Methods for Characterizing and Treating Cognitive Impairment In Aging and Disease

• US 20100081648A1
• Filed: 08/03/2006
• Published: 04/01/2010
• Est. Priority Date: 08/03/2005
• Status: Active Grant

• Current Assignee: Johns Hopkins University
• Original Assignee: Johns Hopkins University
• Inventors: Gallagher, Michela, Haberman, Rebecca
• Granted Patent: US 8,510,055 B2
• Time in Patent Office: Days
• US Class Current: 514/221
• CPC Class Codes: A61K 31/5513 1,4-Benzodiazepines, e.g. diazepam or clozapine
• CPC Class Codes: A61P 25/28 for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
• 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 2600/158 Expression markers
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/10 Signal processing, e.g. from mass spectrometry [MS] or from PCR

Abstract

This invention provides methods for identifying genes associated with cognitive impairment and for identifying compounds useful in the treatment of cognitive impairment. The methods can in particular be used to identify genes associated with, and compounds useful in treating, cognitive impairment in aging.

Claims

1. A method of identifying a gene or a plurality of genes associated with cognitive impairment in a mammal comprising the steps of:

(a) providing an AI population of aged mammals with cognitive impairment;

(b) providing an AU population of aged mammals without cognitive impairment;

(c) providing a Y population of young mammals;

(d) determining the abundance of a plurality of expressed gene products in one or more of the CA1, CA3, and DG hippocampal tissue of each mammal in the AI, AU and Y populations; and

(e) selecting a gene or a plurality of genes based on a significant increase or decrease in the relative abundance of the gene'"'"'s expressed gene product in the AI population of mammals relative to the combined AU and Y populations or in the AU population of mammals relative to the combined AI and Y populations.

3. The method according to claim 1 or 2, wherein the significance of the increase or decrease in the relative abundance is determined using a parametric test.

4. The method according to claim 3, wherein the parametric test is an analysis of variance (ANOVA).

5. The method according to claim 1 or 2, wherein the significance of the increase or decrease in relative abundance is determined using a non-parametric test.

6. The method according to claim 5, wherein the non-parametric test is selected from the group consisting of a Mann-Whitney U test, a Wilcoxon rank-sum test, a Wilcoxon matched pairs signed-rank test, a Mann-Whitney-Wilcoxon test, a Kruskal-Wallis analysis of variance by ranks, a Friedman two way analysis of variance, and a Kolmogorov-Smirnov test.

9. The method according to claim 1 or 2, wherein the abundance of the plurality of expressed gene products is determined by a method selected from the group consisting of microarray analysis, macroarray analysis, in situ hybridization histochemistry, fluorescent in situ hybridization (FISH), immunocytochemistry (ICC), enzyme linked immunosorbent assay (ELISA), immunoprecipitation, quantitative polymerase chain reaction (PCR), serial analysis of gene expression (SAGE) analysis, radioimmunoassay (RIA) and blot analysis.

10. The method according to any one of claims 1 to 9, wherein the mammal is an outbred strain of rat.

11. The method according to any one of claims 1 to 10, wherein the expressed gene products are RNAs.

12. The method according to any one of claims 1 to 11, wherein the expressed gene products are proteins, polypeptides or peptides.

13. A method of identifying a compound useful in the treatment of cognitive impairment comprising the steps of:

(a) determining the abundance or function of an expressed gene product in a mammalian cell of the mammalian cell'"'"'s homologue of a gene or a plurality of genes identified by the method of claim 1 or 2 to increase in abundance in the AI population relative to the combined AU and Y populations or to decrease in abundance in the AU population relative to the combined AI and Y populations or of a gene or genes selected from the group consisting of each of the individual genes listed in Tables 1, 3, 5, 8, 9, 11, 13, 16, 17, 19, 21, 24, 25, 27, 29, 32, 33, 35, 37, 40, 41, 43, 45 and 48 in the presence or absence of a candidate compound; and

(b) identifying a compound from any of the candidate compound(s) that significantly decreases that abundance or attenuates the function of that gene or its expressed gene product in the mammalian cell to which the candidate compound is administered.

