Methods for Identifying Risk of Type II Diabetes and Treatments Thereof

• US 20080199480A1
• Filed: 07/22/2004
• Published: 08/21/2008
• Est. Priority Date: 07/22/2004
• Status: Abandoned Application

• Current Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Original Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Inventors: Braun, Andreas, Denissenko, Mikhail F., Kammerer, Stefan M., Saiah, Eddine, Reneland, Rikard H., Langdown, Maria L., Atienza, Josephine M., Zapf, James W., Nelson, Matthew R.
• Application Number:
  US11/572,420
• Publication Number:
  US 20080199480A1
• Time in Patent Office: Days
• US Class Current: 424/172.1
• CPC Class Codes: A61P 3/10 for hyperglycaemia, e.g. antidiabetics
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/136 Screening for pharmacological compounds
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers

Abstract

Provided herein are methods for identifying a risk of type II diabetes in a subject, reagents and kits for carrying out the methods, methods for identifying candidate therapeutics for treating type II diabetes, and therapeutic and preventative methods applicable to type II diabetes. These embodiments are based upon an analysis of polymorphic variations in nucleotide sequences within the human genome.

Claims

1. A method for identifying a subject at risk of type II diabetes, which comprises detecting the presence or absence of one or more polymorphic variations associated with type II diabetes in a nucleic acid sample from a subject, wherein the one or more polymorphic variations are detected in a nucleotide sequence in SEQ ID NO:

1 or a substantially identical sequence thereof, or a fragment of the foregoing;

whereby the presence of the polymorphic variation is indicative of the subject being at risk of type II diabetes.

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 one or more positions selected from the group consisting of rs1512183, rs1512185, rs1028013, rs987748, rs2881488, rs1157607, rs1157608, rs1912965, rs1912966, rs1054750, rs1499780, rs2117138, rs2346840, rs2048518, rs2048519, rs2048521, rs3762718, rs2196083, rs972030, rs1036286, rs1036285, rs1512188, rs1512189, rs1567657, rs1567658, rs1028012, position 66765 of SEQ ID NO:

1, and position 66794 of SEQ ID NO;

1.

4. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions selected from the group consisting of rs 1512185, rs987748, rs1512183, rs1157607, rs1912966, rs1499780, rs2048519, rs972030, rs1567657 and rs1028012.

5. The method of claim 1, wherein the polymorphic variation is detected at position 66794 of SEQ ID NO:

1.

6. The method of claim 1, wherein a polymorphic variation is detected at position between positions 18716 to 94523 of SEQ ID NO:

1.

7. The method of claim 1, wherein the one or more polymorphic variations are detected at one or more positions in linkage disequilibrium with one or more positions in claim 3.

8. 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.

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

10. A method for identifying a polymorphic variation associated with type II diabetes proximal to an incident polymorphic variation associated with type II diabetes, which comprises:

identifying a polymorphic variation proximal to the incident polymorphic variation associated with type II diabetes, wherein the polymorphic variation is detected in a nucleotide sequence in SEQ ID NO;

1 or a substantially identical sequence thereof, or a fragment of the foregoing;

determining the presence or absence of an association of the proximal polymorphic variant with type II diabetes.

11. The method of claim 10, wherein the incident polymorphic variation is at one or more positions in claim 3.

12. The method of claim 10, 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.

13. The method of claim 10, which further comprises determining whether the proximal polymorphic variation is in linkage disequilibrium with the incident polymorphic variation.

14. The method of claim 10, which further comprises identifying a second polymorphic variation proximal to the identified proximal polymorphic variation associated with type II diabetes and determining if the second proximal polymorphic variation is associated with type II diabetes.

15. The method of claim 14, 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 type II diabetes.

16. An isolated nucleic acid which comprises a cytosine at a position corresponding to position of 66794 in SEQ ID NO:

1.

17. An oligonucleotide comprising a nucleotide sequence complementary to a portion of the nucleic acid of claim 16, wherein the 3′

end of the oligonucleotide is adjacent to position 66794 in SEQ ID NO;

1.

18. A microarray comprising an isolated nucleic acid of claim 16 linked to a solid support.

19. An isolated polypeptide which comprises an amino acid sequence identical to or substantially identical to the amino acid sequence of SEQ ID NO:

4, or a fragment thereof, wherein the polypeptide or fragment thereof comprises a histidine corresponding to position 914 in SEQ ID NO;

4, an arginine corresponding to position 924 in SEQ ID NO;

4, or a histidine corresponding to position 914 in SEQ ID NO;

4 and an arginine corresponding to position 924 in SEQ ID NO;

4.

20-42. -42. (canceled)

43. A method for treating type II diabetes, which comprises administering to a subject in need thereof a molecule that specifically interacts with an EPHA3 polypeptide, whereby the molecule is administered in an amount effective to treat the type II diabetes.

44. The method of claim 43, wherein the molecule is an antibody that specifically binds to EPHA3.

45. The method of claim 43, wherein the molecule is an antibody that inhibits an interaction between EPHA3 and an EPHA3 binding partner, ligand or signal partner.

46. The method of claim 45, wherein the antibody inhibits binding between EPHA3 and Ephrin-A5.

47. The method of claim 43, wherein the molecule modulates one or more levels or activities of cellular molecules selected from the group consisting of glucose uptake by cells;

glucose transport molecule activity or levels in cells;

triacylglycerol content in cells;

resistin levels or activities in cells;

levels or activities of PPARγ

, PI3 kinase, Akt and C/EBPα

in cells;

levels of activities of Ephrin-A2 and Ephrin-A5;

levels or activities of ADAM10;

circulating levels of glucose;

cell or tissue sensitivity to insulin;

progression from impaired glucose tolerance to insulin resistance;

glucose uptake in skeletal muscle cells;

glucose uptake in adipose cells;

glucose uptake in neuronal cells;

glucose uptake in red blood cells;

glucose uptake in the brain; and

postprandial increase in plasma glucose following a meal.

48. A composition comprising a cell from a subject having type II diabetes or at risk of type II diabetes and an antibody that specifically binds to a protein, polypeptide or peptide encoded by a nucleotide sequence identical to or 90% or more identical to a nucleotide sequence in SEQ ID NO:

1-3.

49. The composition of claim 48, wherein the antibody specifically binds to an epitope comprising an arginine at position 924 in an EPHA3 polypeptide (SEQ ID NO:

4).

50. The composition of claim 48, wherein the antibody inhibits the interaction between an EPHA3 polypeptide and a natural binding partner or ligand.

51. The composition of claim 50, wherein the natural binding partner or ligand is Ephrin-A5.

52. A composition comprising a cell from a subject having type II diabetes or at risk of type II diabetes 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 in SEQ ID NO:

1-3, or a complementary sequence of the foregoing.

53. The composition of claim 52, wherein the RNA molecule is a short inhibitory RNA molecule.

54. The method of claim 53, wherein the RNA molecule includes a strand comprising a nucleotide sequence selected from the group consisting of GCGGATGGTAACTTCT (SEQ ID NO:

135), GCTCAAGTTCACTCTACGA (SEQ ID NO;

136), CTCTACGAGACTGCAATAG (SEQ ID NO;

137) and AATTTCGAGCATCAGTT (SEQ ID NO;

138).

55. A method of genotyping a nucleic acid which comprises determining the nucleotide corresponding to position 66794 of SEQ ID NO:

1 in the nucleic acid.

56-59. -59. (canceled)