Fig. 5: Functional annotation and follow-up for the selected V2G pair: chr7:54881563:A:G (rs74504435) and EGFR.
From: Integrated genomic analysis and CRISPRi implicates EGFR in Alzheimer’s disease risk
A Genome browser plot showing the functional annotation of the selected V2G pair in GRCh38 using FILER tracks at the discovery phase, including enhancers from chromHMM and EpiMAP, eQTLs from GTEx and eQTL Catalogue. Bellenguez GWAS identified the sentinel SNP rs76928645 (chr7:54873635:C:T) (p = 1.6 × 10−10), in high LD (r2 = 0.94) with our variant of interest rs74504435, which is annotated to reside in a brain enhancer in four different data sources. Plot is generated using NIAGADS genomicsDB. B ATAC-seq, promoter-focused Capture C, and Hi-C data in brain-relevant cell types showing chromatin state and looping between chr7:54881563:A:G (rs74504435) and EGFR. rs74504435 (highlighted by a yellow line) resides in open chromatin in our own iPSC-derived neural progenitors, neurons, and microglia, and in primary astrocytes. It is involved in a chromatin loop with EGFR in our own iPSC-derived neurons, primary astrocytes, and the microglial cell line HMC3 (promoter-focused Capture C data); as well as in our own iPSC-derived neurons and oligodendrocytes (Hi-C data). C CRISPRi results in a human microglia cell line. We performed CRISPRi in a human microglial cell line (HMC3) expressing dCas9-ZIM3-KRAB using lentiviral delivery of three sgRNA guides targeting the rs74504435 region (G1, G2, and G4) and two non-targeting guides (NTC: mean of control guides). Bar plots show the mean EGFR relative expression compared to a no-guide control as assessed by qPCR; error bars are SEM; N = 3. Statistical analysis via one-way ANOVA followed by Tukey test, **p < 0.001; *p < 0.05.
