Threshold-independent meta-analysis of Alzheimer's disease transcriptomes shows progressive changes in hippocampal functions, epigenetics and microRNA regulation

Current Alzheimer Research

Volumn 9, Issue 4, 2012, Pages 425-435

  Barbash, Shahar ^a   Soreq, Hermona ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

Alzheimer's disease; Disease mechanisms; Epigenetics; Gene group analysis; Microarrays; MicroRNAs; Thresholdindependent statistics

Indexed keywords

MICRORNA; NUCLEOTIDE; TRANSCRIPTOME;

AGED; ALTERNATIVE RNA SPLICING; ALZHEIMER DISEASE; ARTICLE; CLINICAL ARTICLE; COGNITION; CONTROLLED STUDY; DETERIORATION; DISEASE COURSE; DISEASE SEVERITY; EPIGENETICS; GENE CONTROL; HIPPOCAMPUS; HUMAN; HUMAN TISSUE; MICROARRAY ANALYSIS; NERVOUS SYSTEM INFLAMMATION; NEUROFIBRILLARY TANGLE; OXIDATIVE STRESS; PRIORITY JOURNAL; PROTEIN FOLDING; SYNAPTIC TRANSMISSION;

EID: 84859309442     PISSN: 15672050     EISSN: 18755828     Source Type: Journal    
DOI: 10.2174/156720512800492512     Document Type: Article

References (56)

