ABSTRACT Background Genome-wide association studies revealed a robust association between genetic variants in the LIPA (lysosomal acid lipase) gene and coronary artery diseases (CAD), but not lipid traits. QTL studies support that the risk alleles of LIPA CAD variants are associated with higher LIPA mRNA and enzyme activity in human monocytes. Yet the variant-to-function relationship and how this important locus impacts disease etiology has not been fully established. Herein, we aim to determine the causal variant(s), involved cell type, and the target gene, establish the causality of the variant-to-function relationship, and elucidate how increased myeloid LIPA impacts atherosclerosis in vivo . Methods We apply functional genomic datasets, post-GWAS prioritization pipelines, and molecular biology techniques, incuding eQTL, enzyme activity-QTL, high-resolution Tri-HiC, ChIP-seq, and site-directed mutagenesis and luciferase assay to connect functional variants to the candidate genes in the causal cell type. To establish how increased myeloid LIPA impacts atherosclerosis, we generated myeloid-specific Lipa overexpression mice (Lipa Tg ) . Results Post-GWAS pipelines support LIPA as the candidate causal gene at the locus. In human monocyte-derived macrophages, LIPA mRNA, protein and enzyme activity were higher in the risk allele carriers of CAD variants. High-resolution Tri-HiC and luciferase assay confirmed an intronic enhancer region showing strong interaction with the LIPA promoter. Within the enhancer region, the risk alleles of rs1412444/rs1412445 and rs1320496 demonstrate enhanced binding to PU. 1, and acted as the functional variants with risk alleles leading to increased enhancer activity. The risk allele of rs1320496 is predicted to create a motif binding site for PU.1. The functional genomic data together support that LIPA is the candidate causal gene in the locus, and the risk alleles of CAD led to increased LIPA in a myeloid cell-specific manner. Consistently, mice with myeloid-specific Lipa overexpression on a Ldlr -/- background showed significantly increased atherosclerotic lesion size and lesion macrophage area without affecting plasma cholesterol. ScRNA-seq analysis showed that Lipa Tg led to reduced lipid-enriched yet increased inflammatory macrophage subsets, and activation chemokine signaling pathway. This was further confirmed by reduced neutral lipid accumulation in both plaque and peritoneal macrophages and significantly increased monocytes infiltration into the lesion in Lipa Tg mice. Conclusions We established that LIPA risk alleles drive increased myeloid LIPA and aggravate atherosclerosis. CLINICAL PERSPECTIVE What is New? CAD GWAS variants at the LIPA locus led to increased macrophage LIPA expression and enzyme activity. Myeloid-specific overexpression of Lipa exacerbates atherosclerosis. Our study connected the genetic variation to the involved cell type and the target gene, and the disease mechanism for this important locus. What are the Clinical Implications? GWAS and meta-analyses have identified over 200 loci for CAD. Establishing the candidate genes and their mechanistic studies inform novel biological mechanisms and therapeutic application. There is strong statistical evidence linking LIPA with CAD. By leveraging functional genomic studies and transgenic mice, our work established the direct causality that LIPA risk alleles drive increased myeloid LIPA and aggravate atherosclerosis. Establishing the variant-to-function relationship for this locus informs that increasing myeloid LIPA may not be a therapeutic strategy for CAD, despite the essential role of LIPA in regulating lysosomal lipid metabolism.

Decoding the Variant-to-Function Relationship forLIPA, a Risk Locus for CAD