1. Linking non-coding variants to function in microglia in Alzheimer’s disease
- Author
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Yang, Xiaoyu, Wen, Jia, Yang, Han, Jones, Ian R, Zhu, Xiaodong, Liu, Weifang, Li, Bingkun, Clelland, Claire D, Luo, Wenjie, Wong, Man Ying, Ren, Xingjie, Cui, Xiekui, Song, Michael, Liu, Hongjiang, Chen, Cady, Eng, Nicolas, Ravichandran, Mirunalini, Sun, Yang, Lee, David, Van Buren, Eric, Jiang, Min-Zhi, Chan, Candace SY, Ye, Chun Jimmie, Perera, Rushika M, Gan, Li, Li, Yun, and Shen, Yin
- Subjects
Biochemistry and Cell Biology ,Genetics ,Biological Sciences ,Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD) ,Neurodegenerative ,Brain Disorders ,Neurosciences ,Acquired Cognitive Impairment ,Alzheimer's Disease ,Dementia ,Human Genome ,Aging ,Aetiology ,2.1 Biological and endogenous factors ,Neurological ,Humans ,Alzheimer Disease ,Microglia ,Amyloid beta-Peptides ,Genetic Predisposition to Disease ,Biotechnology ,Genome-Wide Association Study ,Cell Membrane ,Phenotype ,Medical and Health Sciences ,Developmental Biology ,Agricultural biotechnology ,Bioinformatics and computational biology - Abstract
Candidate cis-regulatory elements (cCREs) in microglia demonstrate the most substantial enrichment for Alzheimer's disease (AD) heritability compared to other brain cell types. However, whether and how these genome-wide association studies (GWAS) variants contribute to AD remain elusive. Here we prioritize 308 previously unreported AD risk variants at 181 cCREs by integrating genetic information with microglia-specific 3D epigenome annotation. We further establish the link between functional variants and target genes by single-cell CRISPRi screening in microglia. In addition, we show that AD variants exhibit allelic imbalance on target gene expression. In particular, rs7922621 is the effective variant in controlling TSPAN14 expression among other nominated variants in the same cCRE and exerts multiple physiological effects including reduced cell surface ADAM10 and altered soluble TREM2 (sTREM2) shedding. Our work represents a systematic approach to prioritize and characterize AD-associated variants and provides a roadmap for advancing genetic association to experimentally validated cell-type-specific phenotypes and mechanisms.
- Published
- 2023