EGR genes as targets for the diagnosis and treatment of schizophrenia

• US 20050158733A1
• Filed: 06/30/2004
• Published: 07/21/2005
• Est. Priority Date: 06/30/2003
• Status: Abandoned Application

• Current Assignee: Trustees Of Columbia University In The City Of New York (Columbia University), Massachusetts Institute of Technology, Rockefeller University
• Original Assignee: Massachusetts Institute of Technology
• Inventors: Hall, Diana, Karayiorgou, Maria, Tonegawa, Susumu, Gerber, David J., Gogos, Joseph A.
• Application Number:
  US10/881,185
• Publication Number:
  US 20050158733A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: A61P 25/18 Antipsychotics, i.e. neuroleptics; Drugs for mania or schizophrenia
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• 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

The present invention provides targets, methods, and reagents for the diagnosis and treatment of schizophrenia and related conditions. The invention provides methods for the diagnosis of schizophrenia and susceptibility to schizophrenia by detection of polymorphisms, mutations, variations, alterations in expression, etc., in genes encoding an EGR molecule or an EGR interacting molecule, or polymorphisms linked to such genes. The invention provides oligonucleotides, arrays, and antibodies for detection of polymorphisms and variants. The invention provides transgenic mice having alterations in such genes. The invention also provides methods of treating schizophrenia by administering compounds that target these genes. The invention further provides screening methods for identifying such compounds and compounds obtained by perfoming the screens.

Claims

1. A method for the diagnosis of schizophrenia or schizophrenia susceptibility comprising:

(i) providing a sample obtained from a subject to be tested for schizophrenia or schizophrenia susceptibility; and

(ii) detecting a polymorphic variant of a polymorphism in a coding or noncoding portion of a gene encoding an EGR molecule or encoding an EGR interacting molecule, or detecting a polymorphic variant of a polymorphism in a genomic region linked to such a gene, in the sample.

2. The method of claim 1, wherein the gene or a portion thereof is coincident with a schizophrenia susceptibility locus.

3. The method of claim 2, wherein the locus is a genetically identified locus.

4. The method of claim 1, wherein the polymorphism occurs in a coding or noncoding portion of a gene encoding an EGR molecule or encoding an EGR interacting molecule.

5. The method of claim 4, wherein the polymorphism occurs in a coding portion of the gene.

6. The method of claim 5, wherein the polymorphic variant results in an alteration in the amino acid sequence of the EGR protein or EGR interacting molecule encoded by the gene.

7. The method of claim 1, wherein the polymorphism occurs in a genomic region linked to a gene encoding an EGR molecule or encoding an EGR interacting molecule.

8. The method of claim 7, wherein the polymorphism is genetically linked to the gene.

9. The method of claim 1, wherein the gene encodes a polypeptide selected from the group consisting of:

EGR1, EGR2, EGR3, EGR4, NAB1, and NAB2.

10. The method of claim 1, wherein the polymorphism is selected from the markers listed in any of Tables 2, 3, 4, and 5.

11. The method of claim 1, wherein the method is performed so as to detect, either in individually or in parallel, polymorphic variants of multiple polymorphisms in a coding or noncoding portion of one or more genes encoding an EGR molecule or encoding an EGR interacting molecule, or in a genomic region linked to such a gene, in the sample.

12. The method of claim 1, wherein the detecting step comprises:

contacting the sample with an oligonucleotide array, wherein the array comprises a plurality of oligonucleotides designed to specifically detect polymorphic variants of multiple polymorphisms in a coding or noncoding portion of one or more genes encoding an EGR molecule or encoding an EGR interacting molecule, or in a genomic region linked to such a gene, in the sample.

13. The method of claim 11 or 12, wherein the multiple polymorphisms comprise a risk haplotype for schizophrenia.

14. The method of claim 13, wherein at least one of the polymorphisms is selected from markers listed in any of Tables 2, 3, 4, or 5.

15. The method of claim 1, wherein the detecting step comprises:

contacting the sample with an oligonucleotide, wherein the oligonucleotide is designed to specifically detect or amplify a polymorphic variant of the polymorphism.

