Methods to identify polynucleotide and polypeptide sequences which may be associated with physiological and medical conditions

• US 7,247,425 B2
• Filed: 06/30/2004
• Issued: 07/24/2007
• Est. Priority Date: 01/30/1998
• Status: Expired due to Fees

• Current Assignee: Evolutionary Genomics Incorporated
• Original Assignee: Evolutionary Genomics Incorporated
• Inventors: Messier, Walter
• Primary Examiner(s): Horlick; Kenneth R.
• Application Number:
  US10/883,576
• Publication Number:
  US 20050037400A1
• Time in Patent Office: 1,119 Days
• Field of Search: 435/6
• US Class Current: 435/5
• CPC Class Codes: G01N 2333/005 from viruses
• CPC Class Codes: G01N 2500/04 Screening involving studying the effect of compounds C directly on molecule A (e.g. C are potential ligands for a receptor A, or potential substrates for an enzyme A)
• CPC Class Codes: G01N 2500/10 involving cells
• CPC Class Codes: G01N 33/5005 involving human or animal cells immunoassay G01N33/56966; immunoassays of protozoa G01N33/56905; protozoa in screening assays C12Q1/025

Abstract

The present invention provides methods for identifying evolutionarily significant polynucleotide and polypeptide sequences in human and/or non-human primates which may be associated with a physiological condition, such as enhanced resistance to AIDS infection. The invention also provides methods for identifying evolutionarily significant polynucleotides with mutations that are correlated with susceptibility to diseases, such as ICAM 1. The methods employ comparison of human and non-human primate sequences using statistical methods. Sequences thus identified may be useful as host therapeutic targets and/or in screening assays.

Claims

1. A method of determining whether a polynucleotide sequence of a non-human primate which has been or may be associated with a physiological trait in the non-human primate has undergone evolutionarily significant change relative to humans that exhibit the physiological trait to a lesser degree, comprising:

(a) comparing the non-human polynucleotide sequence with the corresponding human primate polynucleotide sequence to identify any nucleotide changes, wherein the polynucleotide sequence is selected from the group consisting of ICAM-1 polynucleotide sequence, ICAM-2 polynucleotide sequence, ICAM-3 polynucleotide sequence, CD98 polynucleotide sequence, p44 polynucleotide sequence, IFN-p56k polynucleotide sequence, and Staf50 polynucleotide sequence; and

(b) determining whether said non-human nucleotide changes are evolutionarily significant, whereby a polynucleotide sequence of a non-human primate which has been or may be associated with a physiological trait in the non-human primate has undergone evolutionarily significant change relative to humans that exhibits the physiological trait to a lesser degree is identified.

2. The method of claim 1, wherein the polynucleotide sequence of a non-human primate is selected from the group consisting of SEQ ID NO:

2, SEQ ID NO;

4, SEQ ID NO;

5, SEQ ID NO;

58, SEQ ID NO;

61, SEQ ID NO;

64, SEQ ID NO;

67, SEQ ID NO;

70, SEQ ID NO;

73, SEQ ID NO;

79, SEQ ID NO;

82, SEQ ID NO;

37, SEQ ID NO;

43, SEQ ID NO;

31, and SEQ ID NO;

49.

3. A method of identifying an agent which may modulate a physiological trait, said method comprising contacting at least one agent to be tested with a cell that has been transfected with the corresponding human polynucleotide sequence of claim 1, wherein an agent is identified by its ability to modulate the function of the polynucleotide sequence.

4. The method of claim 3, wherein the physiological trait is resistance to the progression of a viral disease, the corresponding human polynucleotide is selected from the group consisting of ICAM-1 polynucleotide, ICAM-2 polynucleotide, and ICAM-3 polynucleotide, CD98 polynucleotide, p44 polynucleotide, IFN-p56k polynucleotide, and Staf50 polynucleotide, and the modulated function is increased resistance to the progression of a viral disease.

5. The method of claim 3, wherein the physiological trait is selected from the group consisting of binding of a polypeptide to its ligand, virus-mediated cellular pathogenesis, cell to cell infectivity, virus-mediated cell fusion, virus-mediated syncytia formation, and virus budding rate.

6. The method of claim 5, wherein said polypeptide is selected from the group consisting of ICAM-1, ICAM-2, ICAM-3, CD98, p44, IFN-p56k, and Staf50.

7. The method of claim 4, wherein the polynucleotide is a polynucleotide comprising a polynucleotide selected from the group consisting of SEQ ID NO.:

1, SEQ ID NO.;

55, SEQ ID NO.;

76, SEQ ID NO.;

34, SEQ ID NO.;

40, SEQ ID NO.;

46, and SEQ ID NO.;

52, or fragments thereofof about 18–

225 nucleotides and having at least one human nucleotide that corresponds to a non-human primate evolutionarily significant nucleotide change.

