Combining evidence from human genetic and functional screens to identify pathways altering obesity and fat distribution

Overall adiposity and body fat distribution are heritable traits associated with altered risk of cardiometabolic disease and mortality. Performing rare variant (minor allele frequency<1%) association testing using exome-sequencing data from 402,375 participants in the UK Biobank (UKB) for nine overall and tissue-specific fat distribution traits, we identified 19 genes where putatively damaging rare variation associated with at least one trait (Bonferroni-adjusted P <1.58×10 ^-7 ) and 52 additional genes at FDR≤1% ( P ≤4.37×10 ^-5 ). These 71 genes exhibited higher ( P =3.58×10 ^-18 ) common variant prioritisation scores than genes not significantly enriched for rare putatively damaging variation, with evidence of monotonic allelic series (dose-response relationships) among ultra-rare variants (minor allele count≤10) in 22 genes. Five of the 71 genes have cognate protein UKB Olink data available; all five associated ( P <3.80×10 ^-6 ) with three or more analysed traits. Combining rare and common variation evidence, allelic series and proteomics, we selected 17 genes for CRISPR knockout in human white adipose tissue cell lines. In three previously uncharacterised target genes, knockout increased (two-sided t -test P <0.05) lipid accumulation, a cellular phenotype relevant for fat mass traits, compared to Cas9-empty negative controls: COL5A3 (fold change [FC]=1.72, P =0.0028), EXOC7 (FC=1.35, P =0.0096), and TRIP10 (FC=1.39, P =0.0157); furthermore, knockout of SLTM resulted in reduced lipid accumulation (FC=0.51, P =1.91×10 ^-4 ). Integrating across population-based genetic and in vitro functional evidence, we highlight therapeutic avenues for altering obesity and body fat distribution by modulating lipid accumulation.