NO;

1, a thymine at position 45640 in SEQ ID NO;

1, a thymine at position 48768 in SEQ ID NO;

1, a guanine at position 74247 in SEQ ID NO;

1, an adenine at position 75828 in SEQ ID NO;

1, a thymine at position 76381 in SEQ ID NO;

1, and a guanine at position 84909 in SEQ ID NO;

1.

24. An oligonucleotide comprising a nucleotide sequence complementary to a portion of the nucleotide sequence of (a), (b), (c), or (d) in claim 23, wherein the 3′

end of the oligonucleotide is adjacent to a polymorphic variation associated with melanoma.

25. A microarray comprising an isolated nucleic acid of claim 23 linked to a solid support.

26. An isolated polypeptide encoded by the isolated nucleic acid sequence of claim 23.

27. A method for identifying a candidate molecule that modulates cell proliferation, which comprises:

(a) introducing a test molecule to a system which comprises a nucleic acid comprising a nucleotide sequence selected from the group consisting of;

(i) the nucleotide sequence of SEQ ID NO;

1, 2 or 3;

(ii) a nucleotide sequence which encodes a polypeptide consisting of the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO;

1, 2 or 3;

(iii) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO;

1, 2 or 3; and

(iv) a fragment of a nucleotide sequence of (i), (ii), or (iii);

or

introducing a test molecule to a system which comprises a protein encoded by a nucleotide sequence of (i), (ii), (iii), or (iv); and

(b) determining the presence or absence of an interaction between the test molecule and the nucleic acid or protein,

whereby the presence of an interaction between the test molecule and the nucleic acid or protein identifies the test molecule as a candidate molecule that modulates cell proliferation.

28. The method of claim 27, wherein the system is an animal.

29. The method of claim 27, wherein the system is a cell.

30. The method of claim 27, wherein the nucleotide sequence comprises one or more polymorphic variations associated with melanoma.

31. The method of claim 30, wherein the nucleotide sequence comprises a polymorphic variation associated with melanoma at one or more chromosome positions selected from the group consisting of 33767168, 50495413 and 61089738.

32. The method of claim 30, wherein the nucleotide sequence comprises a polymorphic variation associated with melanoma at chromosome position 50497467.

33. The method of claim 30, wherein the nucleotide sequence comprises a polymorphic variation associated with melanoma at one or more positions in SEQ ID NO:

1 selected from the group consisting of 12008, 32137, 32720, 43721, 44339, 45640, 48768, 74247, 75828, 76381, and 84909.

34. A method for treating melanoma in a subject, which comprises administering a candidate molecule identified by the method of claim 27 to a subject in need thereof, whereby the candidate molecule treats melanoma in the subject.

35. A method for identifying a candidate therapeutic for treating melanoma, which comprises:

(a) introducing a test molecule to a system which comprises a nucleic acid comprising a nucleotide sequence selected from the group consisting of;

(i) the nucleotide sequence of SEQ ID NO;

1, 2 or 3;

(ii) a nucleotide sequence which encodes a polypeptide consisting of the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO;

1, 2 or 3;

(iii) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO;

1, 2 or 3; and

(iv) a fragment of a nucleotide sequence of (i), (ii), or (iii);

or

introducing a test molecule to a system which comprises a protein encoded by a nucleotide sequence of (i), (ii), (iii), or (iv); and

(b) determining the presence or absence of an interaction between the test molecule and the nucleic acid or protein,

whereby the presence of an interaction between the test molecule and the nucleic acid or protein identifies the test molecule as a candidate therapeutic for treating melanoma.

36. A method for treating melanoma in a subject, which comprises contacting one or more cells of a subject in need thereof with a nucleic acid, wherein the nucleic acid comprises a nucleotide sequence selected from the group consisting of:

(a) the nucleotide sequence of SEQ ID NO;

1, 2 or 3;

(b) a nucleotide sequence which encodes a polypeptide consisting of the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO;

1, 2 or 3;

(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO;

1, 2 or 3; and

(d) a fragment of a nucleotide sequence of (a), (b), or (c); and

(e) a nucleotide sequence complementary to the nucleotide sequences of (a), (b), (c), or (d);

whereby contacting the one or more cells of the subject with the nucleic acid treats melanoma in the subject.

37. The method of claim 36, wherein the nucleic acid is duplex RNA.

38. The method of claim 37, wherein the duplex RNA comprises a strand comprising the nucleotide sequence AGAGAGGTCCTGAATGTTC (SEQ ID NO:

250);

GATTATCCTTGCTCTGGAA (SEQ ID NO;

251;

GCACCATACAATCAGAGTT (SEQ ID NO;

     252);

or GCCAGGCAATGTGTTGAAG (SEQ ID NO;

     253).

39. A method for treating melanoma in a subject, which comprises contacting one or more cells of a subject in need thereof with a protein, wherein the protein is encoded by a nucleotide sequence which comprises a polynucleotide sequence selected from the group consisting of:

(a) the nucleotide sequence of SEQ ID NO;

1, 2 or 3;

(b) a nucleotide sequence which encodes a polypeptide consisting of the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO;

1, 2 or 3;

(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO;

1, 2 or 3; and

(d) a fragment of a nucleotide sequence of (a), (b), or (c);

whereby contacting the one or more cells of the subject with the protein treats melanoma in the subject.

