FRI455 Polycystic Ovary Syndrome-Associated DENND1A Non-Coding Risk Loci Alter Gene Expression

Abstract Disclosure: L. Sankaranarayanan: None. G. Johnson: None. A. Barrera: None. A.E. Dunaif: None. T. Reddy: None. Polycystic ovary syndrome (PCOS) is a leading cause of infertility and type 2 diabetes affecting 10-15% of menstruating people worldwide. PCOS is characterized by increased circulating testosterone levels, ovulatory dysfunction and insulin resistance. Genome wide association studies (GWAS) have identified ∼20 replicated common PCOS susceptibility loci in European and Han Chinese cohorts. The associated variants are predominantly non-coding and implicate neuroendocrine, reproductive, and metabolic causal pathways. Rare non-coding variants in DENND1A, a GWAS candidate gene that regulates androgen biosynthesis, were present in ∼50% of PCOS families by whole genome sequencing. These associations suggest non-coding genetic contributions to the development of PCOS. We tested the hypothesis that PCOS GWAS risk loci contribute to PCOS pathogenesis by altering gene regulation. We first identified ∼1500 functioning regulatory elements across the GWAS associated regions using a high throughput reporter assay, STARR-seq, in two different cell lines. We used H295R, an adrenal cell line model for testosterone production and COV434, an ovarian granulosa cell line. We identified cell-line specific and overlapping regulatory regions suggesting that there is context specific gene regulation. Sixty percent of the identified regions are in previously documented open chromatin regions from DNase-seq and ATAC-seq studies supporting our hypothesis that these regulatory regions are functional. We additionally experimentally tested the regulatory effect of five of the regulatory regions identified in the DENND1A locus in H295R cells using CRISPR-based epigenetic editing tools. This endogenous perturbation increases DENND1A gene levels (measured by qPCR) and also increased testosterone produced by the H295R cells (measured by ELISA), suggesting that these regions are biologically relevant to PCOS pathogenesis.We investigated allele-specific regulatory activity in a multi-ethnic pool of five genomes from healthy individuals. We identified 21 common genetic variants (minor allele frequency in the population >0.05) that alter regulatory activity in the DENND1A locus, including two that are ancestry-specific. Further, rs12237685 and rs28441318 are also eQTLS for DENND1A from the GTEX project and reside within open chromatin regions in ovarian cells. The functional consequences of non-coding genetic variants associated with complex traits has been exceptionally difficult to elucidate. Our findings suggest that both the common genetic variants and rare PCOS patient-associated DENND1A variants and altered gene expression. Further, some of those variants may contribute to allele-specific genetic risk for PCOS. Presentation Date: Friday, June 16, 2023