16. The method of claim 1, wherein the detecting step comprises:

contacting the sample with an oligonucleotide array, wherein the array comprises one or more oligonucleotides designed to specifically detect a polymorphic variant of the polymorphism.

17. The method of claim 1, further comprising the step of:

determining that the subject is susceptible to or suffers from schizophrenia if the polymorphic variant is associated with an increased risk of schizophrenia.

42. The method of any of claim 27, further comprising the step of:

identifying the subject as at risk of or suffering from schizophrenia using the method of claim 1 or any other appropriate method.

66. The method of claim 65, further comprising the step of identifying the subject as at risk of or suffering from schizophrenia according to the method of claim 1.

18. A method for the diagnosis of schizophrenia or schizophrenia susceptibility comprising:

(i) providing a sample obtained from a subject to be tested for schizophrenia or schizophrenia susceptibility; and

(ii) detecting an alteration or variation in expression or activity of an EGR molecule or an EGR interacting molecule, in the sample, relative to the expression or activity of the EGR molecule or EGR interacting molecule that would be expected in a sample obtained from a normal subject.

19. The method of claim 18, wherein the alteration or variation comprises an increase or decrease in abundance of an mRNA that encodes the EGR molecule or EGR interacting molecule, or an increase or decrease in abundance of the EGR molecule or EGR interacting molecule.

20. The method of claim 18, wherein the EGR molecule or EGR interacting molecule is selected from the group consisting of:

EGR1, EGR2, EGR3, EGR4, NAB 1, and NAB2.

21. The method of claim 18, wherein the alteration or variation results in an increase or decrease in transcription of an EGR target gene.

22. A method for the diagnosis of schizophrenia or schizophrenia susceptibility comprising:

(i) providing a sample obtained from a subject to be tested for schizophrenia or schizophrenia susceptibility; and

(ii) detecting an alteration or variation in an EGR molecule or EGR interacting molecule in the sample.

23. The method of claim 22, wherein the alteration or variation comprises an alteration or variation in the amino acid sequence, size, or tissue or subcellular distribution of the EGR molecule or EGR interacting molecule.

24. The method of claim 22, wherein the EGR molecule or EGR interacting molecule is selected from the group consisting of:

EGR1, EGR2, EGR3, EGR4, NAB1, and NAB2.

25. The method of claim 22, wherein the detecting step comprises employing an antibody that specifically binds to the EGR molecule or EGR interacting molecule.

26. The method of claim 22, wherein the detecting step comprises employing an antibody that specifically binds to a variant of the EGR molecule or EGR interacting molecule, the presence of which variant is indicative of susceptibility or presence of schizophrenia.

27. A method for treating schizophrenia or susceptibility to schizophrenia comprising:

providing a subject at risk of or suffering from schizophrenia; and

administering a compound that modulates activity or abundance of an EGR molecule or EGR interacting molecule to the subject.

28. The method of claim 27, wherein the compound enhances activity or abundance of the EGR molecule or EGR interacting molecule.

29. The method of claim 27, wherein the compound reduces activity or abundance of the EGR molecule or EGR interacting molecule.

30. The method of claim 27, wherein the compound modulates activity of the EGR molecule or EGR interacting molecule.

31. The method of claim 30, wherein the compound enhances activity of the EGR molecule or EGR interacting molecule.

32. The method of claim 30, wherein the compound reduces activity of the EGR molecule or EGR interacting molecule.

33. The method of claim 27, wherein the compound modulates expression of the EGR molecule or EGR interacting molecule.

34. The method of claim 33, wherein the compound enhances expression of the EGR molecule or EGR interacting molecule.

35. The method of claim 33, wherein the compound reduces expression of the EGR molecule or EGR interacting molecule.

36. The method of claim 27, wherein the compound binds to the EGR molecule or EGR interacting molecule.

37. The method of claim 27, wherein the compound disrupts binding of EGR molecule or EGR interacting molecule to a second molecule.

38. The method of claim 37, wherein the compound disrupts binding of an EGR molecule and either NAB1 or NAB2.

39. The method of claim 27, wherein the EGR molecule or EGR interacting molecule is selected from the group consisting of:

EGR1, EGR2, EGR3, EGR4, NAB1, and NAB2.

