Human single nucleotide polymorphisms associated with dose-dependent weight gain and methods of use thereof

• US 20070202512A1
• Filed: 08/17/2006
• Published: 08/30/2007
• Est. Priority Date: 08/19/2005
• Status: Abandoned Application

• Current Assignee: Bristol-Myers Squibb Company
• Original Assignee: Bristol-Myers Squibb Company
• Inventors: Ranade, Koustubh
• Application Number:
  US11/505,577
• Publication Number:
  US 20070202512A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/136 Screening for pharmacological compounds
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/172 Haplotypes

Abstract

The invention provides novel polynucleotides and polypeptides associated with the incidence of PPAR-agonist associated weight gain and lower HbA1C levels. The invention also provides polynucleotide fragments corresponding to the genomic and/or coding regions of these polynucleotides which comprise at least one polymorphic locus per fragment. Allele-specific primers and probes which hybridize to these regions, and/or which comprise at least one polymorphic locus are also provided. The polynucleotides, primers, and probes of the present invention are useful in phenotype correlations, medicine, and genetic analysis. Also provided are vectors, host cells, antibodies, and recombinant and synthetic methods for producing said polynucleotides and/or polypeptides. The invention further relates to diagnostic methods for using these novel polynucleotides in the diagnosis, treatment, and/or prevention of various PPAR-related diseases and/or disorders, including weight gain.

Claims

1. An isolated nucleic acid molecule comprising a polynucleotide sequence selected from the group consisting of the polynucleotide sequence provided as SEQ ID NO:

1, 3, 14, and 16.

2. The isolated nucleic acid molecule according to claim 1, wherein said nucleic acid comprises at least one polymorphic locus selected from the group consisting of:

(a) nucleotide position 696 of SEQ ID NO;

1;

(b) nucleotide position 696 of SEQ ID NO;

3;

(c) nucleotide position 1220 of SEQ ID NO;

14; and

(d) nucleotide position 1220 of SEQ ID NO;

16.

3. A method of identifying a patient who may be at risk of developing dose-dependent weight gain upon administration of a PPAR-agonist comprising the step of determining whether said patient has a reference or variable allele at one or more polymorphic loci of the human PPAR-alpha gene.

4. The method according to claim 3, wherein the presence of a variable allele at the polymorphic locus at nucleotide position 696 of SEQ ID NO:

1 or 3 is indicative of an decreased risk of developing dose-dependent weight gain in a patient receiving PPAR-agonist therapy, whereas the presence of the reference allele at said polymorphic position is indicative of an increased risk of developing dose-dependent weight gain in a patient receiving PPAR-agonist therapy.

5. A method of identifying a patient who may be at risk of developing dose-dependent weight gain upon administration of a PPAR-agonist comprising the step of determining whether said patient has a reference or variable allele at one or more polymorphic loci of the human glucocorticoid receptor gene.

6. The method according to claim 5, wherein the presence of a variable allele at the polymorphic locus at nucleotide position 1220 of SEQ ID NO:

14 or 16 is indicative of an increased risk of developing dose-dependent weight gain in a patient receiving PPAR-agonist therapy, whereas the presence of the reference allele at said polymorphic position is indicative of a decreased risk of developing dose-dependent weight gain in a patient receiving PPAR-agonist therapy.

7. An isolated polypeptide comprising a sequence selected from the group consisting of the polypeptide sequence provided as SEQ ID NO:

2, and SEQ ID NO;

4, wherein said polypeptide comprises at least one polymorphic locus, wherein said polymorphic locus is located at amino acid position 162.

8. A method of identifying a patient who may be at risk of developing dose-dependent weight gain upon administration of a PPAR-agonist comprising the step of determining whether said patient has a reference or variable allele at one or more polymorphic loci of the human PPAR-alpha polypeptide.

9. The method according to claim 8, wherein the presence of a variable allele at the polymorphic locus at amino acid position 162 of SEQ ID NO:

2 or 4, is indicative of a decreased risk of developing dose-dependent weight gain in a patient receiving PPAR-agonist therapy, whereas the presence of the reference allele at said polypeptide polymorphic position is indicative of an increased risk of developing dose-dependent weight gain in a patient receiving PPAR-agonist therapy.

10. An isolated polypeptide comprising a sequence selected from the group consisting of the polypeptide sequence provided as SEQ ID NO:

15, and SEQ ID NO;

17, wherein said polypeptide comprises at least one polymorphic locus, wherein said polymorphic locus is located at amino acid position 363.

11. A method of identifying a patient who may be at risk of developing dose-dependent weight gain upon administration of a PPAR-agonist comprising the step of determining whether said patient has a reference or variable allele at one or more polymorphic loci of the human glucocorticoid receptor polypeptide.

12. The method according to claim 11, wherein the presence of a variable allele at the polymorphic locus at amino acid position 363 of SEQ ID NO:

15 or 17, is indicative of an increased risk of developing dose-dependent weight gain in a patient receiving PPAR-agonist therapy, whereas the presence of the reference allele at said polypeptide polymorphic position is indicative of a decreased risk of developing dose-dependent weight gain in a patient receiving PPAR-agonist therapy.

19. A kit comprising the method of claim 3, 4, 5, 6, 8, 9, 11, 12, 13, 14, 15, 16, 17 or 18.

13. A method of identifying a patient who may be have a higher likelihood of achieving lower levels of glycosylated hemoglobin (HbA1C) upon administration of a PPAR-agonist comprising the step of determining whether said patient has a reference or variable allele at one or more polymorphic loci of the human glucocorticoid receptor polynucleotide.

14. The method according to claim 13, wherein the presence of a variable allele at said one or more polymorphic loci is indicative of an increased likelihood of achieving lower levels of glycosylated hemoglobin (HbA1C) in a patient receiving PPAR-agonist therapy, whereas the presence of a reference allele at said one or more polymorphic loci is indicative of a decreased likelihood of achieving lower levels of glycosylated hemoglobin (HbA1C) in a patient receiving PPAR-agonist therapy.

16. The method according to claim 13, wherein the presence of a variable allele at said one or more polymorphic loci is indicative of an increased likelihood of achieving lower levels of glycosylated hemoglobin (HbA1C) in a patient receiving PPAR-agonist therapy, whereas the presence of a reference allele at said one or more polymorphic loci is indicative of a decreased likelihood of achieving lower levels of glycosylated hemoglobin (HbA1C) in a patient receiving PPAR-agonist therapy.

15. A method of identifying a patient who may be have a higher likelihood of achieving lower levels of glycosylated hemoglobin (HbA1C) upon administration of a PPAR-agonist comprising the step of determining whether said patient has a reference or variable allele at one or more polymorphic loci of the human glucocorticoid receptor polypeptide.

17. A method of identifying the likelihood that a patient will achieve lower levels of glycosylated hemoglobin (HbA1C) upon administration of a PPAR-agonist comprising the step of determining the systemic cortisol level in a test sample from said patient and comparing said cortisol level to a reference or control sample, wherein elevated levels of cortisol in said test sample is indicative of an increased likelihood of said patient achieving lower levels of glycosylated hemoglobin (HbA1C), and an increased likelihood of having an increased response to PPAR-agonist therapy, relative to a patient having lower levels of cortisol.

18. A method of identifying the likelihood that a patient will be at risk of developing dose-dependent weight gain upon administration of a PPAR-agonist comprising the step of determining the systemic cortisol level in a test sample from said patient and comparing said cortisol level to a reference or control sample, wherein elevated levels of cortisol in said test sample is indicative of an increased risk of developing dose-dependent weight gain relative to a patient having lower levels of cortisol.