Cited by 206Alzheimer's disease research and treatmentsGenomics and Chromatin DynamicsEpigenetics and DNA Methylation

Epigenomic dissection of Alzheimer’s disease pinpoints causal variants and reveals epigenome erosion

Open access
Xiong, Xushen, James, Benjamin T., Boix, Carles A., Park, Yongjin P., Galani, Kyriaki, Victor, Matheus B., Sun, Na, Hou, Lei +9 more·2023·Cell

Abstract

Recent work has identified dozens of non-coding loci for Alzheimer's disease (AD) risk, but their mechanisms and AD transcriptional regulatory circuitry are poorly understood. Here, we profile epigenomic and transcriptomic landscapes of 850,000 nuclei from prefrontal cortexes of 92 individuals with and without AD to build a map of the brain regulome, including epigenomic profiles, transcriptional regulators, co-accessibility modules, and peak-to-gene links in a cell-type-specific manner. We develop methods for multimodal integration and detecting regulatory modules using peak-to-gene linking. We show AD risk loci are enriched in microglial enhancers and for specific TFs including SPI1, ELF2, and RUNX1. We detect 9,628 cell-type-specific ATAC-QTL loci, which we integrate alongside peak-to-gene links to prioritize AD variant regulatory circuits. We report differential accessibility of regulatory modules in late AD in glia and in early AD in neurons. Strikingly, late-stage AD brains show global epigenome dysregulation indicative of epigenome erosion and cell identity loss.

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Crossref · 10.1016/j.cell.2023.08.040

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  • Recent single-cell studies of human AD revealed links between DNA damage and epigenome erosion during disease progression.

    “Recent single-cell studies of human AD revealed the links between DNA damage and epigenome erosion during disease progression77,78.”
  • These works estimated damage burden by measuring chimeric gene fusions arising from DSBs.

    “These work estimated damage burden by measuring chimeric gene fusions arose from DSBs.”
  • The rs10792832-flanking OCR peak identified in iMG is present in brain microglia but not in other brain cell types.

    “Note the rs10792832-flanking peak (highlighted in the vertical yellow box) identified in our iMG is only present in brain microglia but not in other cell types.”
  • These severely affected donors had lower transcription and reduced chromatin accessibility that may correspond to senescent states or global epigenome dysregulation that is indicative of cell identity loss.

    “These severely affected donors had lower transcription and reduced chromatin accessibility that may correspond to senescent states97, or global epigenome dysregulation that is indicative of cell identity loss98.”

    From Integrated multimodal cell atlas of Alzheimer’s disease (2024) · cites this paper as [98]

  • The accompanying manuscript by Xiong et al. describes widespread changes in cell-type specific chromatin accessibility within excitatory neurons in human AD samples, termed epigenome erosion.

    “the accompanying manuscript by Xiong et al. describes widespread changes in cell-type specific chromatin accessibility within excitatory neurons in human AD samples which they term “epigenome erosion””

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Authors
Xiong, X., James, B. T., Boix, C. A., Park, Y. P., Galani, K., Victor, M. B., Sun, N., Hou, L., Ho, L.-L., Mantero, J., Scannail, A. N., Dileep, V., Dong, W., Mathys, H., Bennett, D. A., Tsai, L.-H., & Kellis, M.
Affiliations
  • MIT Computer Science and Artificial Intelligence Laboratory (US)
  • Broad Institute (US)
  • Massachusetts Institute of Technology (US)
  • University of California San Diego (US)
  • University of Pittsburgh (US)
  • Rush University Medical Center (US)
Corresponding author
  • Tsai, Li-Huei
  • Kellis, Manolis
Venue
Cell
Publisher
Elsevier BV
Published
2023-09
Volume
186
Issue
20
Pages
4422-4437.e21
ISSN
0092-8674 (ISSN-L)
OpenAlex
W4387142583
Cited by
205
References
86
Citations by year
2026: 70 · 2025: 72 · 2024: 51 · 2023: 11 · 2022: 1
FWCI
36.23
Type
journal article
Language
en
Open access
Locations
  • Cell (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion, other-oa)
Funders
  • Cure Alzheimer's Fund
  • National Institutes of Health (AG062377, P30AG10161, NS110453, U01AG46152, AG058002, MH119509, R01AG57473, U01AG61356, AG054012, NS127187, R01AG17917, P30AG72975, AG062335, NS115064, HG008155, MH109978, DA053631, R01AG15819, AG067151, AG074003, AG081017, AG077227, NS129032)
  • Russian Science Foundation
  • National Science Foundation (1745302)
Topics
  • Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
Alzheimer's disease, prefrontal cortex, PU.1, RUNX1, chromatin accessibility, glial cells, neurons
MeSH terms
Epigenome, Alzheimer Disease, Brain, Gene Expression Regulation, Humans, Genome-Wide Association Study, Epigenomics

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