14. A method of identifying a compound useful in the treatment of cognitive impairment comprising the steps of:

(a) determining the abundance or function of an expressed gene product in a mammalian cell of the mammalian cell'"'"'s homologue of a gene or a plurality of genes identified by the method of claim 1 or 2 to decrease in abundance in the AI population relative to the combined AU and Y populations or to increase in abundance in the AU population relative to the combined AI and Y populations or of a gene or genes selected from the group consisting of each of the individual genes listed in Tables 2, 4, 6, 7, 10, 12, 14, 15, 18, 20, 22, 23, 26, 28, 30, 31, 34, 36, 38, 39, 42, 44, 46 and 47 in the presence or absence of a candidate compound; and

(b) identifying a compound from any of the candidate compound(s) that significantly increases that abundance or enhances the function of that gene or its expressed gene product in the mammalian cell to which the candidate compound is administered.

15. The method according to claim 13 or 14, wherein the mammalian cell is selected from the group consisting of a neuronal cell and a glial cell.

16. The method according to claim 15, wherein the mammalian cell is a hippocampal cell.

17. The method according to claim 16, wherein the hippocampal cell is selected from the group of a CA1 cell, a CA3 cell or a DG cell.

18. A method of identifying a compound useful in the treatment of cognitive impairment comprising:

(a) determining the abundance or function of an expressed gene product, in the hippocampus of a mammal, of the mammal'"'"'s homologue of a gene or a plurality of genes identified by the method of claim 1 or 2 to increase in abundance in the AI population relative to the combined AU and Y populations or to decrease in abundance in the AU population relative to the combined AI and Y populations or a gene or genes selected from the group consisting of each of the individual genes listed in Tables 1, 3, 5, 8, 9, 11, 13, 16, 17, 19, 21, 24, 25, 27, 29, 32, 33, 35, 37, 40, 41, 43, 45 and 48 in the presence or absence of a candidate compound; and

(b) identifying a compound from any of the candidate compound(s) that significantly decreases that abundance or attenuates the function of that gene or its expressed gene product in the mammal to whom the candidate compound is administered.

19. A method of identifying a compound useful in the treatment of cognitive impairment comprising:

(a) determining the abundance or function of an expressed gene product, in the hippocampus of a mammal, of the mammal'"'"'s homologue of a gene or a plurality of genes identified by the method of claim 1 or 2 to decrease in abundance in the AI population relative to the combined AU and Y populations or to increase in abundance in the AU population relative to the combined AI and Y populations or a gene or genes selected from the group consisting of each of the individual genes listed in Tables 2, 4, 6, 7, 10, 12, 14, 15, 18, 20, 22, 23, 26, 28, 30, 31, 34, 36, 38, 39, 42, 44, 46 and 47 in the presence or absence of a candidate compound; and

(b) identifying a compound from any of the candidate compound(s) that significantly increases that abundance or enhances the function of that gene or its expressed gene product in the mammal to whom the candidate compound is administered.

20. The method according to claim 18 or 19, wherein the mammal is an aged mammal.

21. The method according to claim 20, wherein the aged mammal is cognitively impaired.

22. A method of identifying a compound useful in the treatment of cognitive impairment in aging comprising:

(a) determining the abundance or function of an expressed gene product, in the hippocampus of an aged mammal with cognitive impairment, of the mammal'"'"'s homologue of a gene or a plurality of genes identified by the method of claim 1 or 2 to increase in abundance in the AI population relative to the combined AU and Y populations or to decrease in abundance in the AU population relative to the combined AI and Y populations or a gene or genes selected from the group consisting of each of the individual genes listed in Tables 1, 3, 5, 8, 9, 11, 13, 16, 17, 19, 21, 24, 25, 27, 29, 32, 33, 35, 37, 40, 41, 43, 45 and 48 in the presence or absence of a candidate compound; and

(b) identifying a compound from among the candidate compound(s) that significantly decreases that abundance or attenuates the function of that gene or its expressed gene product in the aged mammal with cognitive impairment to whom the compound is administered relative to a member of the group consisting of an aged mammal without cognitive impairment, a young mammal, an aged cognitively impaired mammal in the absence of the compound, and two or more of them.

