Skip to main content
Erschienen in: Acta Neuropathologica 4/2019

02.02.2019 | Original Paper

Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer’s disease

verfasst von: Stephen A. Semick, Rahul A. Bharadwaj, Leonardo Collado-Torres, Ran Tao, Joo Heon Shin, Amy Deep-Soboslay, James R. Weiss, Daniel R. Weinberger, Thomas M. Hyde, Joel E. Kleinman, Andrew E. Jaffe, Venkata S. Mattay

Erschienen in: Acta Neuropathologica | Ausgabe 4/2019

Einloggen, um Zugang zu erhalten

Abstract

Late-onset Alzheimer’s disease (AD) is a complex age-related neurodegenerative disorder that likely involves epigenetic factors. To better understand the epigenetic state associated with AD, we surveyed 420,852 DNA methylation (DNAm) sites from neurotypical controls (N = 49) and late-onset AD patients (N = 24) across four brain regions (hippocampus, entorhinal cortex, dorsolateral prefrontal cortex and cerebellum). We identified 858 sites with robust differential methylation collectively annotated to 772 possible genes (FDR < 5%, within 10 kb). These sites were overrepresented in AD genetic risk loci (p = 0.00655) and were enriched for changes during normal aging (p < 2.2 × 10−16), and nearby genes were enriched for processes related to cell-adhesion, immunity, and calcium homeostasis (FDR < 5%). To functionally validate these associations, we generated and analyzed corresponding transcriptome data to prioritize 130 genes within 10 kb of the differentially methylated sites. These 130 genes were differentially expressed between AD cases and controls and their expression was associated with nearby DNAm (p < 0.05). This integrated analysis implicates novel genes in Alzheimer’s disease, such as ANKRD30B. These results highlight DNAm differences in Alzheimer’s disease that have gene expression correlates, further implicating DNAm as an epigenetic mechanism underlying pathological molecular changes associated with AD. Furthermore, our framework illustrates the value of integrating epigenetic and transcriptomic data for understanding complex disease.
Anhänge
Nur mit Berechtigung zugänglich
Literatur
5.
Zurück zum Zitat Braak H, Braak E (1991) Neuropathological stageing of Alzheimer-related changes. Acta Neuropathologica 82(4):239–259CrossRefPubMed Braak H, Braak E (1991) Neuropathological stageing of Alzheimer-related changes. Acta Neuropathologica 82(4):239–259CrossRefPubMed
7.
Zurück zum Zitat Collado-Torres L, Burke EE, Peterson A, Shin JH, Straub RE, Rajpurohi A et al (2018) Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia. bioRxiv. https://doi.org/10.1101/426213 CrossRef Collado-Torres L, Burke EE, Peterson A, Shin JH, Straub RE, Rajpurohi A et al (2018) Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia. bioRxiv. https://​doi.​org/​10.​1101/​426213 CrossRef
8.
Zurück zum Zitat Conejero-Goldberg C, Hyde TM, Chen S, Herman MM, Kleinman JE, Davies P et al (2015) Cortical Transcriptional Profiles in APOE4 Carriers with Alzheimer's disease: patterns of protection and degeneration. J Alzheimers Dis 48(4):969–978CrossRefPubMed Conejero-Goldberg C, Hyde TM, Chen S, Herman MM, Kleinman JE, Davies P et al (2015) Cortical Transcriptional Profiles in APOE4 Carriers with Alzheimer's disease: patterns of protection and degeneration. J Alzheimers Dis 48(4):969–978CrossRefPubMed
10.
Zurück zum Zitat Corder EH, Saunders AM, Strittmatter WJ, Schmechel DE, Gaskell PC, Small GW et al (1993) Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer’s disease in late onset families. Science 261:921–923CrossRefPubMed Corder EH, Saunders AM, Strittmatter WJ, Schmechel DE, Gaskell PC, Small GW et al (1993) Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer’s disease in late onset families. Science 261:921–923CrossRefPubMed
13.
Zurück zum Zitat Farrer LA, Cupples LA, Haines JL, Hyman B, Kukull WA, Mayeux R et al (1997) Effects of age, sex, and ethnicity on the association between apolipoprotein E genotype and Alzheimer disease. A meta-analysis. APOE and Alzheimer Disease Meta Analysis Consortium. JAMA 278:1349–1356CrossRefPubMed Farrer LA, Cupples LA, Haines JL, Hyman B, Kukull WA, Mayeux R et al (1997) Effects of age, sex, and ethnicity on the association between apolipoprotein E genotype and Alzheimer disease. A meta-analysis. APOE and Alzheimer Disease Meta Analysis Consortium. JAMA 278:1349–1356CrossRefPubMed
14.
