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Basic Science and Pathogenesis.

Julianna N Brutman1, Eli J Kaufman1, Evangelos Nizamis1

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Summary
This summary is machine-generated.

Double-strand breaks (DSBs) in the APOE gene are linked to Alzheimer's disease (AD) risk variants. These DNA repair events may alter APOE function and AD pathogenesis.

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Area of Science:

  • Genetics
  • Neuroscience
  • Molecular Biology

Background:

  • Apolipoprotein E (APOE) genotype is the primary genetic risk factor for Alzheimer's disease (AD).
  • The precise biological mechanisms driving APOE-related AD pathogenesis remain unclear.
  • Double-strand breaks (DSBs) are implicated in both normal memory formation and early AD pathology, but their specific role in AD is not well-defined.

Purpose of the Study:

  • To investigate the occurrence and characteristics of DNA double-strand breaks (DSBs) within the APOE gene in human samples.
  • To determine if DSBs are associated with specific APOE risk variants, particularly APOE-ε4.
  • To explore the transcriptional consequences of these DSB events in the context of AD.

Main Methods:

  • Analysis of single-nuclei RNA sequencing (snRNAseq) data from human brain tissue.
  • Examination of DNA sequencing data from the Alzheimer's Disease Sequencing Project (ADSP) for evidence of DSBs.
  • Identification and characterization of sequence reads exhibiting gaps or split-reads indicative of DSB and repair events.

Main Results:

  • Approximately 1,999 DNA sequence reads from the ADSP dataset showed DSB and repair events within the APOE gene, averaging 334bp in length.
  • These DSBs frequently occurred in the last exon of APOE and were associated with risk variants like APOE-ε4, APOE-ε2, and APOE-Christchurch, sometimes excising them.
  • Transcribed DSB events (split-reads) were detected in astrocytes and microglia, with a significant enrichment in AD samples compared to controls, particularly originating near the APOE-ε4 SNP rs429358.

Conclusions:

  • APOE is subject to extensive double-strand break and repair events that can excise critical risk variants.
  • These findings suggest a novel mechanism by which APOE genotype influences AD risk.
  • The study highlights the potential role of DNA repair dynamics in AD pathogenesis and APOE's complex function.