40. A method for treating melanoma in a subject, which comprises:

detecting the presence or absence of one or more polymorphic variations associated with melanoma in a nucleic acid sample from a subject, wherein the polymorphic variation is detected in a nucleotide sequence selected from the group consisting of;

(a) the nucleotide sequence of SEQ ID NO;

1, 2 or 3;

(b) a nucleotide sequence which encodes a polypeptide consisting of the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO;

1, 2 or 3;

(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO;

1, 2 or 3; and

(d) a fragment of a nucleotide sequence of (a), (b), or (c) comprising the polymorphic variation; and

administering a melanoma treatment to a subject in need thereof based upon the presence or absence of the one or more polymorphic variations in the nucleic acid sample.

41. The method of claim 40, wherein the one or more polymorphic variations are detected at one or more chromosome positions selected from the group consisting of 33767168, 50495413 and 61089738.

42. The method of claim 40, wherein a polymorphic variation is detected at chromosome position 50497467.

43. The method of claim 40, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO:

1 selected from the group consisting of 12008, 32137, 32720, 43721, 44339, 45640, 48768, 74247, 75828, 76381, and 84909.

44. The method of claim 40, which further comprises extracting and analyzing a tissue biopsy sample from the subject.

45. The method of claim 40, wherein the treatment is one or more selected from the group consisting of administering cisplatin, administering carmustine, administering vinblastine, administering vincristine, administering bleomycin, administering a combination of the foregoing, and surgery.

46. A method for preventing melanoma in a subject, which comprises:

detecting the presence or absence of one or more polymorphic variations associated with melanoma in a nucleic acid sample from a subject, wherein the polymorphic variation is detected in a nucleotide sequence selected from the group consisting of;

(a) the nucleotide sequence of SEQ ID NO;

1, 2 or 3;

(b) a nucleotide sequence which encodes a polypeptide consisting of the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO;

1, 2 or 3;

(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO;

1, 2 or 3,; and

(d) a fragment of a nucleotide sequence of (a), (b), or (c) comprising the polymorphic variation; and

administering a melanoma preventative to a subject in need thereof based upon the presence or absence of the one or more polymorphic variations in the nucleic acid sample.

47. The method of claim 46, wherein the one or more polymorphic variations are detected at one or more chromosome positions selected from the group consisting of 33767168, 50495413 and 61089738.

48. The method of claim 46, wherein a polymorphic variation is detected at chromosome position 50497467.

49. The method of claim 46, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO:

1 selected from the group consisting of 12008, 32137, 32720, 43721, 44339, 45640, 48768, 74247, 75828, 76381, and 84909.

50. The method of claim 46, wherein the preventative reduces ultraviolet (UV) light exposure to the subject.

51. A method of targeting information for preventing or treating melanoma to a subject in need thereof, which comprises:

detecting the presence or absence of one or more polymorphic variations associated with melanoma in a nucleic acid sample from a subject, wherein the polymorphic variation is detected in a nucleotide sequence selected from the group consisting of;

(a) the nucleotide sequence of SEQ ID NO;

1, 2 or 3;

(b) a nucleotide sequence which encodes a polypeptide consisting of the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO;

1, 2 or 3;

(c) a nucleotide sequence which encodes a polypeptide that is 90% or more identical to the amino acid sequence encoded by the nucleotide sequence of SEQ ID NO;

1,2 or 3; and

(d) a fragment of a nucleotide sequence of (a), (b), or (c) comprising the polymorphic variation comprising the polymorphic variation; and

directing information for preventing or treating melanoma to a subject in need thereof based upon the presence or absence of the one or more polymorphic variations in the nucleic acid sample.

52. The method of claim 51, wherein the one or more polymorphic variations are detected at one or more chromosome positions selected from the group consisting of 33767168, 50495413 and 61089738.

53. The method of claim 51, wherein a polymorphic variation is detected at chromosome position 50497467.

54. The method of claim 51, wherein the one or more polymorphic variations are detected at one or more positions in SEQ ID NO:

1 selected from the group consisting of 12008, 32137, 32720, 43721,44339, 45640, 48768, 74247, 75828, 76381, and 84909.

55. The method of claim 51, wherein the information comprises a description of methods for reducing ultraviolet (UV) light exposure to the subject.

56. The method of claim 51, wherein the information comprises a description of chemotherapeutic treatments and surgical treatments of melanoma.

57. A composition comprising a melanoma cell and an antibody that specifically binds to a protein, polypeptide or peptide encoded by a nucleotide sequence 90% or more identical to the nucleotide sequence of SEQ ID NO:

1, 2 or 3.

58. The composition of claim 57, wherein the antibody specifically binds to an epitope comprising a serine at amino acid 656 in a NID2 protein, polypeptide or peptide.

59. A composition comprising a melanoma cell and a RNA, DNA, PNA or ribozyme molecule comprising a nucleotide sequence identical to or 90% or more identical to a portion of a nucleotide sequence of SEQ ID NO:

1, 2 or 3.

60. The composition of claim 59, wherein the RNA molecule is a short inhibitory RNA molecule.