Cited by 223Alzheimer's disease research and treatmentsDNA Repair MechanismsCancer Genomics and Diagnostics

Somatic genomic changes in single Alzheimer’s disease neurons

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Miller, Michael B., Huang, August Yue, Kim, Junho, Zhou, Zinan, Kirkham, Samantha L., Maury, Eduardo A., Ziegenfuss, Jennifer S., Reed, Hannah C. +12 more·2022·Nature

Abstract

Dementia in Alzheimer's disease progresses alongside neurodegeneration 1-4, but the specific events that cause neuronal dysfunction and death remain poorly understood. During normal ageing, neurons progressively accumulate somatic mutations 5 at rates similar to those of dividing cells 6,7 which suggests that genetic factors, environmental exposures or disease states might influence this accumulation 5. Here we analysed single-cell whole-genome sequencing data from 319 neurons from the prefrontal cortex and hippocampus of individuals with Alzheimer's disease and neurotypical control individuals. We found that somatic DNA alterations increase in individuals with Alzheimer's disease, with distinct molecular patterns. Normal neurons accumulate mutations primarily in an age-related pattern (signature A), which closely resembles 'clock-like' mutational signatures that have been previously described in healthy and cancerous cells 6-10. In neurons affected by Alzheimer's disease, additional DNA alterations are driven by distinct processes (signature C) that highlight C>A and other specific nucleotide changes. These changes potentially implicate nucleotide oxidation 4,11, which we show is increased in Alzheimer's-disease-affected neurons in situ. Expressed genes exhibit signature-specific damage, and mutations show a transcriptional strand bias, which suggests that transcription-coupled nucleotide excision repair has a role in the generation of mutations. The alterations in Alzheimer's disease affect coding exons and are predicted to create dysfunctional genetic knockout cells and proteostatic stress. Our results suggest that known pathogenic mechanisms in Alzheimer's disease may lead to genomic damage to neurons that can progressively impair function. The aberrant accumulation of DNA alterations in neurodegeneration provides insight into the cascade of molecular and cellular events that occurs in the development of Alzheimer's disease.

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Authors
Miller, M. B., Huang, A. Y., Kim, J., Zhou, Z., Kirkham, S. L., Maury, E. A., Ziegenfuss, J. S., Reed, H. C., Neil, J. E., Rento, L., Ryu, S. C., Ma, C. C., Luquette, L. J., Ames, H. M., Oakley, D. H., Frosch, M. P., Hyman, B. T., Lodato, M. A., Lee, E. A., & Walsh, C. A.
Affiliations
  • Broad Institute (US)
  • Boston Children's Hospital (US)
  • University of Massachusetts Chan Medical School (US)
  • Allegheny College (US)
  • Harvard University (US)
  • University of Maryland, Baltimore (US)
Corresponding author
  • Lodato, Michael A.
  • Lee, Eunjung Alice
  • Walsh, Christopher A.
Venue
Nature
Published
2022-04-20
Volume
604
Issue
7907
Pages
714-722
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
OpenAlex
W4224234680
Cited by
223
References
84
Citations by year
2026: 41 · 2025: 52 · 2024: 57 · 2023: 53 · 2022: 20
FWCI
28.33
Type
journal article
Language
en
Open access
Locations
  • Nature (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
Funders
  • Howard Hughes Medical Institute
  • National Institutes of Health (1t15lm007098-01)
  • National Institute on Aging (K08AG065502, DP2AG072437, K01AG051791, R00AG054748, R01AG070921, P30AG062421)
  • National Heart, Lung, and Blood Institute (T32HL007627)
  • National Human Genome Research Institute (T32HG002295)
  • National Institute of General Medical Sciences (T32GM007753)
  • National Institute of Neurological Disorders and Stroke (R01NS032457)
  • Eunice Kennedy Shriver National Institute of Child Health and Human Development (P50HD105351)
Topics
  • Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
Keywords
Alzheimer's disease, somatic mutations, neuronal DNA damage, mutational signatures, nucleotide oxidation, transcription-coupled repair, prefrontal cortex, hippocampus, neurodegeneration, aging, single-cell whole-genome sequencing
MeSH terms
Whole Genome Sequencing, Aging, Alzheimer Disease, DNA, Exons, Hippocampus, Humans, Neurons, Nucleotides, Prefrontal Cortex, Genomics, Mutation Rate

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