Identification of genes associated with dissociation of cognitive performance and neuropathological burden: Multistep analysis of genetic, epigenetic, and transcriptional data
Philip De Jager and colleagues conduct a multistep analysiso of genetic, epigenetic and transcriptional data to identify genes associated with residual cognition.
Vyšlo v časopise:
Identification of genes associated with dissociation of cognitive performance and neuropathological burden: Multistep analysis of genetic, epigenetic, and transcriptional data. PLoS Med 14(4): e32767. doi:10.1371/journal.pmed.1002287
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pmed.1002287
Souhrn
Philip De Jager and colleagues conduct a multistep analysiso of genetic, epigenetic and transcriptional data to identify genes associated with residual cognition.
Zdroje
1. Boyle PA, Wilson RS, Yu L, Barr AM, Honer WG, Schneider JA, et al. Much of late life cognitive decline is not due to common neurodegenerative pathologies. Ann Neurol. 2013;74(3):478–89. doi: 10.1002/ana.23964 23798485
2. Yu L, Boyle PA, Segawa E, Leurgans S, Schneider JA, Wilson RS, et al. Residual decline in cognition after adjustment for common neuropathologic conditions. Neuropsychology. 2015;29(3):335–43. doi: 10.1037/neu0000159 25495832
3. Boyle PA, Yu L, Wilson RS, Schneider JA, Bennett DA. Relation of neuropathology with cognitive decline among older persons without dementia. Front Aging Neurosci. 2013;5:50. doi: 10.3389/fnagi.2013.00050 24058343
4. Negash S, Wilson RS, Leurgans SE, Wolk DA, Schneider JA, Buchman AS, et al. Resilient brain aging: characterization of discordance between Alzheimer’s disease pathology and cognition. Curr Alzheimer Res. 2013;10(8):844–51. 23919768
5. Wilson RS, Barnes LL, Mendes de Leon CF, Aggarwal NT, Schneider JS, Bach J, et al. Depressive symptoms, cognitive decline, and risk of AD in older persons. Neurology. 2002;59(3):364–70. 12177369
6. Yu L, Dawe RJ, Buchman AS, Boyle PA, Schneider JA, Arfanakis K, et al. Ex vivo MRI transverse relaxation in community based older persons with and without Alzheimer’s dementia. Behav Brain Res. 2016;322:233–40. doi: 10.1016/j.bbr.2016.09.001 27596378
7. Dawe RJ, Yu L, Leurgans SE, Schneider JA, Buchman AS, Arfanakis K, et al. Postmortem MRI: a novel window into the neurobiology of late life cognitive decline. Neurobiol Aging. 2016;45:169–77. doi: 10.1016/j.neurobiolaging.2016.05.023 27459937
8. Katzman R, Terry R, DeTeresa R, Brown T, Davies P, Fuld P, et al. Clinical, pathological, and neurochemical changes in dementia: a subgroup with preserved mental status and numerous neocortical plaques. Ann Neurol. 1988;23(2):138–44. doi: 10.1002/ana.410230206 2897823
9. Wilson RS, Nag S, Boyle PA, Hizel LP, Yu L, Buchman AS, et al. Neural reserve, neuronal density in the locus ceruleus, and cognitive decline. Neurology. 2013;80(13):1202–8. doi: 10.1212/WNL.0b013e3182897103 23486878
10. Stern Y. Cognitive reserve in ageing and Alzheimer’s disease. Lancet Neurol. 2012;11(11):1006–12. doi: 10.1016/S1474-4422(12)70191-6 23079557
11. Perez-Nievas BG, Stein TD, Tai HC, Dols-Icardo O, Scotton TC, Barroeta-Espar I, et al. Dissecting phenotypic traits linked to human resilience to Alzheimer’s pathology. Brain. 2013;136(Pt 8):2510–26. doi: 10.1093/brain/awt171 23824488
12. Snowdon DA, Greiner LH, Mortimer JA, Riley KP, Greiner PA, Markesbery WR. Brain infarction and the clinical expression of Alzheimer disease. The Nun Study. JAMA. 1997;277(10):813–7. 9052711
