Translational gene mapping of cognitive decline

Neurobiology of Aging

Volumn 29, Issue 4, 2008, Pages 524-541

  Wilmot, Beth ^a   McWeeney, Shannon K ^a   Nixon, Randal R ^a   Montine, Thomas J ^b   Laut, Jamie ^c   Harrington, Christina A ^a   Kaye, Jeffrey A ^c   Kramer, Patricia L ^a,c  

^a OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

Author keywords

Alzheimer's disease; Cognitive decline; Cognitive reserve; Gene expression profiling; Healthy brain aging; Intersectin 1; Synaptic plasticity

Indexed keywords

INTERSECTIN;

AGING; ALZHEIMER DISEASE; ARTICLE; COGNITION; DOWN REGULATION; GENE EXPRESSION; GENE MAPPING; HUMAN; NERVE CELL PLASTICITY; NEUROFIBRILLARY TANGLE; PHENOTYPE; PRIORITY JOURNAL; RNA TRANSLATION; UPREGULATION;

AGED; AGED, 80 AND OVER; BRAIN; CHROMOSOME MAPPING; COGNITION DISORDERS; FEMALE; GENE EXPRESSION PROFILING; HUMANS; MALE; PROTEIN BIOSYNTHESIS;

EID: 39749187335     PISSN: 01974580     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.neurobiolaging.2006.11.008     Document Type: Article

References (73)

