Expression profiling in the aging brain: A perspective

Ageing Research Reviews

Volumn 4, Issue 4, 2005, Pages 529-547

  Galvin, James E ^a   Ginsberg, Stephen D ^b,c  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NATHAN S KLINE INSTITUTE FOR PSYCHIATRIC RESEARCH   (United States)

^c NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Alzheimer's disease; Functional genomics; Gene expression; Microarray; Senescence; Single cell profiling

Indexed keywords

GENOMIC DNA; MESSENGER RNA;

AGING; ALZHEIMER DISEASE; BRAIN; FUNCTIONAL GENOMICS; FUNCTIONAL PROTEOMICS; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GERONTOLOGY; HUMAN; MICROARRAY ANALYSIS; MOSAICISM; NONHUMAN; REVIEW; SENESCENCE; TRANSCRIPTION REGULATION;

ANIMALIA;

EID: 33644558377     PISSN: 15681637     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.arr.2005.06.009     Document Type: Short Survey

References (89)

1. T. Aittokallio, M. Kurki, O. Nevalainen, T. Nikula, A. West, and R. Lahesmaa Computational strategies for analyzing data in gene expression microarray experiments J. Bioinform. Comput. Biol. 1 2003 541 586
2. O. Alter, P.O. Brown, and D. Botstein Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms Proc. Natl. Acad. Sci. U.S.A. 100 2003 3351 3356
3. S.E. Baranzini Gene expression profiling in neurological disorders: toward a systems-level understanding of the brain Neuromol. Med. 6 2004 31 52
4. A.J. Becker, J. Chen, A. Zien, D. Sochivko, S. Normann, J. Schramm, C.E. Elger, O.D. Wiestler, and I. Blumcke Correlated stage- and subfield-associated hippocampal gene expression patterns in experimental and human temporal lobe epilepsy Eur. J. Neurosci. 18 2003 2792 2802
5. Y.N. Berner, and F. Stern Energy restriction controls aging through neuroendocrine signal transduction Ageing Res. Rev. 3 2004 189 198
6. E.M. Blalock, K.C. Chen, K. Sharrow, J.P. Herman, N.M. Porter, T.C. Foster, and P.W. Landfield Gene microarrays in hippocampal aging: statistical profiling identifies novel processes correlated with cognitive impairment J. Neurosci. 23 2003 3807 3819
7. E.M. Blalock, J.W. Geddes, K.C. Chen, N.M. Porter, W.R. Markesbery, and P.W. Landfield Incipient Alzheimer's disease: microarray correlation analyses reveal major transcriptional and tumor suppressor responses Proc. Natl. Acad. Sci. U.S.A. 101 2004 2173 2178
8. G. Blander, and L. Guarente The Sir2 family of protein deacetylases Annu. Rev. Biochem. 73 2004 417 435
9. P.O. Brown, and D. Botstein Exploring the new world of the genome with DNA microarrays Nat. Genet. 21 Suppl. 1999 33 37
10. G.J. Burbach, D. Dehn, D. Del Turco, M. Staufenbiel, and T. Deller Laser microdissection reveals regional and cellular differences in GFAP mRNA upregulation following brain injury, axonal denervation, and amyloid plaque deposition Glia 48 2004 76 84
11. S.R. Burzynski Aging: gene silencing or gene activation? Med. Hypotheses 64 2005 201 208
12. S.X. Cao, J.M. Dhahbi, P.L. Mote, and S.R. Spindler Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice Proc. Natl. Acad. Sci. U.S.A. 98 2001 10630 10635
13. H.Y. Chan, and N.M. Bonini Drosophila models of human neurodegenerative disease Cell Death Differ. 7 2000 1075 1080
14. S. Che, and S.D. Ginsberg Amplification of transcripts using terminal continuation Lab. Invest. 84 2004 131 137
15. V. Colangelo, J. Schurr, M.J. Ball, R.P. Pelaez, N.G. Bazan, and W.J. Lukiw 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 2002 462 473
16. S.E. Counts, M. Nadeem, J. Wuu, S.D. Ginsberg, H.U. Saragovi, and E.J. Mufson Reduction of cortical TrkA but not p75(NTR) protein in early-stage Alzheimer's disease Ann. Neurol. 56 2004 520 531
17. J.P. de Magalhaes From cells to ageing: a review of models and mechanisms of cellular senescence and their impact on human ageing Exp. Cell Res. 300 2004 1 10
18. J.P. de Magalhaes, J. Costa, and O. Toussaint HAGR: the human ageing genomic resources Nucleic Acids Res. 33 2005 D537 D543
