Abstract 4370075: Leveraging Single-Nucleus Chromatin Accessibility and Transcriptome Profiling to Define the Regulatory Landscape of Dilated Cardiomyopathy
Abstract
Introduction: While genetic variants linked to dilated cardiomyopathy (DCM) are increasingly well characterized, the molecular mechanisms driving pathogenesis remain poorly understood. Traditional bulk and in vitro methods lack the resolution to capture the cellular heterogeneity and complexity of DCM. Here, we use single-nucleus multiome chromatin accessibility and RNA sequencing to resolve cell-type-specific gene regulatory changes in genetic DCM. Methods: We performed 10X Genomics Multiome (simultaneous RNA and chromatin accessibility) profiling on nuclei isolated from left ventricular tissue of 13 DCM patients with diverse genetic etiologies ( LMNA , PLN , RBM20 , TNNT2 , TTN ) and 5 non-failing hearts. Integrated analysis identified 12 distinct cardiac cell types based on joint transcriptomic and epigenomic signatures. Intercellular communication networks were inferred using CellChat. We leveraged paired RNA and chromatin accessibility data to elucidate potential enhancer-gene interactions driving disease-associated cell state changes. Results: We observed disease-specific alterations in cellular composition and signaling networks across DCM genetic etiologies. Integrated chromatin accessibility and gene expression data revealed changes in the gene regulatory networks of cardiomyocytes, fibroblasts, and endothelial cells. Notably, the transcription factor PRRX1 emerged as a key differentially regulated gene in LMNA -related DCM. Functional assays in iPSC-derived cardiomyocytes demonstrated that PRRX1 knockdown significantly improved calcium handling and reduced arrythmia incidence. Conclusions: This single nucleus multiomic atlas of genetic DCM provides insights into cell-type-specific gene regulation and cell communication programs associated with disease states. Our findings highlight PRRX1 as a potential therapeutic target in LMNA -related DCM and underscore the value of multiomic profiling for uncovering the regulatory basis of cardiomyopathies.
Article Details
Authors (17)
Logan Dunkenberger
Stanford University, Stanford, California, United States
Casey Gilles
Stanford University, Stanford, California, United States
Nadjet Belbachir
Stanford Cardiovascular Institute, Stanford University, CA (L.R., N.B., H.Z., R.H., W.Z., X.W., M.X., J.G., H.Y.K., T.L., J.S., J.C.W.).
Eyal Metzl Raz
Stanford University, Stanford, California, United States
Lasemahang Limbu
Stanford University, Stanford, California, United States
Spencer Bonham
Stanford University, Stanford, California, United States
Jennifer Arthur
Stanford University, Stanford, California, United States
Alex Dalal
Stanford University, Menlo Park, California, United States
Maryam Kay
Stanford University, Stanford, California, United States
Rachel Baum
Stanford University, Stanford, California, United States
Evgenios Neofytou
Stanford University, Stanford, California, United States
Rohin Ramchandani
Stanford University, Stanford, California, United States
Mo Ameen
Stanford University, Stanford, California, United States
Kevin Wang
Department of Neurobiology and Behavior, University of California
Michael Fischbein
Stanford University, Menlo Park, California, United States
Y Joseph Woo
STANFORD UNIV SCHOOL MEDICINE, Stanford, California, United States
Ioannis Karakikes
Stanford University, Stanford, California, United States