13. Schneider JA, Arvanitakis Z, Bang W, Bennett DA. Mixed brain pathologies account for most dementia cases in community-dwelling older persons. Neurology. 2007;69(24):2197–204. doi: 10.1212/01.wnl.0000271090.28148.24 17568013
14. Arnold SE, Louneva N, Cao K, Wang LS, Han LY, Wolk DA, et al. Cellular, synaptic, and biochemical features of resilient cognition in Alzheimer’s disease. Neurobiol Aging. 2013;34(1):157–68. doi: 10.1016/j.neurobiolaging.2012.03.004 22554416
15. Honer WG, Barr AM, Sawada K, Thornton AE, Morris MC, Leurgans SE, et al. Cognitive reserve, presynaptic proteins and dementia in the elderly. Transl Psychiatry. 2012;2:e114. doi: 10.1038/tp.2012.38 22832958
16. Allen GI, Amoroso N, Anghel C, Balagurusamy V, Bare CJ, Beaton D, et al. Crowdsourced estimation of cognitive decline and resilience in Alzheimer’s disease. Alzheimers Dement. 2016;12(6):645–53. doi: 10.1016/j.jalz.2016.02.006 27079753
17. Bennett DA, Schneider JA, Arvanitakis Z, Wilson RS. Overview and findings from the religious orders study. Curr Alzheimer Res. 2012;9(6):628–45. 22471860
18. Bennett DA, Schneider JA, Buchman AS, Barnes LL, Boyle PA, Wilson RS. Overview and findings from the Rush Memory and Aging Project. Curr Alzheimer Res. 2012;9(6):646–63. 22471867
19. De Jager PL, Srivastava G, Lunnon K, Burgess J, Schalkwyk LC, Yu L, et al. Alzheimer’s disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. Nat Neurosci. 2014;17(9):1156–63. doi: 10.1038/nn.3786 25129075
20. Bennett DA, Wilson RS, Schneider JA, Evans DA, Beckett LA, Aggarwal NT, et al. Natural history of mild cognitive impairment in older persons. Neurology. 2002;59(2):198–205. 12136057
21. Replogle JM, Chan G, White CC, Raj T, Winn PA, Evans DA, et al. A TREM1 variant alters the accumulation of Alzheimer-related amyloid pathology. Ann Neurol. 2015;77(3):469–77. doi: 10.1002/ana.24337 25545807
22. Bennett DA, Yu L, De Jager PL. Building a pipeline to discover and validate novel therapeutic targets and lead compounds for Alzheimer’s disease. Biochem Pharmacol. 2014;88(4):617–30. doi: 10.1016/j.bcp.2014.01.037 24508835
23. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81(3):559–75. doi: 10.1086/519795 17701901
24. De Jager PL, Shulman JM, Chibnik LB, Keenan BT, Raj T, Wilson RS, et al. A genome-wide scan for common variants affecting the rate of age-related cognitive decline. Neurobiol Aging. 2012;33(5):1017.e1–15. doi: 10.1016/j.neurobiolaging.2011.09.033 22054870
25. Shulman JM, Chen K, Keenan BT, Chibnik LB, Fleisher A, Thiyyagura P, et al. Genetic susceptibility for Alzheimer disease neuritic plaque pathology. JAMA Neurol. 2013;70(9):1150–7. doi: 10.1001/jamaneurol.2013.2815 23836404
26. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet. 2006;38(8):904–9. doi: 10.1038/ng1847 16862161
27. Browning BL, Browning SR. A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet. 2009;84(2):210–23. doi: 10.1016/j.ajhg.2009.01.005 19200528
28. 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. 1997;18(4 Suppl):S1–2. 9330978
29. Arvanitakis Z, Leurgans SE, Wang Z, Wilson RS, Bennett DA, Schneider JA. Cerebral amyloid angiopathy pathology and cognitive domains in older persons. Ann Neurol. 2011;69(2):320–7. doi: 10.1002/ana.22112 21387377
30. Gorelick PB, Scuteri A, Black SE, Decarli C, Greenberg SM, Iadecola C, et al. Vascular contributions to cognitive impairment and dementia: a statement for healthcare professionals from the American Heart Association/American Stroke Association. Stroke. 2011;42(9):2672–713. doi: 10.1161/STR.0b013e3182299496 21778438
31. Schneider JA, Bennett DA. Where vascular meets neurodegenerative disease. Stroke. 2010;41(10 Suppl):S144–6. doi: 10.1161/STROKEAHA.110.598326 20876491