19. J.P. de Magalhaes, and O. Toussaint GenAge: a genomic and proteomic network map of human ageing FEBS Lett. 571 2004 243 247
20. C.A. Dickey, J.F. Loring, J. Montgomery, M.N. Gordon, P.S. Eastman, and D. Morgan Selectively reduced expression of synaptic plasticity-related genes in amyloid precursor protein + presenilin-1 transgenic mice J. Neurosci. 23 2003 5219 5226
21. P.A. Doris Hypertension genetics, single nucleotide polymorphisms, and the common disease: common variant hypothesis Hypertension 39 2002 323 331
22. J. Eberwine, J.E. Kacharmina, C. Andrews, K. Miyashiro, T. McIntosh, K. Becker, T. Barrett, D. Hinkle, G. Dent, and P. Marciano mRNA expression analysis of tissue sections and single cells J. Neurosci. 21 2001 8310 8314
23. M.G. Edwards, D. Sarkar, R. Klopp, J.D. Morrow, R. Weindruch, and T.A. Prolla Impairment of the transcriptional responses to oxidative stress in the heart of aged C57BL/6 mice Ann. NY Acad. Sci. 1019 2004 85 95
24. J.A. Eisman Genetics of osteoporosis Endocr. Rev. 20 1999 788 804
25. P. Fabrizio, L. Li, and V.D. Longo Analysis of gene expression profile in yeast aging chronologically Mech. Ageing Dev. 126 2005 11 16
26. M.E. Fortini, and N.M. Bonini Modeling human neurodegenerative diseases in Drosophila: on a wing and a prayer Trends Genet. 16 2000 161 167
27. W.M. Freeman, and S.E. Hemby Proteomics for protein expression profiling in neuroscience Neurochem. Res. 29 2004 1065 1081
28. J.E. Galvin Neurodegenerative diseases: pathology and the advantage of single-cell profiling Neurochem. Res. 29 2004 1041 1051
29. J.E. Galvin, and S.D. Ginsberg Expression profiling and pharmacotherapeutic development in the central nervous system Alzheimer Dis. Assoc. Disord. 18 2004 264 269
30. D. Gems, and J.J. McElwee Ageing: microarraying mortality Nature 424 2003 259 261
31. Ginsberg, S.D., 2005. RNA amplification strategies for small sample populations. Methods.
32. S.D. Ginsberg, and S. Che RNA amplification in brain tissues Neurochem. Res. 27 2002 981 992
33. S.D. Ginsberg, and S. Che Combined histochemical staining, RNA amplification, regional, and single cell analysis within the hippocampus Lab. Invest. 84 2004 952 962
34. S.D. Ginsberg, and S. Che Expression profile analysis within the human hippocampus: comparison of CA1 and CA3 pyramidal neurons J. Comp. Neurol. 487 2005 107 118
35. S.D. Ginsberg, P.B. Crino, S.E. Hemby, J.A. Weingarten, V.M.-Y. Lee, J.H. Eberwine, and J.Q. Trojanowski Predominance of neuronal mRNAs in individual Alzheimer's disease senile plaques Ann. Neurol. 45 1999 174 181
36. S.D. Ginsberg, I. Elarova, M. Ruben, F. Tan, S.E. Counts, J.H. Eberwine, J.Q. Trojanowski, S.E. Hemby, E.J. Mufson, and S. Che Single cell gene expression analysis: implications for neurodegenerative and neuropsychiatric disorders Neurochem. Res. 29 2004 1054 1065
37. S.D. Ginsberg, S.E. Hemby, V.M.-Y. Lee, J.H. Eberwine, and J.Q. Trojanowski Expression profile of transcripts in Alzheimer's disease tangle-bearing CA1 neurons Ann. Neurol. 48 2000 77 87
38. Ginsberg, S.D., Hemby, S.E., Mufson, E.J., Martin, L.J., in press. Cell and tissue microdissection in combination with genomic and proteomic applications. In: Zaborszky, L., Wouterlood, F., Lanciego, J.L. (Eds.), Neuroanatomical Tract Tracing 3: Molecules-Neurons-Systems, Springer/Kluwer/ Plenum, New York.
39. T.R. Golden, and S. Melov Microarray analysis of gene expression with age in individual nematodes Aging Cell 3 2004 111 124
40. E. Grunblatt, S. Mandel, J. Jacob-Hirsch, S. Zeligson, N. Amariglo, G. Rechavi, J. Li, R. Ravid, W. Roggendorf, P. Riederer, and M.B. Youdim Gene expression profiling of Parkinsonian substantia nigra pars compacta; alterations in ubiquitin-proteasome, heat shock protein, iron and oxidative stress regulated proteins, cell adhesion/cellular matrix and vesicle trafficking genes J. Neural. Transm. 111 2004 1543 1573
41. L. Guarente, and F. Picard Calorie restriction - the SIR2 connection Cell 120 2005 473 482