40. The method of claim 27, wherein the administering step comprises introducing a gene therapy vector into the subject.

41. The method of claim 40, wherein the gene therapy vector comprises a nucleic acid that encodes an EGR molecule or EGR interacting molecule or an expression product of a target gene of an EGR molecule or an EGR interacting molecule.

43. A method of identifying a polymorphism useful in diagnosis of schizophrenia or susceptibility to schizophrenia comprising steps of:

identifying one or more polymorphisms in or linked to a gene encoding an EGR molecule or EGR interacting molecule;

providing a set of samples including samples obtained from subjects affected with schizophrenia;

testing the samples for linkage or association of one or more variants of the polymorphism with schizophrenia; and

identifying the polymorphism as useful in diagnosis of schizophrenia if linkage or association exists between one or more variants of the polymorphism and schizophrenia susceptibility.

44. A method of identifying a mutation that contributes to or causes schizophrenia or susceptibility to schizophrenia comprising steps of:

identifying a polymorphism in or linked to a gene encoding an EGR molecule or EGR interacting molecule;

determining that a polymorphic variant of the polymorphism is linked to or associated with susceptibilty to schizophrenia;

sequencing the gene and optionally regulatory regions of the gene in a sample obtained from one or more subjects suffering from schizophrenia;

comparing the sequence obtained with a normal or wild type sequence of the same gene;

identifying the polymorphic variant as representing a mutation that causes or contributes to schizophrenia if the sequence obtained in the sequencing step differs from the normal or wild type sequence.

45. A method for identifying a candidate compound for treatment of schizophrenia or susceptibility to schizophrenia comprising steps of:

providing a biological system comprising an EGR molecule and an EGR reporter;

contacting the biological system with a compound;

comparing the transcriptional response of the reporter in the presence of the compound with the response or expected response in the absence of the compound; and

identifying the compound as a candidate compound for treatment of schizophrenia or susceptibility to schizophrenia if the transcriptional response in the presence of the compound is different from the transcriptional response that occurs or would be expected in the absence of the compound.

46. The method of claim 45, wherein the biological system is a cell or population of cells.

47. The method of claim 45, wherein the biological system further comprises an NAB molecule.

52. The method of any of claims 45, 48, or 51, further comprising the step of testing the compound in an animal model for schizophrenia or in human subjects at risk of or suffering from schizophrenia.

63. A compound identified according to the method of any of claims 45, 48, 51, 53, or 54, or a derivative thereof, wherein the derivative optionally displays enhanced bioavailability, enhanced ability to cross the blood-brain barrier, or an improved safety profile.

64. A pharmaceutical composition comprising:

the compound of claim 63;

and

a pharmaceutically acceptable carrier.

65. A method of treating schizophrenia or susceptibility to schizophrenia comprising steps of:

providing a subject at risk of or suffering from schizophrenia; and

administering any of the pharmaceutical compositions of claim 64 to the subject either alone or concurrently with a second compound for treatment of schizophrenia or schizophrenia susceptibility or a compound that reduces side effects of such a compound.

48. A method of identifying a candidate compound for treatment of schizophrenia or susceptibility to schizophrenia comprising steps of:

providing a biological system comprising an EGR molecule and an endogenous EGR modulator;

contacting the biological system with the compound;

comparing extent or rate of binding of the EGR molecule and the endogenous EGR modulator in the presence of the compound with the extent or rate of binding that occurs or would be expected to occur in the absence of the compound; and

identifying the compound as a candidate compound for treatment of schizophrenia or susceptibility to schizophrenia if the extent or rate of binding of the EGR molecule and the endogenous EGR inhibitor in the presence of the compound is different from the extent or rate of binding that occurs or would be expected in the absence of the compound.

49. The method of claim 48, wherein the endogenous EGR modulator is an NAB protein.

50. The method of claim 48, wherein the comparing step comprises performing a two or three hybrid screen.

51. A method for identifying a candidate compound for treatment of schizophrenia or schizophrenia susceptibility comprising steps of:

providing a molecular structure of an EGR molecule;

identifying a structure that is expected to bind to the EGR molecule or to prevent binding of the EGR molecule to an EGR interacting molecule; and

selecting a compound having such a structure as a candidate compound for treatment of schizophrenia or schizophrenia susceptibility.

