High‐throughput CRISPRi screening to investigate mechanisms underlying Alzheimer’s risk loci

AbstractBackgroundAlzheimer’s disease (AD) is a highly (60‐80%) heritable disease with 75 known genetic risk loci. Interestingly, preliminary data from human tissues suggests that these risk loci predominantly act through myeloid cells, implicating microglia, the brain’s resident immune cell, as playing a critical role in AD risk. However, whether the mechanisms underlying these risk loci can be studied in induced pluripotent stem cell (iPSC)‐derived systems, which are currently the only physiologically relevant human model system, remains unknown.MethodWe generated neural progenitors, excitatory neurons, astrocytes and microglia from two human iPSC lines, and performed RNA‐seq to identify all expressed genes and ChIP‐seq for H3K27ac to identify all active gene promoters and enhancers. We compared these data to ChIP‐seq data from primary uncultured (ex vivo) adult human microglia to compare the enrichment of AD risk loci polymorphisms in active promoters and enhancers, as well as a larger panel of neuropsychiatric and neurodegenerative conditions.ResultiPSC‐derived microglia‐like cells (iMGLs) recapitulated an enrichment of AD risk loci polymorphisms in microglial promoters and enhancers previously seen in ex vivo primary human microglia. Furthermore, the enrichments of polymorphisms conferring risk for other neurological and neurodegenerative conditions were similar in iMGLs and ex vivo microglia, suggesting that the epigenome of iMGLs is similar to that of in vivo human microglia.ConclusioniMGLs will serve as a useful cell‐based model for studying AD risk loci, and we are currently developing high‐throughput CRISPR‐based genome and epigenome editing systems to dissect the molecular and cellular mechanisms at these loci, which will nominate novel genes and pathways for therapeutic development.