23. A method of identifying a compound useful in the treatment of cognitive impairment in aging comprising:

(a) determining the abundance or function of an expressed gene product, in the hippocampus of an aged mammal with cognitive impairment, of the mammal'"'"'s homologue of a gene or a plurality of genes identified by the method of claim 1 or 2 to decrease in abundance in the AI population relative to the combined AU and Y populations or to increase in abundance in the AU population relative to the combined AI and Y populations or a gene or genes selected from the group consisting of each of the individual genes listed in Tables 2, 4, 6, 7, 10, 12, 14, 15, 18, 20, 22, 23, 26, 28, 30, 31, 34, 36, 38, 39, 42, 44, 46 and 47 in the presence or absence of a candidate compound; and

(b) identifying a compound from among the candidate compound(s) that significantly increases that abundance or enhances the function of that gene or its expressed gene product in the aged mammal with cognitive impairment to whom the compound is administered relative to a member of the group consisting of an aged mammal without cognitive impairment, a young mammal, an aged cognitively impaired mammal in the absence of the compound, and two or more of them.

24. The method according to claim 22 or 23, wherein the compound does not significantly alter that abundance or function in a member of the group consisting of a young mammal, an aged cognitively unimpaired mammal and both, to whom the candidate compound is administered.

25. A method of identifying a compound useful in the treatment of cognitive impairment comprising:

(a) determining the cognitive status of a mammal in the presence or absence of a candidate compound believed to decrease the abundance or attenuate the function of an expressed gene product of a gene or a plurality of genes identified by the method of claim 1 or 2 to increase in abundance in the AI population relative to the combined AU and Y populations or to decrease in abundance in the AU population relative to the combined AI and Y populations or a gene or genes selected from the group consisting of each of the individual genes listed in Tables 1, 3, 5, 8, 9, 11, 13, 16, 17, 19, 21, 24, 25, 27, 29, 32, 33, 35, 37, 40, 41, 43, 45 and 48; and

(b) identifying the compound from among the candidate compound(s) that beneficially alters the cognitive status of the mammal to whom the compound is administered.

26. A method of identifying a compound useful in the treatment of cognitive impairment comprising:

(a) determining the cognitive status of a mammal in the presence or absence of a candidate compound believed to increase the abundance or enhance the function of an expressed gene product of a gene or a plurality of genes identified by the method of claim 1 or 2 to decrease in abundance in the AI population relative to the combined AU and Y populations or to increase in abundance in the AU population relative to the combined AI and Y populations or a gene or genes selected from the group consisting of each of the individual genes listed in Tables 2, 4, 6, 7, 10, 12, 14, 15, 18, 20, 22, 23, 26, 28, 30, 31, 34, 36, 38, 39, 42, 44, 46 and 47; and

(b) identifying the compound from among the candidate compound(s) that beneficially alters the cognitive status of the mammal to whom the compound is administered.

27. The method according to claim 25 or 26, wherein the mammal is an aged mammal.

28. The method according to claim 27, wherein the aged mammal is cognitively impaired.

29. A method of identifying a compound useful in the treatment of cognitive impairment in aging comprising:

(a) determining the cognitive status of an aged mammal with cognitive impairment, in the presence or absence of a candidate compound believed to decrease the abundance or attenuate the function of an expressed gene product of a gene or a plurality of genes identified by the method of claim 1 or 2 to increase in abundance in the AI population relative to the combined AU and Y populations or to decrease in abundance in the AU population relative to the combined AI and Y populations or a gene or genes selected from the group consisting of each of the individual genes listed in Tables 1, 3, 5, 8, 9, 11, 13, 16, 17, 19, 21, 24, 25, 27, 29, 32, 33, 35, 37, 40, 41, 43, 45 and 48; and

(b) identifying a compound from among the candidate compound(s) that beneficially alters the cognitive function in the aged mammal with cognitive impairment to whom the compound is administered relative to a member of the group consisting of an aged mammal without cognitive impairment, a young mammal, an aged cognitively impaired mammal to whom the compound is not administered, and two or more of them.

30. A method of identifying a compound useful in the treatment of cognitive impairment in aging comprising:

(a) determining the cognitive status of an aged mammal with cognitive impairment, in the presence or absence of a candidate compound believed to increase the abundance or enhance the function of an expressed gene product of a gene or a plurality of genes identified by the method of claim 1 or 2 to decrease in abundance in the AI population relative to the combined AU and Y populations or to increase in abundance in the AU population relative to the combined AI and Y populations or a gene or genes selected from the group consisting of each of the individual genes listed in Tables 2, 4, 6, 7, 10, 12, 14, 15, 18, 20, 22, 23, 26, 28, 30, 31, 34, 36, 38, 39, 42, 44, 46 and 47; and

(b) identifying a compound from among the candidate compound(s) that beneficially alters the cognitive function in the aged mammal with cognitive impairment to whom the compound is administered relative to a member of the group consisting of an aged mammal without cognitive impairment, a young mammal, an aged cognitively impaired mammal to whom the compound is not administered, and two or more of them.