53. A method of identifying a compound for treatment of schizophrenia comprising steps of:

providing a subject or subjects;

administering a candidate compound to the subject or subjects, wherein the candidate compound modulates activity or abundance of an EGR molecule or EGR interacting molecule;

comparing severity or incidence of the phenotype in the subject or subjects to severity or incidence of the phenotype to that existing or expected to exist in a subject or subjects to which the candidate compound is not administered; and

identifying the candidate compound as a compound for the treatment of schizophrenia or schizophrenia susceptibility if severity or incidence of the phenotype in the subject or subjects is less than that existing or expected to exist in a subject or subjects to which the compound is not administered.

54. A method of identifying a compound for treatment of schizophrenia comprising steps of:

providing a subject or subjects at risk of or exhibiting one or more phenotypes suggestive of schizophrenia, wherein the subject or subjects have an alteration in at least one EGR molecule or EGR interacting molecule or in a gene encoding such a molecule;

administering a candidate compound to the subject or subjects;

comparing severity or incidence of the phenotype in the subject or subjects to severity or incidence of the phenotype to that existing or expected to exist in a subject or subjects to which the candidate compound is not administered; and

identifying the candidate compound as a compound for the treatment of schizophrenia or schizophrenia susceptibility if severity or incidence of the phenotype in the subject or subjects is less than that existing or expected to exist in a subject or subjects to which the compound is not administered.

55. The method of claim 54, wherein the alteration is an alteration in expression level or expression pattern.

56. The method of claim 54, wherein the alteration is an alteration in amino acid sequence.

57. The method of claim 54, wherein the subject or subjects exhibit a polymorphic variant of a gene encoding an EGR molecule or EGR interacting molecule, wherein presence of the variant is associated with one or more phenotypes suggestive of schizophrenia.

58. The method of claim 54, wherein the subject or subjects are mice.

59. The method of claim 54, wherein the subject or subjects are humans.

60. The method of claim 54, wherein the subject or subjects are genetically engineered.

61. The method of claim 54, wherein the subject or subjects have an alteration in at least two molecules selected from the group consisting of EGR molecules and EGR interacting molecules.

62. The method of claim 54, wherein the subject or subjects are deficient in expression of at least one EGR molecule or EGR interacting molecule.

67. An oligonucleotide designed to specifically detect or amplify a naturally occurring polymorphic variant of a polymorphism in a coding or noncoding portion of a gene encoding an EGR molecule or EGR interacting molecule, or a polymorphic variant of a polymorphism in a genomic region linked to such a gene, wherein the gene or a portion thereof is coincident with a schizophrenia susceptibility locus.

68. The oligonucleotide of claim 67, wherein the gene is selected from the group consisting of:

EGR1, EGR2, EGR3, EGR4, NAB 1, and NAB2.

69. The oligonucleotide of claim 68, wherein the polymorphism is the selected from the markers listed in any of Tables 2, 3, 4, and 5.

74. A pair of oligonucleotides as set forth in claim 67 or 70, wherein the oligonucleotides hybridize to opposite DNA strands on either side of the polymorphic site.

75. A kit comprising the oligonucleotide of claim 67 or 70 and one or more items selected from the group consisting of:

packaging and instructions for use, a buffer, nucleotides, a polymerase, an enzyme, a positive control sample, a negative control sample, and a negative control primer or probe.

76. An oligonucleotide array comprising a plurality of oligonucleotides as set forth in claim 67 or 70.

77. The oligonucleotide array of claim 76, wherein the oligonucleotides detect polymorphic variants at a plurality of different polymorphic sites.

78. A kit comprising the oligonucleotide array of claim 76 and one or more items selected from the group consisting of:

packaging and instructions for use, a buffer, nucleotides, a polymerase, an enzyme, a positive control sample, a negative control sample, and a negative control primer or probe.