32. Nelson PT, Schmitt FA, Lin Y, Abner EL, Jicha GA, Patel E, et al. Hippocampal sclerosis in advanced age: clinical and pathological features. Brain. 2011;134(Pt 5):1506–18. doi: 10.1093/brain/awr053 21596774
33. Arvanitakis Z, Leurgans SE, Barnes LL, Bennett DA, Schneider JA. Microinfarct pathology, dementia, and cognitive systems. Stroke. 2011;42(3):722–7. doi: 10.1161/STROKEAHA.110.595082 21212395
34. Boyle PA, Yu L, Nag S, Leurgans S, Wilson RS, Bennett DA, et al. Cerebral amyloid angiopathy and cognitive outcomes in community-based older persons. Neurology. 2015;85(22):1930–6. doi: 10.1212/WNL.0000000000002175 26537052
35. Yip AG, McKee AC, Green RC, Wells J, Young H, Cupples LA, et al. APOE, vascular pathology, and the AD brain. Neurology. 2005;65(2):259–65. doi: 10.1212/01.wnl.0000168863.49053.4d 16043796
36. 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. 2006;66(12):1837–44. doi: 10.1212/01.wnl.0000219668.47116.e6 16801647
37. Yu L, De Jager PL, Yang J, Trojanowski JQ, Bennett DA, Schneider JA. The TMEM106B locus and TDP-43 pathology in older persons without FTLD. Neurology. 2015;84(9):927–34. doi: 10.1212/WNL.0000000000001313 25653292
38. Wilson RS, Yu L, Trojanowski JQ, Chen EY, Boyle PA, Bennett DA, et al. TDP-43 pathology, cognitive decline, and dementia in old age. JAMA Neurol. 2013;70(11):1418–24. doi: 10.1001/jamaneurol.2013.3961 24080705
39. Chan G, White CC, Winn PA, Cimpean M, Replogle JM, Glick LR, et al. CD33 modulates TREM2: convergence of Alzheimer loci. Nat Neurosci. 2015;18(11):1556–8. doi: 10.1038/nn.4126 26414614
40. Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics. 2007;8(1):118–27. doi: 10.1093/biostatistics/kxj037 16632515
41. Ramos-Miguel A, Hercher C, Beasley CL, Barr AM, Bayer TA, Falkai P, et al. Loss of Munc18-1 long splice variant in GABAergic terminals is associated with cognitive decline and increased risk of dementia in a community sample. Mol Neurodegener. 2015;10:65. doi: 10.1186/s13024-015-0061-4 26628003
42. Ward LD, Kellis M. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res. 2012;40(Database issue):D930–4. doi: 10.1093/nar/gkr917 22064851
43. Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods. 2012;9(3):215–6. doi: 10.1038/nmeth.1906 22373907
44. Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015;518(7539):317–30. doi: 10.1038/nature14248 25693563
45. Stranger BE, Montgomery SB, Dimas AS, Parts L, Stegle O, Ingle CE, et al. Patterns of cis regulatory variation in diverse human populations. PLoS Genet. 2012;8(4):e1002639. doi: 10.1371/journal.pgen.1002639 22532805
46. Yu L, Chibnik LB, Srivastava GP, Pochet N, Yang J, Xu J, et al. Association of brain DNA methylation in SORL1, ABCA7, HLA-DRB5, SLC24A4, and BIN1 with pathological diagnosis of Alzheimer disease. JAMA Neurol. 2015;72(1):15–24. doi: 10.1001/jamaneurol.2014.3049 25365775
47. Chen-Plotkin AS, Unger TL, Gallagher MD, Bill E, Kwong LK, Volpicelli-Daley L, et al. TMEM106B, the risk gene for frontotemporal dementia, is regulated by the microRNA-132/212 cluster and affects progranulin pathways. J Neurosci. 2012;32(33):11213–27. doi: 10.1523/JNEUROSCI.0521-12.2012 22895706
48. GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nat Genet. 2013;45(6):580–5. doi: 10.1038/ng.2653 23715323
49. Pruim RJ, Welch RP, Sanna S, Teslovich TM, Chines PS, Gliedt TP, et al. LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics. 2010;26(18):2336–7. doi: 10.1093/bioinformatics/btq419 20634204