Zurück zum Zitat Fleminger S (2003) Head injury as a risk factor for Alzheimer's disease: the evidence 10 years on; a partial replication. J Neurol Neurosurg Psychiatry 74(7):857–862CrossRefPubMedPubMedCentral Fleminger S (2003) Head injury as a risk factor for Alzheimer's disease: the evidence 10 years on; a partial replication. J Neurol Neurosurg Psychiatry 74(7):857–862CrossRefPubMedPubMedCentral
23.
Zurück zum Zitat Hyman BT, Trojanowski JQ (1997) Consensus recommendations for the postmortem diagnosis of Alzheimer disease from the National Institute on Aging and the Reagan Institute Working Group on diagnostic criteria for the neuropathological assessment of Alzheimer disease. J Neuropathol Exp Neurol 56(10):1095–1097CrossRefPubMed Hyman BT, Trojanowski JQ (1997) Consensus recommendations for the postmortem diagnosis of Alzheimer disease from the National Institute on Aging and the Reagan Institute Working Group on diagnostic criteria for the neuropathological assessment of Alzheimer disease. J Neuropathol Exp Neurol 56(10):1095–1097CrossRefPubMed
27.
Zurück zum Zitat Jager D, Stockert E, Gure AO, Scanlan MJ, Karbach J, Jager E et al (2001) Identification of a tissue-specific putative transcription factor in breast tissue by serological screening of a breast cancer library. Cancer Res 61:2055–2061PubMed Jager D, Stockert E, Gure AO, Scanlan MJ, Karbach J, Jager E et al (2001) Identification of a tissue-specific putative transcription factor in breast tissue by serological screening of a breast cancer library. Cancer Res 61:2055–2061PubMed
36.
Zurück zum Zitat Lindsay J, Laurin D, Verreault R, Hebert R, Helliwell B, Hill GB et al (2002) Risk factors for Alzheimer’s disease: a prospective analysis from the Canadian Study of Health and Aging. Am J Epidemiol 156:445–453CrossRefPubMed Lindsay J, Laurin D, Verreault R, Hebert R, Helliwell B, Hill GB et al (2002) Risk factors for Alzheimer’s disease: a prospective analysis from the Canadian Study of Health and Aging. Am J Epidemiol 156:445–453CrossRefPubMed
52.
Zurück zum Zitat Price AJ, Collado-Torres L, Ivanov NA, Xia W, Burke EE, Shin JH et al (2018) Divergent neuronal DNA methylation patterns across human cortical development: critical periods and a unique role of CpH methylation. bioRxiv. https://doi.org/10.1101/428391 CrossRef Price AJ, Collado-Torres L, Ivanov NA, Xia W, Burke EE, Shin JH et al (2018) Divergent neuronal DNA methylation patterns across human cortical development: critical periods and a unique role of CpH methylation. bioRxiv. https://​doi.​org/​10.​1101/​428391 CrossRef
55.
Zurück zum Zitat Rizzardi LF, Hickey PF, DiBlasi VR, Tryggvadóttir R, Callahan CM, Idrizi A et al (2019) Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability. Nature Neurosci 22(2):307–316CrossRefPubMed Rizzardi LF, Hickey PF, DiBlasi VR, Tryggvadóttir R, Callahan CM, Idrizi A et al (2019) Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability. Nature Neurosci 22(2):307–316CrossRefPubMed
62.
Zurück zum Zitat Smith AR, Mill J, Smith RG, Lunnon K (2016) Elucidating novel dysfunctional pathways in Alzheimer's disease by integrating loci identified in genetic and epigenetic studies. Neuroepigenetics 6:32–50CrossRef Smith AR, Mill J, Smith RG, Lunnon K (2016) Elucidating novel dysfunctional pathways in Alzheimer's disease by integrating loci identified in genetic and epigenetic studies. Neuroepigenetics 6:32–50CrossRef
68.
Zurück zum Zitat Yamamoto T, Hirano A (1986) A comparative study of modified Bielschowsky, Bodian and thioflavin S stains on Alzheimer's neurofibrillary tangles. Neuropathol Appl Neurobiol 12(1):3–9CrossRefPubMed Yamamoto T, Hirano A (1986) A comparative study of modified Bielschowsky, Bodian and thioflavin S stains on Alzheimer's neurofibrillary tangles. Neuropathol Appl Neurobiol 12(1):3–9CrossRefPubMed
Metadaten
Titel
Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer’s disease
verfasst von
Stephen A. Semick
Rahul A. Bharadwaj
Leonardo Collado-Torres
Ran Tao
Joo Heon Shin
Amy Deep-Soboslay
James R. Weiss
Daniel R. Weinberger
Thomas M. Hyde
Joel E. Kleinman
Andrew E. Jaffe
Venkata S. Mattay
Publikationsdatum
02.02.2019
Verlag
Springer Berlin Heidelberg
Erschienen in
Acta Neuropathologica / Ausgabe 4/2019
Print ISSN: 0001-6322
Elektronische ISSN: 1432-0533
DOI
https://doi.org/10.1007/s00401-019-01966-5

Weitere Artikel der Ausgabe 4/2019

Acta Neuropathologica 4/2019 Zur Ausgabe

Leitlinien kompakt für die Neurologie

Mit medbee Pocketcards sicher entscheiden.

Seit 2022 gehört die medbee GmbH zum Springer Medizin Verlag

Update Neurologie

Bestellen Sie unseren Fach-Newsletter und bleiben Sie gut informiert.