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Basic Science and Pathogenesis.

Luciana Bertholim Nasciben1, Derek Van Booven2, Wanying Xu3

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A protective allele for Alzheimer's disease (AD) interacts with the APOE gene. This interaction involves a unique VNTR region, offering potential therapeutic targets for AD.

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Area of Science:

  • Genomics
  • Neuroscience
  • Human Genetics

Background:

  • A specific allele (rs10423769 A) confers up to 75% reduced Alzheimer's disease (AD) risk in APOEε4 homozygotes.
  • Understanding the mechanism of this protective variant could lead to novel therapeutics for APOEε4 carriers.
  • The genomic region surrounding the protective variant is complex, featuring segmental duplications (SD) and structural variants (SVs).

Purpose of the Study:

  • To investigate the genomic region between the protective rs10423769 A allele and the APOE gene using advanced techniques.
  • To elucidate potential AD-protective mechanisms conferred by this variant.
  • To analyze the complex genomic landscape including SDs and SVs.

Main Methods:

  • High-coverage PacBio HiFi whole genome sequencing was performed on 9 samples.
  • Genome assembly and comparative analysis were conducted using hifiasm, minigraph, and Bandage.
  • Hi-C sequencing and in-house bioinformatics tools (eHiCA) were employed to identify potential chromatin interactions.

Main Results:

  • Long read sequencing identified an expanded VNTR with MEF2D transcription factor binding sites in the protective haplotype.
  • An increased number of SVs were detected in the SD region surrounding the rs10423769 A haplotype.
  • eHiCA revealed evidence of long-range physical interactions between the rs10423769 locus, the APOE promoter, and intervening regions including ZNF genes.

Conclusions:

  • The African-origin protective haplotype exhibits long-range physical interactions with the APOE promoter and other chr19 regions.
  • This protective haplotype contains an expanded VNTR with multiple transcription factor binding sites.
  • These findings provide insights into the genomic mechanisms underlying AD risk reduction.