70. An oligonucleotide designed to specifically detect or amplify a naturally occurring nucleic acid region comprising a polymorphic site in a coding or noncoding portion of a gene encoding an EGR molecule or EGR interacting molecule, or a polymorphic variant of a polymorphism in a genomic region linked to such a gene, wherein the gene or a portion thereof is coincident with a schizophrenia susceptibility locus.

71. The oligonucleotide of claim 70, wherein the schizophrenia susceptibility locus is genetically identified.

72. The oligonucleotide of claim 70, wherein the gene is selected from the group consisting of:

EGR1, EGR2, EGR3, EGR4, NAB1, and NAB2.

73. The oligonucleotide of claim 72, wherein the polymorphism is the selected from the markers listed in any of Tables 2, 3, 4, and 5.

79. A primer that terminates at the nucleotide position immediately adjacent to a naturally occurring polymorphic site on the 3′

side and extends at least 8 and less than 100 nucleotides in the 5′

direction from this site, wherein the polymorphic site is the site of a polymorphism in a coding or noncoding portion of a gene encoding an EGR molecule or EGR interacting molecule or is the site of a polymorphism in a genomic region linked to such a gene.

80. The primer of claim 79, wherein the gene or a portion thereof is coincident with a schizophrenia susceptibility locus.

81. The primer of claim 80, wherein the schizophrenia susceptiblity locus is genetically identified.

82. The primer of claim 80, wherein the gene is selected from the group consisting of:

EGR1, EGR2, EGR3, EGR4, NAB1, and NAB2.

83. The primer of claim 80, wherein the polymorphism is the selected from the markers listed in any of Tables 2, 3, 4, and 5.

84. A pair of primers as set forth in claim 79, wherein the primers hybridize to opposite DNA strands adjacent to the location of the polymorphic site.

85. A kit comprising the primer of claim 79 and one or more items selected from the group consising of:

packaging and instructions for use, a buffer, nucleotides, a polymerase, an enzyme, a positive control sample, a negative control sample, and a negative control primer or probe.

86. An siRNA or shRNA molecule targeted to a transcript encoding an EGR molecule or EGR interacting molecule.

87. The siRNA or shRNA molecule of claim 86, wherein the EGR molecule or EGR interacting molecule is encoded by a gene that is coincident with a schizophrenia susceptibility locus.

88. The siRNA or shRNA molecule of claim 87, wherein the schizophrenia susceptibility locus is genetically identified.

89. The siRNA or shRNA molecule of claim 86, wherein the molecule is selectively or specifically targeted to a transcript encoding a polymorphic variant of such a transcript, wherein existence of the polymorphic variant in a subject is indicative of susceptibility to or presence of schizophrenia.

90. The siRNA or shRNA molecule of claim 86, wherein the transcript encodes a molecule selected from the group consisting of:

EGR1, EGR2, EGR3, EGR4, NAB1, and NAB2.

91. A kit comprising the siRNA or shRNA molecule of claim 86 and one or more items selected from the group consisting of:

packaging and instructions for use, a buffer, a positive control sample, and a negative control siRNA or shRNA.

92. An antibody that specifically binds to a variant of an EGR molecule or EGR interacting molecule, wherein the calcineurin subunit or calcineurin interacting molecule is encoded by a gene comprising a polymorphic variant, wherein existence of the polymorphic variant in a subject is indicative of susceptibility to or presence of schizophrenia.

93. The antibody of claim 92, wherein the calcineurin subunit or calcineurin interacting molecule is selected from the group consisting of:

EGR1, EGR2, EGR3, EGR4, NAB 1, and NAB2.

94. A kit comprising the antibody of claim 92 and one or more items selected from the group consisting of:

packaging and instructions for use, a buffer, a substrate, a secondary antibody, an enzyme, a positive control sample, a negative control sample, and a negative control antibody.

95. A database comprising a list of polymorphic sequences stored on a computer-readable medium, wherein the polymorphic sequences occur in a coding or noncoding portion of a gene encoding an EGR molecule or EGR interacting molecule, or in a genomic region linked to such a gene, and wherein the list is largely or entirely limited to polymorphisms have been identified as useful in performing genetic diagnosis of schizophrenia or susceptibility to schizophrenia, or for performing genetic studies of schizophrenia or susceptibility to schizophrenia.