1. Masliah E, Mallory M, Hansen L, Alford M, Albright T, DeTeresa R, et al. Patterns of aberrant sprouting in Alzheimer's disease. Neuron 6: 729-739 (1991).
2. Forman MS, Lee VM, Trojanowski JQ. 'Unfolding' pathways in neurodegenerative disease. Trends Neurosci 26: 407-410 (2003).
3. Chouliaras L, Rutten BP, Kenis G, Peerbooms O, Visser PJ, Verhey F, et al. Epigenetic regulation in the pathophysiology of Alzheimer's disease. Prog Neurobiol 90: 498-510 (2010).
4. Mucke L, Masliah E, Yu GQ, Mallory M, Rockenstein EM, Tatsuno G, et al. High-level neuronal expression of abeta 1-42 in wild-type human amyloid protein precursor transgenic mice: synaptotoxicity without plaque formation. J Neurosci 20: 4050-4058 (2000).
5. Bossers K, Wirz KT, Meerhoff GF, Essing AH, van Dongen JW, Houba P, et al. Concerted changes in transcripts in the prefrontal cortex precede neuropathology in Alzheimer's disease. Brain 133: 3699-3723 (2010).
6. Blalock EM, Geddes JW, Chen KC, Porter NM, Markesbery WR, Landfield PW, et al. Incipient Alzheimer's disease: microarray correlation analyses reveal major transcriptional and tumor suppressor responses. Proc Natl Acad Sci USA 101: 2173-2178 (2004).
7. Liang WS, Dunckley T, Beach TG, Grover A, Mastroeni D, Ramsey K, et al. Altered neuronal gene expression in brain regions differentially affected by Alzheimer's disease: a reference data set. Physiol Genomics 33: 240-256 (2008).
8. Galasko D, Hansen LA, Katzman R, Wiederholt W, Masliah E, Terry R, et al. Clinical-neuropathological correlations in Alzheimer's disease and related dementias. Arch Neurol 51: 888-895 (1994).
9. Soreq L, Bergman H, Goll Y, Greenberg DS, Israel Z, Soreq H, et al. Deep brain stimulation induces rapidly reversible transcript changes in Parkinson's leukocytes. J Cell Mol Med: (2011).
10. Soreq L, Bergman H, Goll Y et al. Deep brain stimulation induces rapidly reversible transcript changes in Parkinson's leukocytes. J Cell Mol Med: (2011).
11. Cahoy JD, Emery B, Kaushal A, Foo LC, Zamanian JL, Christopherson KS, et al. A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J Neurosci 28: 264-278 (2008).
12. Du H, Guo L, Yan S, Sosunov AA, McKhann GM, Yan SS. Early deficits in synaptic mitochondria in an Alzheimer's disease mouse model. Proc Natl Acad Sci USA 107: 18670-18675 (2010).
13. Bernardi G. The vertebrate genome: isochores and evolution. Mol Biol Evol 10: 186-204 (1993).
14. Eimerl S, Schramm M. The quantity of calcium that appears to induce neuronal death. J Neurochem 62: 1223-1226 (1994).
15. Hebert SS, De Strooper B. Alterations of the microRNA network cause neurodegenerative disease. Trends Neurosci 32: 199-206 (2009).
16. Szaro BG, Strong MJ. Post-transcriptional control of neurofilaments: New roles in development, regeneration and neurodegenerative disease. Trends Neurosci 33: 27-37 (2010).
17. Nunez-Iglesias J, Liu CC, Morgan TE, Finch CE, Zhou XJ. Joint genome-wide profiling of miRNA and mRNA expression in Alzheimer's disease cortex reveals altered miRNA regulation. PLoS One 5: e8898 (2010).
18. Schonrock N, Ke YD, Humphreys D, Staufenbiel M, Ittner LM, Preiss T, et al. Neuronal microRNA deregulation in response to Alzheimer's disease amyloid-beta. PLoS One 5: e11070 (2010).
19. Long JM, Lahiri DK. MicroRNA-101 downregulates Alzheimer's amyloid-beta precursor protein levels in human cell cultures and is differentially expressed. Biochem Biophys Res Commun 404: 889-895 (2011).
20. Vilardo E, Barbato C, Ciotti M, Cogoni C, Ruberti F. MicroRNA-101 regulates amyloid precursor protein expression in hippocampal neurons. J Biol Chem 285: 18344-18351 (2010).
21. Shaked I, Meerson A, Wolf Y, Avni R, Greenberg D, Gilboa-Geffen A, et al. MicroRNA-132 potentiates cholinergic antiinflammatory signaling by targeting acetylcholinesterase. Immunity 31: 965-973 (2009).
22. Cogswell JP, Ward J, Taylor IA, Waters M, Shi Y, Cannon B, et al. Identification of miRNA changes in Alzheimer's disease brain and CSF yields putative biomarkers and insights into disease pathways. J Alzheimers Dis 14: 27-41 (2008).
23. Berson A, Knobloch M, Hanan M, Diamant S, Sharoni M, Schuppli D, et al. Changes in readthrough acetylcholinesterase expression modulate amyloid-beta pathology. Brain 131: 109-119 (2008).
24. Friedman Y, Naamati G, Linial M. MiRror: a combinatorial analysis web tool for ensembles of microRNAs and their targets. Bioinformatics 26: 1920-1921 (2010).
25. Guo H, Ingolia NT, Weissman JS, Bartel DP. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466: 835-840 (2010).
26. Cheng C, Li LM. Inferring microRNA activities by combining gene expression with microRNA target prediction. PLoS One 3: e1989 (2008).
27. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, et al. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769-773 (2005).