1. Anon., 1997. Consensus recommendations for the postmortem diagnosis of Alzheimer's disease. The National Institute on Aging, and Reagan Institute Working Group on Diagnostic Criteria for the Neuropathological Assessment of Alzheimer's disease. Neurobiol. Aging 18 (4 Suppl.), S1-S2.
2. Bannai H., Fukatsu K., Mizutani A., Natsume T., Iemura S., Ikegami T., Inoue T., and Mikoshiba K. An RNA-interacting protein, SYNCRIP (heterogeneous nuclear ribonuclear protein Q1/NSAP1) is a component of mRNA granule transported with inositol 1,4,5-trisphosphate receptor type 1 mRNA in neuronal dendrites. J. Biol. Chem. 279 51 (2004) 53427-53434
3. Beissbarth T., and Speed T.P. GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 20 9 (2004) 1464-1465
4. Benjamini Y., and Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Annal. Stat. 29 4 (2001) 1165-1188
5. Bernardini S., Bellincampi L., Ballerini S., Federici G., Iori R., Trequattrini A., Ciappi F., Baldinetti F., Bossu P., Caltagirone C., and Spalletta G. Glutathione S-transferase P1 *C allelic variant increases susceptibility for late-onset Alzheimer disease: association study and relationship with apolipoprotein E epsilon4 allele. Clin. Chem. 51 6 (2005) 944-951
6. Bertram L., and Tanzi R.E. Alzheimer's disease: one disorder, too many genes?. Hum. Mol. Genet. 13 Spec No. 1 (2004) R135-R141
7. Bierer L.M., Hof P.R., Purohit D.P., Carlin L., Schmeidler J., Davis K.L., and Perl D.P. Neocortical neurofibrillary tangles correlate with dementia severity in Alzheimer's disease. Arch. Neurol. 52 1 (1995) 81-88
8. Blalock E.M., Geddes J.W., Chen K.C., Porter N.M., Markesbery W.R., and Landfield P.W. Incipient Alzheimer's disease: microarray correlation analyses reveal major transcriptional and tumor Suppressor responses. Proc. Natl. Acad. Sci. USA 101 7 (2004) 2173-2178
9. Braak H., and Braak E. Argyrophilic grain disease: frequency of occurrence in different age categories and neuropathological diagnostic criteria. J. Neural. Trans. 105 8-9 (1998) 801-819
10. Carey R.M., Balcz B.A., Lopez-Coviella I., and Slack B.E. Inhibition of dynamin-dependent endocytosis increases shedding of the amyloid precursor protein ectodomain and reduces generation of amyloid beta protein. BMC Cell. Biol. 6 (2005) 30
11. Cataldo A.M., Peterhoff C.M., Troncoso J.C., Gomez-Isla T., Hyman B.T., and Nixon R.A. Endocytic pathway abnormalities precede amyloid beta deposition in sporadic Alzheimer's disease and Down syndrome: differential effects of APOE genotype and presenilin mutations. Am. J. Pathol. 157 1 (2000) 277-286
12. Cheung V.G., Jen K.Y., Weber T., Morley M., Devlin J.L., Ewens K.G., and Spielman R.S. Genetics of quantitative variation in human gene expression. Cold Spring Harb. Symp. Quant. Biol. 68 (2003) 403-407
13. Chyung J.H., and Selkoe D.J. Inhibition of receptor-mediated endocytosis demonstrates generation of amyloid beta-protein at the cell surface. J. Biol. Chem. 278 51 (2003) 51035-51043
14. Colangelo V., Schurr J., Ball M.J., Pelaez R.P., Bazan N.G., and Lukiw W.J. Gene expression profiling of 12633 genes in Alzheimer hippocampal CA1: transcription and neurotrophic factor down-regulation and up-regulation of apoptotic and pro-inflammatory signaling. J. Neurosci. Res. 70 3 (2002) 462-473
15. Dallas P.B., Gottardo N.G., Firth M.J., Beesley A.H., Hoffmann K., Terry P.A., Freitas J.R., Boag J.M., Cummings A.J., and Kees U.R. Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR-how well do they correlate?. BMC Genomics 6 1 (2005) 59
16. de la Monte S.M., and Wands J.R. Review of insulin and insulin-like growth factor expression, signaling, and malfunction in the central nervous system: relevance to Alzheimer's disease. J. Alzheimers Dis. 7 1 (2005) 45-61
17. Dimakopoulos A.C. Protein aggregation in Alzheimer's disease and other neuropathological disorders. Curr. Alzheimer Res. 2 1 (2005) 19-28
18. Dresios J., Aschrafi A., Owens G.C., Vanderklish P.W., Edelman G.M., and Mauro V.P. Cold stress-induced protein Rbm3 binds 60S ribosomal subunits, alters microRNA levels, and enhances global protein synthesis. Proc. Natl. Acad. Sci. USA 102 6 (2005) 1865-1870
19. Dudoit S., Yang Y., Callow M., and Speed T. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica 12 (2002) 111-139
20. Dunckley T., Beach T.G., Ramsey K.E., Grover A., Mastroeni D., Walker D.G., Lafleur B.J., Coon K.D., Brown K.M., Caselli R., Kukull W., Higdon R., McKeel D., Morris J.C., Hulette C., Schmechel D., Reiman E.M., Rogers J., and Stephan D.A. Gene expression correlates of neurofibrillary tangles in Alzheimer's disease. Neurobiol. Aging (2005)
21. Farrall M. Quantitative genetic variation: a post-modern view. Hum. Mol. Genet. 13 Suppl. 1 (2004) R1-R7
