Genetic dependency of atrial fibrillation-associated risk genes across tissue types: Discovering novel therapeutic targets

Abstract

BackgroundAddressing the underlying causes of atrial fibrillation (AFib) is critically important. While potential AFib-related genes have been recognized, the impact of modifying these genes in humans remains poorly understood. ObjectiveWe assessed the cellular dependencies of 309 genes previously associated with AFib through genome-wide association studies using data from the Cancer Dependency Map project, aiming to prioritize potential therapeutic targets with minimal off-target effects. MethodsWe analyzed CRISPR-Cas9 knockout (CHRONOS scores) and RNA interference (RNAi) knockdown (DEMETER2 scores) screening data from 1,927 human cell lines across 24 tissue types, focusing on tissues associated with AFib initiation, presentation, and progression: autonomic ganglia, central nervous system (CNS), and soft tissue. We examined the expression and dependency scores of the AFib-associated genes, identifying significant correlations between gene expression and cellular dependency within specific tissues using Pearson correlation coefficients and controlling the false discovery rate (FDR) at 5%. ResultsOut of the 309 AFib-associated genes, 206 genes (66.7%) had CHRONOS dependency scores and 229 (74.1%) had DEMETER2 dependency scores available. Several genes showed significant negative dependency scores (CHRONOS < -0.5) across multiple tissues, indicating potential off-target effects if inhibited. In contrast, we identified 12 genes with significant expression-driven dependencies within AFib-associated tissues. In CNS cell lines, HAND2 (R = -0.456, FDR = 0.002) and VGLL2 (R = -0.434, FDR = 0.005) showed significant negative correlations between gene expression and cellular dependency. In soft tissue cell lines, BEST3 (R = -0.679, FDR = 0.001) and PITX2 (R = -0.679, FDR = 0.001) also demonstrated strong negative correlations. Additionally, ERBB4 in CNS lines showed a significant negative correlation (R = -0.361, FDR = 0.048). These findings suggest that inhibiting these genes may selectively affect high-expressing cells in AFib-associated tissues while minimizing effects on other tissues. ConclusionOur analysis identified HAND2, VGLL2, BEST3, and ERBB4 as potential therapeutic targets for AFib, demonstrating significant expression-driven dependencies in AFib-associated tissues with no pan-tissue essentiality. These results provide a quantitative basis for developing targeted therapies with reduced off-target effects. CONDENSED ABSTRACTAtrial fibrillation (AFIB) is one of the most common cardiac arrhythmias with numerous known risk factors. Although many AFIB-associated genes have been identified, the impact of screening or the effects of modifying these genes in humans remain poorly understood. We examined CRISPR knockout and RNAi knockdown screen data from nearly 2,000 human cell lines to assess the cellular dependencies of 309 genes associated with AFIB, previously identified through genome-wide association studies. Some genes demonstrate broad cell dependencies across various tissue types, indicating potential off-target effects if inhibited. Conversely, HAND2, VGLL2, BEST3, and ERBB4 were identified as genes of interest because their genetic knockouts specifically impacted high-expressing cells from tissue lineages pertinent to AFIB and/or were not pan-dependent. Overall, analyses of genetic screen data identified AFIB-associated genes whose knockout or knockdown selectively affected cell lines of relevant tissue lineages, prioritizing targets for potential AFIB treatments.