28. Wang WX, Rajeev BW, Stromberg AJ, Ren N, Tang G, Huang Q, et al. The expression of microRNA miR-107 decreases early in Alzheimer's disease and may accelerate disease progression through regulation of beta-site amyloid precursor protein-cleaving enzyme 1. J Neurosci 28: 1213-1223 (2008).
29. Provost P. Interpretation and applicability of microRNA data to the context of Alzheimer's and age-related diseases. Aging (Albany NY) 2: 166-169 (2010).
30. Leskovjan AC, Kretlow A, Lanzirotti A, Barrea R, Vogt S, Miller LM, et al. Increased brain iron coincides with early plaque formation in a mouse model of Alzheimer's disease. Neuroimage 55: 32-38 (2011).
31. Long JC, Caceres JF. The SR protein family of splicing factors: master regulators of gene expression. Biochem J 417: 15-27 (2009).
32. Matlin AJ, Clark F, Smith CW. Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol 6: 386-398 (2005).
33. Scheff SW, Price DA. Alzheimer's disease-related synapse loss in the cingulate cortex. J Alzheimers Dis 3: 495-505 (2001).
34. Shi J, Qian W, Yin X, Iqbal K, Grundke-Iqbal I, Gu X, et al. Cyclic AMP-dependent Protein Kinase Regulates the Alternative Splicing of Tau Exon 10: A MECHANISM INVOLVED IN TAU PATHOLOGY OF ALZHEIMER DISEASE. J Biol Chem 286: 14639-14648 (2011).
35. Bowser R, Smith MA. Cell cycle proteins in Alzheimer's disease: plenty of wheels but no cycle. J Alzheimers Dis 4: 249-254 (2002).
36. Pimplikar SW, Nixon RA, Robakis NK, Shen J, Tsai LH. Amyloidindependent mechanisms in Alzheimer's disease pathogenesis. J Neurosci 30: 14946-14954 (2010).
37. Supnet C, Bezprozvanny I. Neuronal calcium signaling, mitochondrial dysfunction, and Alzheimer's disease. J Alzheimers Dis 20 Suppl 2: S487-498 (2010).
38. Thomas SN, Cripps D, Yang AJ. Proteomic analysis of protein phosphorylation and ubiquitination in Alzheimer's disease. Methods Mol Biol 566: 109-121 (2009).
39. Perry VH, Nicoll JA, Holmes C. Microglia in neurodegenerative disease. Nat Rev Neurol 6: 193-201 (2010).
40. Aksenov MY, Aksenova MV, Butterfield DA, Geddes JW, Markesbery WR. Protein oxidation in the brain in Alzheimer's disease. Neuroscience 103: 373-383 (2001).
41. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledgebased approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102: 15545-15550 (2005).
42. Grond-Ginsbach C, Hummel M, Wiest T, Wiest T, Horstmann S, Pfleger K, et al. Gene expression in human peripheral blood mononuclear cells upon acute ischemic stroke. J Neurol 255: 723-731 (2008).
43. Chong MS, Sahadevan S. Preclinical Alzheimer's disease: diagnosis and prediction of progression. Lancet Neurol 4: 576-579 (2005).
44. Rachakonda V, Pan TH, Le WD. Biomarkers of neurodegenerative disorders: how good are they? Cell Res 14: 347-358 (2004).
45. Harris JA, Devidze N, Verret L, Ho K, Halabisky B, Thwin MT, et al. Transsynaptic progression of amyloid-beta-induced neuronal dysfunction within the entorhinal-hippocampal network. Neuron 68: 428-441 (2010).
46. Geddes JW, Tekirian TL, Soultanian NS, Ashford JW, Davis DG, Markesbery WR. Comparison of neuropathologic criteria for the diagnosis of Alzheimer's disease. Neurobiol Aging 18: S99-105 (1997).
47. Hyman BT. The neuropathological diagnosis of Alzheimer's disease: clinical-pathological studies. Neurobiol Aging 18: S27-32 (1997).
48. Riley KP, Snowdon DA, Markesbery WR. Alzheimer's neurofibrillary pathology and the spectrum of cognitive function: findings from the Nun Study. Ann Neurol 51: 567-577 (2002).
49. Bennett DA, Schneider JA, Arvanitakis Z, Kelly JF, Aggarwal NT, Shah RC, et al. Neuropathology of older persons without cognitive impairment from two community-based studies. Neurology 66: 1837-1844 (2006).
50. Price JL, McKeel DW, Jr., Buckles VD, Roe CM, Xiong C, Grundman M, et al. Neuropathology of nondemented aging: presumptive evidence for preclinical Alzheimer disease. Neurobiol Aging 30: 1026-1036 (2009).
51. Juhasz G, Foldi I, Penke B. Systems biology of Alzheimer's disease: How diverse molecular changes result in memory impairment in AD. Neurochem Int: (2011).
52. Wang SC, Oelze B, Schumacher A. Age-specific epigenetic drift in late-onset Alzheimer's disease. PLoS One 3: e2698 (2008).
53. West RL, Lee JM, Maroun LE. Hypomethylation of the amyloid precursor protein gene in the brain of an Alzheimer's disease patient. J Mol Neurosci 6: 141-146 (1995).
54. Tollervey JR, Wang Z, Hortobagyi T, Witten JT, Zarnack K, Kayikci M, et al. Analysis of alternative splicing associated with aging and neurodegeneration in the human brain. Genome Res 21: 1572-1582 (2011).
55. Bruno AM, Huang JY, Bennett DA, Marr RA, Hastings ML, Stutzmann GE. Altered ryanodine receptor expression in mild cognitive impairment and Alzheimer's disease. Neurobiol Aging: (2011).
56. Karni S, Soreq H, Sharan R. A network-based method for predicting disease-causing genes. J Comput Biol 16: 181-189 (2009).