42. S.P. Gygi, Y. Rochon, B.R. Franza, and R. Aebersold Correlation between protein and mRNA abundance in yeast Mol. Cell. Biol. 19 1999 1720 1730
43. E.R. Hauser, and M.A. Pericak-Vance Genetic analysis for common complex disease Am. Heart J. 140 2000 S36 S44
44. S.E. Hemby, J.Q. Trojanowski, and S.D. Ginsberg Neuron-specific age-related decreases in dopamine receptor subtype mRNAs J. Comp. Neurol. 456 2003 176 183
45. K. Hiratsuka, Y. Kamino, T. Nagata, Y. Takahashi, S. Asai, K. Ishikawa, and Y. Abiko Microarray analysis of gene expression changes in aging in mouse submandibular gland J. Dent. Res. 81 2002 679 682
46. D.L. Hoyert, H.C. Kung, and B.L. Smith Deaths: preliminary data for 2003 Natl. Vital Stat. Rep. 53 2005 1 48
47. W. Jin, R.M. Riley, R.D. Wolfinger, K.P. White, G. Passador-Gurgel, and G. Gibson The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster Nat. Genet. 29 2001 389 395
48. T.E. Johnson, S. Henderson, S. Murakami, E. de Castro, S.H. de Castro, J. Cypser, B. Rikke, P. Tedesco, and C. Link Longevity genes in the nematode Caenorhabditis elegans also mediate increased resistance to stress and prevent disease J. Inherit. Metab. Dis. 25 2002 197 206
49. J.E. Kacharmina, P.B. Crino, and J. Eberwine Preparation of cDNA from single cells and subcellular regions Meth. Enzymol. 303 1999 3 18
50. C. Kenyon, J. Chang, E. Gensch, A. Rudner, and R. Tabtiang A C. elegans mutant that lives twice as long as wild type Nature 366 1993 461 464
51. S.N. Kim, J.H. Rhee, Y.H. Song, D.Y. Park, M. Hwang, S.L. Lee, J.E. Kim, B.S. Gim, J.H. Yoon, Y.J. Kim, and J. Kim-Ha Age-dependent changes of gene expression in the Drosophila head Neurobiol. Aging 26 2005 1083 1091
52. B.W. Kirk, M. Feinsod, R. Favis, R.M. Kliman, and F. Barany Single nucleotide polymorphism seeking long term association with complex disease Nucleic Acids Res. 30 2002 3295 3311
53. T.B. Kirkwood Understanding the odd science of aging Cell 120 2005 437 447
54. V.B. Kumar, M.W. Franko, S.A. Farr, H.J. Armbrecht, and J.E. Morley Identification of age-dependent changes in expression of senescence-accelerated mouse (SAMP8) hippocampal proteins by expression array analysis Biochem. Biophys. Res. Commun. 272 2000 657 661
55. K.J. Kyng, A. May, S. Kolvraa, and V.A. Bohr Gene expression profiling in Werner syndrome closely resembles that of normal aging Proc. Natl. Acad. Sci. U.S.A. 100 2003 12259 12264
56. C.H. Lee, and P.F. Macgregor Using microarrays to predict resistance to chemotherapy in cancer patients Pharmacogenomics 5 2004 611 625
57. D.J. Lockhart, H. Dong, M.C. Byrne, M.T. Follettie, M.V. Gallo, M.S. Chee, M. Mittmann, C. Wang, M. Kobayashi, H. Horton, and E.L. Brown Expression monitoring by hybridization to high-density oligonucleotide arrays Nat. Biotechnol. 14 1996 1675 1680
58. J.F. Loring, X. Wen, J.M. Lee, J. Seilhamer, and R. Somogyi A gene expression profile of Alzheimer's disease DNA Cell Biol. 20 2001 683 695
59. T. Lu, Y. Pan, S.Y. Kao, C. Li, I. Kohane, J. Chan, and B.A. Yankner Gene regulation and DNA damage in the ageing human brain Nature 429 2004 883 891
60. K. Lukasiuk, and A. Pitkänen Large-scale analysis of gene expression in epilepsy research: is synthesis already possible? Neurochem. Res. 29 2004 1164 1173
61. W.J. Lukiw Gene expression profiling in fetal, aged, and Alzheimer hippocampus: a continuum of stress-related signaling Neurochem. Res. 29 2004 1287 1297
62. P.G. Marciano, J.H. Eberwine, R. Ragupathi, K.E. Saatman, D.F. Meaney, and T.K. McIntosh Expression profiling following traumatic brain injury: a review Neurochem. Res. 27 2002 1147 1155
63. E.R. Marcotte, L.K. Srivastava, and R. Quirion cDNA microarray and proteomic approaches in the study of brain diseases: focus on schizophrenia and Alzheimer's disease Pharmacol. Ther. 100 2003 63 74
64. S.A. McCarroll, C.T. Murphy, S. Zou, S.D. Pletcher, C.S. Chin, Y.N. Jan, C. Kenyon, C.I. Bargmann, and H. Li Comparing genomic expression patterns across species identifies shared transcriptional profile in aging Nat. Genet. 36 2004 197 204
