Integrative analysis of uterine leiomyoma genetics, epigenomics, and single-cell transcriptomics reveals causal genetic variants, gene targets, and cell types

Abstract

Abstract Uterine fibroids (UF), also called leiomyomas, are observed in nearly 70% of women of reproductive age. These tumors disrupt normal uterine function and cause significant physical and psychological health problems. Although heritable genetics is a significant risk factor, specific genetic variations and gene targets causally associated with UL are poorly understood. We performed a meta-analysis on existing fibroid genome-wide association studies (GWAS) and integrated the identified risk loci and potentially causal single nucleotide polymorphisms (SNPs) with epigenomics (H3K27me3), transcriptomics (RNA-Seq), 3D chromatin organization (Hi-C) and single-cell atlas (scRNA-Seq) of primary samples from UF patients. The integrative analysis identified 24 risk loci and 394 potential gene targets associated with UF. Among these, 106 of them were differentially expressed in UF tumors. Critically, the integrative analysis with single-cell RNA sequencing revealed the cell types with aberrant expression of these target genes in normal and UF tissue. Finally, CRISPR-based epigenetic manipulation (dCas9-KRAB) of two risk loci in a disease-relevant cell type fine-mapped the gene targets. These findings and the methodological approach indicate the effectiveness of integrative multi-omics data combined with locus-specific epigenetic editing approaches to identify disease-relevant risk loci and their target genes.