8. The method of claim 3, wherein the physiological trait is resistance to the progression of a viral disease, the polynucleotide is selected from the group consisting of CD98, p44, IFN-p56k, and Staf50, and the modulated function is increased resistance to the progression of hepatitis C—

caused hepatitis.

9. The method of claim 3, wherein the physiological trait is resistance to the progression of a viral disease, the polynucleotide is selected from the group consisting of CD98, p44, IFN-p56k, and Staf50, and the modulated function is increased resistance to the progression of AIDS.

10. The method of claim 9, wherein the polynucleotide is a polynucleotide selected from the group consisting of SEQ ID NO.:

34, SEQ ID NO.;

40, SEQ ID NO.;

46, and SEQ ID NO.;

52.

11. The method of claim 3, wherein the physiological trait is resistance to the progression of AIDS, the polynucleotide is selected from the group consisting of human ICAM-1 polynucleotide, human ICAM-2 polynucleotide, and human ICAM-3 polynucleotide, and the modulated function is increased resistance to the progression of AIDS.

12. The method of claim 11, wherein the polynucleotide is selected from the group consisting of SEQ ID NO.1, SEQ ID NO.:

55, SEQ ID NO.;

76, a polynucleotide encoding the polypeptide SEQ ID NO;

6, a polynucleotide encoding the polypeptide SEQ ID NO;

7, a polynucleotide encoding the polypeptide SEQ ID NO;

8, a polynucleotide encoding the polypeptide SEQ ID NO;

57, and a polynucleotide encoding the polypeptide SEQ ID NO;

78.

13. The method of claim 3, wherein the physiological trait is resistance to the progression of AIDS, the polynucleotide is a human ICAM-1 polynucleotide, and the modulated function is dimerization of two ICAM-1 polypeptides.

14. The method of claim 13, wherein the polynucleotide is a polynucleotide selected from the group consisting of SEQ ID NO.1, and a polynucleotide encoding the polypeptide SEQ ID NO:

6.

15. A method of identifying an agent which may modulate a physiological trait, said method comprising contacting at least one agent to be tested with a polypeptide encoded by a corresponding human polynucleotide sequence of claim 1, or a composition comprising said polypeptide, wherein an agent is identified by its ability to modulate function of the human polypeptide.

16. The method of claim 15, wherein the physiological trait is resistance to the progression of AIDS, the polynucleotide is selected from the group consisting of a human ICAM-1 polynucleotide, human ICAM-2 polynucleotide, and human ICAM-3 polynucleotide, and the modulated function is increased resistance to the progression of AIDS.

17. The method of claim 15, wherein the physiological trait is resistance to the progression of AIDS, the polynucleotide is a human ICAM-1 polynucleotide, and the modulated function is dimerization of two ICAM-1 polypeptides.

19. A method for identifying a target site on a human polypeptide which may be suitable for therapeutic intervention, comprising identifying amino acid changes in the human polypeptide corresponding to evolutionarily significant nucleotide changes identified according to the method of claim 1, as target sites.

20. A method for identifying a target site on a human polynucleotide which may be suitable for therapeutic intervention, comprising identifying nucleotide changes in the human polynucleotide that are evolutionarily significant according to the method of claim 1 as target sites.

21. A method of identifying an agent which may modulate a physiological trait, said method comprising contacting at least one agent to be tested with a cell that has been transfected with the human polynucleotide sequence of claim 1, wherein an agent is identified by its ability to modulate function of the polynucleotide.

22. A method of identifying an agent which may modulate a physiological trait, said method comprising contacting at least one agent to be tested with a polypeptide encoded by the polynucleotide sequence of claim 1, or a composition comprising said polypeptide, wherein an agent is identified by its ability to modulate function of the polypeptide.

18. A method of correlating a polynucleotide sequence of a non-human primate with greater resistance to progression of an infectious disease relative to humans, comprising:

(a) identifying a human polynucleotide sequence, wherein the expression is modulated upon infection of a human cell with an infectious agent that causes the infectious disease;

(b) comparing the human polynucleotide sequences of (a) with a corresponding polynucleotide sequence of a non-human primate that exhibits greater resistance to progression of disease caused by the infectious agent to identify any nucleotide changes; and

(c) determining whether said non-human primate nucleotide changes are evolutionarily significant, whereby the polynucleotide sequence of the non-human primate is correlated with greater resistance to progression of an infectious disease relative to humans.