65. K.L. McClain, Y.H. Cai, J. Hicks, L.E. Peterson, X.T. Yan, S. Che, and S.D. Ginsberg Expression profiling using human tissues in combination with RNA amplification and microarray analysis: assessment of Langerhans cell histiocytosis Amino Acids 28 2005 279 290
66. J.J. McElwee Addressing the age-old question of old age Genome Biol. 5 2004 337
67. M.A. McMurray, and D.E. Gottschling Aging and genetic instability in yeast Curr. Opin. Microbiol. 7 2004 673 679
68. Melov, S., Hubbard, A., 2004. Microarrays as a tool to investigate the biology of aging: a retrospective and a look to the future. Sci. Aging Knowledge Environ. 2004: re7.
69. R.A. Miller, A. Galecki, and R.J. Shmookler-Reis Interpretation, design, and analysis of gene array expression experiments J. Gerontol. A: Biol. Sci. Med. Sci. 56 2001 B52 B57
70. E.J. Mufson, S.E. Counts, and S.D. Ginsberg Single cell gene expression profiles of nucleus basalis cholinergic neurons in Alzheimer's disease Neurochem. Res. 27 2002 1035 1048
71. C.T. Murphy, S.A. McCarroll, C.I. Bargmann, A. Fraser, R.S. Kamath, J. Ahringer, H. Li, and C. Kenyon Genes that act downstream of DAF-16 to influence the lifespan of Caenorhabditis elegans Nature 424 2003 277 283
72. P.N. Nair, T. Golden, and S. Melov Microarray workshop on aging Mech. Ageing Dev. 124 2003 133 138
73. Y. Nomura, and Y. Okuma Age-related defects in lifespan and learning ability in SAMP8 mice Neurobiol. Aging 20 1999 111 115
74. S.D. Pletcher, and M.P. Stumpf Population genomics: ageing by association Curr. Biol. 12 2002 R328 R330
75. J.H. Powers Antimicrobial drug development - the past, the present, and the future Clin. Microbiol. Infect. 10 2004 23 31
76. T.A. Prolla DNA microarray analysis of the aging brain Chem. Senses 27 2002 299 306
77. T.A. Prolla Multiple roads to the aging phenotype: insights from the molecular dissection of progerias through DNA microarray analysis Mech. Ageing Dev. 126 2005 461 465
78. P.H. Reddy, S. McWeeney, B.S. Park, M. Manczak, R.V. Gutala, D. Partovi, Y. Jung, V. Yau, R. Searles, M. Mori, and J. Quinn Gene expression profiles of transcripts in amyloid precursor protein transgenic mice: up-regulation of mitochondrial metabolism and apoptotic genes is an early cellular change in Alzheimer's disease Hum. Mol. Genet. 13 2004 1225 1240
79. R. Ricciarelli, C. d'Abramo, S. Massone, U. Marinari, M. Pronzato, and M. Tabaton Microarray analysis in Alzheimer's disease and normal aging IUBMB Life 56 2004 349 354
80. D.S. Rickman, M.P. Bobek, D.E. Misek, R. Kuick, M. Blaivas, D.M. Kurnit, J. Taylor, and S.M. Hanash Distinctive molecular profiles of high-grade and low-grade gliomas based on oligonucleotide microarray analysis Cancer Res. 61 2001 6885 6891
81. M.R. Rose, L.D. Mueller, and A.D. Long Pharmacology, genomics, and the evolutionary biology of ageing Free Radic. Res. 36 2002 1293 1297
82. L. Seroude, T. Brummel, P. Kapahi, and S. Benzer Spatio-temporal analysis of gene expression during aging in Drosophila melanogaster Aging Cell 1 2002 47 56
83. G. Shaulsky, and W.F. Loomis Gene expression patterns in Dictyostelium using microarrays Protist 153 2002 93 98
84. R.S. Sohal, and R. Weindruch Oxidative stress, caloric restriction, and aging Science 273 1996 59 63
85. G. Suji, and S. Sivakami Glucose, glycation and aging Biogerontology 5 2004 365 373
86. J. Vijg, and Y. Suh Genetics of longevity and aging Annu. Rev. Med. 56 2005 193 212
87. D.J. Villeneuve, and A.M. Parissenti The use of DNA microarrays to investigate the pharmacogenomics of drug response in living systems Curr. Top. Med. Chem. 4 2004 1329 1345
88. R. Weindruch, T. Kayo, C.K. Lee, and T.A. Prolla Microarray profiling of gene expression in aging and its alteration by caloric restriction in mice J. Nutr. 131 2001 918S 923S
89. R. Weindruch, and T.A. Prolla Gene expression profile of the aging brain Arch. Neurol. 59 2002 1712 1714