22. Fathallah-Shaykh H.M. Microarrays: applications and pitfalls. Arch. Neurol. 62 11 (2005) 1669-1672
23. Gautier L., Cope L., Bolstad B.M., and Irizarry R.A. Affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20 3 (2004) 307-315
24. Gentleman R.C., Carey V.J., Bates D.M., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y., Gentry J., Hornik K., Hothorn T., Huber W., Iacus S., Irizarry R., Leisch F., Li C., Maechler M., Rossini A.J., Sawitzki G., Smith C., Smyth G., Tierney L., Yang J.Y., and Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5 10 (2004) R80
25. Hegde A.N. Ubiquitin-proteasome-mediated local protein degradation and synaptic plasticity. Prog. Neurobiol. 73 5 (2004) 311-357
26. Hermani A., De Servi B., Medunjanin S., Tessier P.A., and Mayer D. S100A8 and S100A9 activate MAP kinase and NF-kappaB signaling pathways and trigger translocation of RAGE in human prostate cancer cells. Exp. Cell Res. 312 2 (2006) 184-197
27. Hsu Y.C., and Perin M.S. Human neuronal pentraxin II (NPTX2): conservation, genomic structure, and chromosomal localization. Genomics 28 2 (1995) 220-227
28. Huber W., von Heydebreck A., Sultmann H., Poustka A., and Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18 Suppl. 1 (2002) S96-S104
29. Irizarry R.A., Bolstad B.M., Collin F., Cope L.M., Hobbs B., and Speed T.P. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31 4 (2003) e15
30. Jais P.H. How frequent is altered gene expression among susceptibility genes to human complex disorders?. Genet. Med. 7 2 (2005) 83-96
31. Kanai Y., Dohmae N., and Hirokawa N. Kinesin transports RNA: isolation and characterization of an RNA-transporting granule. Neuron 43 4 (2004) 513-525
32. Katzman R., Terry R., DeTeresa R., Brown T., Davies P., Fuld P., Renbing X., and Peck A. Clinical, pathological, and neurochemical changes in dementia: a subgroup with preserved mental status and numerous neocortical plaques. Ann. Neurol. 23 2 (1988) 138-144
33. Keating D.J., Chen C., and Pritchard M.A. Alzheimer's disease and endocytic dysfunction: clues from the Down syndrome-related proteins, DSCR1 and ITSN1. Ageing Res. Rev. (2006)
34. Kita H., Carmichael J., Swartz J., Muro S., Wyttenbach A., Matsubara K., Rubinsztein D.C., and Kato K. Modulation of polyglutamine-induced cell death by genes identified by expression profiling. Hum. Mol. Genet. 11 19 (2002) 2279-2287
35. Layfield R., Lowe J., and Bedford L. The ubiquitin-proteasome system and neurodegenerative disorders. Essays Biochem. 41 (2005) 157-171
36. Lee J.H. Genetic evidence for cognitive reserve: variations in memory and related cognitive functions. J. Clin. Exp. Neuropsychol. 25 5 (2003) 594-613
37. Loring J.F., Wen X., Lee J.M., Seilhamer J., and Somogyi R. A gene expression profile of Alzheimer's disease. DNA Cell Biol. 20 11 (2001) 683-695
38. Maekawa M., Ishizaki T., Boku S., Watanabe N., Fujita A., Iwamatsu A., Obinata T., Ohashi K., Mizuno K., and Narumiya S. Signaling from Rho to the actin cytoskeleton through protein kinases ROCK and LIM-kinase. Science 285 5429 (1999) 895-898
39. Marshall E. Getting the noise out of gene arrays. Science 306 5696 (2004) 630-631
40. Martin K.C., and Kosik K.S. Synaptic tagging-who's it?. Nat. Rev. Neurosci. 3 10 (2002) 813-820
41. Mattick J.S., and Makunin I.V. Small regulatory RNAs in mammals. Hum. Mol. Genet. 14 Spec No. 1 (2005) R121-R132
42. McPherson P.S., Kay B.K., and Hussain N.K. Signaling on the endocytic pathway. Traffic 2 6 (2001) 375-384
43. Mirra S.S., Heyman A., McKeel D., Sumi S.M., Crain B.J., Brownlee L.M., Vogel F.S., Hughes J.P., van Belle G., and Berg L. The Consortium to Establish a Registry for Alzheimer's Disease (CERAD). Part II. Standardization of the neuropathologic assessment of Alzheimer's disease. Neurology 41 4 (1991) 479-486
44. Mizutani A., Fukuda M., Ibata K., Shiraishi Y., and Mikoshiba K. SYNCRIP, a cytoplasmic counterpart of heterogeneous nuclear ribonucleoprotein R, interacts with ubiquitous synaptotagmin isoforms. J. Biol. Chem. 275 13 (2000) 9823-9831
45. Mohney R.P., Das M., Bivona T.G., Hanes R., Adams A.G., Philips M.R., and O'Bryan J.P. Intersectin activates Ras but stimulates transcription through an independent pathway involving JNK. J. Biol. Chem. 278 47 (2003) 47038-47045
46. Morley M., Molony C.M., Weber T.M., Devlin J.L., Ewens K.G., Spielman R.S., and Cheung V.G. Genetic analysis of genome-wide variation in human gene expression. Nature 430 7001 (2004) 743-747
47. Mosconi L. Brain glucose metabolism in the early and specific diagnosis of Alzheimer's disease. FDG-PET studies in MCI and AD. Eur. J. Nucl. Med. Mol. Imaging 32 4 (2005) 486-510