31. The method according to claim 29 or 30, wherein the compound does not significantly alter the cognitive status of a member of the group consisting of a young mammal, an aged cognitively unimpaired mammal, and both, to whom the compound is administered.

32. The method according to any one of claims 25 to 31, wherein cognitive function is hippocampal-dependent function.

33. The method according to claim 32, wherein the hippocampal-dependent function is selected from the group consisting of spatial memory acquisition, long-term spatial memory, and spatial memory retrieval.

34. The method according to any one of claims 19 to 33, wherein the mammal is an outbred strain of rat.

35. The method according to any one of claims 19 to 33, wherein the mammal is a human.

36. The method according to any one of claims 19 to 24, wherein the abundance is determined in CA1, CA3 or DG hippocampal tissue.

37. The method according to claim 1, wherein the identified gene(s) are selected from the group consisting of each of the individual genes listed in Tables 1-48.

39. The method according to any one of claims 14, 19, 23, 26 and 30 wherein the expressed gene product is the product of the GABA-5 α

5 receptor gene (GENBANK®

accession number NM_—

017295) or its homologues.

2. A method of identifying a gene or a plurality of genes associated with cognitive impairment in a mammal comprising the steps of:

(a) providing an AI population of aged mammals with cognitive impairment;

(b) providing an AU population of aged mammals without cognitive impairment;

(c) providing a Y population of young mammals;

(d) determining the abundance of a plurality of expressed gene products in one or more of the CA1, CA3, and DG hippocampal tissue of each mammal in the AI, AU and Y populations;

(e) selecting a gene or a plurality of genes based on a significant increase or decrease in the relative abundance of the gene'"'"'s expressed gene product in the AI population of mammals relative to the combined AU and Y populations or in the AU population of mammals relative to the combined AI and Y populations;

(f) correlating the increased or decreased abundance of a selected gene'"'"'s expressed gene products with the level of cognitive impairment in each mammal of the AU and AI populations; and

(g) selecting a gene or a plurality of genes based on a significant correlation between the relative abundance of the gene'"'"'s expressed gene product and the level of cognitive impairment in the mammals.

7. The method according to claim 2, wherein the significance of the correlation is determined using a parametric Pearson correlation coefficient.

8. The method according to claim 2, wherein the significance of the correlation is determined using a nonparametric Spearman rank correlation coefficient.

38. The method according to claim 2, wherein the identified gene(s) are selected from the group consisting of each of the individual genes listed in Tables 1, 2, 5, 6, 9, 10, 13, 14, 17, 18, 21, 22, 25, 26, 29, 30, 33, 34, 37, 38, 41, 42, 45 and 46.

40. A method for treating cognitive impairment in a mammal in need of such treatment, the method comprising the step of treating the mammal with GABA-5 α

5 receptor agonist.

41. The method according to claim 40, wherein the mammal is a human.

42. The method according to claims 40 and 41, wherein the agonist is selected from the group consisting of 1-methyl-7-acetyleno-5-phenyl-1,3-dihydro-benzo[e]-1,4-diazepin-2-one, S(CH₂)₃OH, and 8-ethylthio-3-methyl-5-(1-oxidopyridin-2-yl)-3,4-dihydronaphthalen-1(2H)-one.

43. A pharmaceutical composition for treating cognitive impairment, the composition comprising pharmaceutically effective amount of a GABA-5 α

5 receptor agonist and a pharmaceutically acceptable carrier.

44. The pharmaceutical composition according to claim 43, wherein the agonist is selected from the group consisting of 1-methyl-7-acetyleno-5-phenyl-1,3-dihydro-benzo[e]-1,4-diazepin-2-one, S(CH₂)₃OH, and 8-ethylthio-3-methyl-5-(1-oxidopyridin-2-yl)-3,4-dihydronaphthalen-1(2H)-one.