50. Yu L, Boyle PA, Leurgans S, Schneider JA, Bennett DA. Disentangling the effects of age and APOE on neuropathology and late life cognitive decline. Neurobiol Aging. 2014;35(4):819–26. doi: 10.1016/j.neurobiolaging.2013.10.074 24199961
51. Lambert JC, Ibrahim-Verbaas CA, Harold D, Naj AC, Sims R, Bellenguez C, et al. Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer’s disease. Nat Genet. 2013;45(12):1452–8. doi: 10.1038/ng.2802 24162737
52. Davies G, Marioni RE, Liewald DC, Hill WD, Hagenaars SP, Harris SE, et al. Genome-wide association study of cognitive functions and educational attainment in UK Biobank (N = 112 151). Mol Psychiatry. 2016;21(6):758–67. doi: 10.1038/mp.2016.45 27046643
53. Davies G, Armstrong N, Bis JC, Bressler J, Chouraki V, Giddaluru S, et al. Genetic contributions to variation in general cognitive function: a meta-analysis of genome-wide association studies in the CHARGE consortium (N = 53949). Mol Psychiatry. 2015;20(2):183–92. doi: 10.1038/mp.2014.188 25644384
54. Kim Y, Xia K, Tao R, Giusti-Rodriguez P, Vladimirov V, van den Oord E, et al. A meta-analysis of gene expression quantitative trait loci in brain. Translational psychiatry. 2014;4:e459. doi: 10.1038/tp.2014.96 25290266
55. Van Deerlin VM, Sleiman PM, Martinez-Lage M, Chen-Plotkin A, Wang LS, Graff-Radford NR, et al. Common variants at 7p21 are associated with frontotemporal lobar degeneration with TDP-43 inclusions. Nat Genet. 2010;42(3):234–9. doi: 10.1038/ng.536 20154673
56. Ackerman SL, Kozak LP, Przyborski SA, Rund LA, Boyer BB, Knowles BB. The mouse rostral cerebellar malformation gene encodes an UNC-5-like protein. Nature. 1997;386(6627):838–42. doi: 10.1038/386838a0 9126743
57. Leonardo ED, Hinck L, Masu M, Keino-Masu K, Ackerman SL, Tessier-Lavigne M. Vertebrate homologues of C. elegans UNC-5 are candidate netrin receptors. Nature. 1997;386(6627):833–8. doi: 10.1038/386833a0 9126742
58. Bernet A, Mazelin L, Coissieux MM, Gadot N, Ackerman SL, Scoazec JY, et al. Inactivation of the UNC5C Netrin-1 receptor is associated with tumor progression in colorectal malignancies. Gastroenterology. 2007;133(6):1840–8. doi: 10.1053/j.gastro.2007.08.009 17967459
59. Wetzel-smith MK, Hunkapiller J, Bhangale TR, Srinivasan K, Maloney JA, Atwal JK, et al. A rare mutation in UNC5C predisposes to late-onset Alzheimer’s disease and increases neuronal cell death. Nat Med. 2014;20:1452–7. doi: 10.1038/nm.3736 25419706
60. Hernandez MC, Andres-Barquin PJ, Martinez S, Bulfone A, Rubenstein JL, Israel MA. ENC-1: a novel mammalian kelch-related gene specifically expressed in the nervous system encodes an actin-binding protein. J Neurosci. 1997;17(9):3038–51. 9096139
61. Kim TA, Lim J, Ota S, Raja S, Rogers R, Rivnay B, et al. NRP/B, a novel nuclear matrix protein, associates with p110(RB) and is involved in neuronal differentiation. J Cell Biol. 1998;141(3):553–66. 9566959
62. Lei H, Li J, Zhao Z, Liu L. Inhibition of ectodermal-neural cortex 1 protects neural cells from apoptosis induced by hypoxia and hypoglycemia. J Mol Neurosci. 2016;59(1):126–34. doi: 10.1007/s12031-016-0742-7 27039095
63. Lee H, Ahn HH, Lee W, Oh Y, Choi H, Shim SM, et al. ENC1 modulates the aggregation and neurotoxicity of mutant huntingtin through p62 under ER stress. Mol Neurobiol. 2015;53:6620–34. doi: 10.1007/s12035-015-9557-8 26637326
64. Vass R, Ashbridge E, Geser F, Hu WT, Grossman M, Clay-Falcone D, et al. Risk genotypes at TMEM106B are associated with cognitive impairment in amyotrophic lateral sclerosis. Acta Neuropathol. 2011;121(3):373–80. doi: 10.1007/s00401-010-0782-y 21104415
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