48. O'Bryan J.P., Mohney R.P., and Oldham C.E. Mitogenesis and endocytosis: What's at the intersection?. Oncogene 20 44 (2001) 6300-6308
49. Ohki-Hamazaki H., Watase K., Yamamoto K., Ogura H., Yamano M., Yamada K., Maeno H., Imaki J., Kikuyama S., Wada E., and Wada K. Mice lacking bombesin receptor subtype-3 develop metabolic defects and obesity. Nature 390 6656 (1997) 165-169
50. Ohki-Hamazaki H., Iwabuchi M., and Maekawa F. Development and function of bombesin-like peptides and their receptors. Int. J. Dev. Biol. 49 2-3 (2005) 293-300
51. Ohtsuka T., Hata Y., Ide N., Yasuda T., Inoue E., Inoue T., Mizoguchi A., and Takai Y. nRap GEP: a novel neural GDP/GTP exchange protein for rap1 small G protein that interacts with synaptic scaffolding molecule (S-SCAM). Biochem. Biophys. Res. Commun. 265 1 (1999) 38-44
52. Pfaffl M.W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29 9 (2001) e45
53. Predescu S.A., Predescu D.N., Timblin B.K., Stan R.V., and Malik A.B. Intersectin regulates fission and internalization of caveolae in endothelial cells. Mol. Biol. Cell 14 12 (2003) 4997-5010
54. Pucharcos C., Estivill X., and de la Luna S. Intersection 2, a new multimodular protein involved in clathrin-mediated endocytosis. FEBS Lett. 478 1-2 (2000) 43-51
55. Ramakers C., Ruijter J.M., Deprez R.H., and Moorman A.F. Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci. Lett. 339 1 (2003) 62-66
56. Salehi A., Delcroix J.D., and Swaab D.F. Alzheimer's disease and NGF signaling. J. Neural Transm. 111 3 (2004) 323-345
57. Savdie C., Ferguson S.S., Vincent J.P., Beaudet A., and Stroh T. Cell-type-specific pathways of neurotensin endocytosis. Cell Tissue Res. (2005) 1-17
58. Scarmeas N., and Stern Y. Cognitive reserve: implications for diagnosis and prevention of Alzheimer's disease. Curr. Neurol. Neurosci. Rep. 4 5 (2004) 374-380
59. Scearce L.M., Brestelli J.E., McWeeney S.K., Lee C.S., Mazzarelli J., Pinney D.F., Pizarro A., Stoeckert Jr. C.J., Clifton S.W., Permutt M.A., Brown J., Melton D.A., and Kaestner K.H. Functional genomics of the endocrine pancreas: the pancreas clone set and PancChip, new resources for diabetes research. Diabetes 51 7 (2002) 1997-2004
60. Scheff S.W., Price D.A., Schmitt F.A., and Mufson E.J. Hippocampal synaptic loss in early Alzheimer's disease and mild cognitive impairment. Neurobiol. Aging (2005)
61. Schmitt F.A., Davis D.G., Wekstein D.R., Smith C.D., Ashford J.W., and Markesbery W.R. Preclinical" AD revisited: neuropathology of cognitively normal older adults. Neurology 55 3 (2000) 370-376
62. Singleton A., Myers A., and Hardy J. The law of mass action applied to neurodegenerative disease: a hypothesis concerning the etiology and pathogenesis of complex diseases. Hum. Mol. Genet. 13 Spec No. 1 (2004) R123-R126
63. Smyth G. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3 1 (2004) 1-23
64. Stern Y. What is cognitive reserve? Theory and research application of the reserve concept. J. Int. Neuropsychol. Soc. 8 3 (2002) 448-460
65. Storey J.D., and Tibshirani R. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA 100 16 (2003) 9440-9445
66. Stroombergen M.C., and Waring R.H. Determination of glutathione S-transferase mu and theta polymorphisms in neurological disease. Hum. Exp. Toxicol. 18 3 (1999) 141-145
67. Sun-Wada G.H., Wada Y., and Futai M. Diverse and essential roles of mammalian vacuolar-type proton pump ATPase: toward the physiological understanding of inside acidic compartments. Biochim. Biophys. Acta 1658 1-2 (2004) 106-114
68. Team RDC, 2005. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, http://www.R-project.org.
69. Tong X.K., Hussain N.K., Adams A.G., O'Bryan J.P., and McPherson P.S. Intersection can regulate the Ras/MAP kinase pathway independent of its role in endocytosis. J. Biol. Chem. 275 38 (2000) 29894-29899
70. Tsui C.C., Copeland N.G., Gilbert D.J., Jenkins N.A., Barnes C., and Worley P.F. Narp, a novel member of the pentraxin family, promotes neurite outgrowth and is dynamically regulated by neuronal activity. J. Neurosci. 16 8 (1996) 2463-2478
71. Wellmann S., Buhrer C., Moderegger E., Zelmer A., Kirschner R., Koehne P., Fujita J., and Seeger K. Oxygen-regulated expression of the RNA-binding proteins RBM3 and CIRP by a HIF-1-independent mechanism. J. Cell Sci. 117 Pt 9 (2004) 1785-1794
72. Yan H., Yuan W., Velculescu V.E., Vogelstein B., and Kinzler K.W. Allelic variation in human gene expression. Science 297 5584 (2002) 1143
73. Yao P.J., Zhu M., Pyun E.I., Brooks A.I., Therianos S., Meyers V.E., and Coleman P.D. Defects in expression of genes related to synaptic vesicle trafficking in frontal cortex of Alzheimer's disease. Neurobiol. Dis. 12 2 (2003) 97-109