An integrative genomic and single-cell atlas identifies PLAGL1+ FB_c1 fibroblasts as candidate mediators of human cardiac fibrosis

Cardiomyopathy constitutes a principal cause of heart failure globally and is characterized by pathological cardiac fibrosis, which is a central feature of disease progression and is primarily driven by activated fibroblasts. Despite its clinical importance, the comprehensive cellular heterogeneity and the exact molecular mechanisms driving fibrotic remodelling are inadequately understood, thereby constraining the advancement of targeted therapeutic interventions. To elucidate these mechanisms, we conducted a comprehensive multiomics analysis. This study utilized single-cell RNA sequencing (scRNA-seq) data derived from 24 human heart samples, comprising 4 normal and 20 diseased samples. These data were integrated with genome-wide association study (GWAS) summary statistics and bulk transcriptomic datasets. Our analytical framework encompassed the construction of a cellular atlas, the application of Single-cell Disease Relevance Score (scDRS) and Augur perturbation analyses, the exploration of protein‒protein interaction networks, pseudotime trajectory inference, regulatory network analysis using SCENIC, and in silico gene knockout modelling via scTenifoldKnk. We constructed a high-resolution single-cell atlas of human cardiomyopathic hearts. Diseased hearts showed immune cell enrichment and a disease-associated activated fibroblast subpopulation, FB_c1, which was enriched in both ischaemic cardiomyopathy and dilated cardiomyopathy and showed elevated extracellular matrix-related gene expression. Integrative scDRS and Augur analyses identified fibroblasts as a disease-associated cell population linked to heart failure genetic risk and transcriptional perturbation. Multicohort transcriptomic analysis and PPI-based prioritization revealed LUM as a fibrosis-associated ECM candidate gene. The results of pseudotime analysis suggest a transcriptional continuum of fibroblast activation rather than definitive lineage progression. The results of regulatory network analysis, in silico perturbation, and PLAGL1 knockdown experiments support PLAGL1 as a candidate regulator associated with fibroblast activation and ECM remodelling. This research presents an in depth, high-resolution analysis of the cellular and molecular architecture associated with cardiomyopathy. It identifies fibroblasts, specifically the FB_c1 subpopulation, as disease-associated contributors to extracellular matrix remodelling and identifies LUM and PLAGL1 as candidate molecules linked to fibroblast activation. The findings provide a single-cell and multiomics framework for understanding fibroblast-associated cardiac fibrosis. FB_c1 was identified as a disease-associated activated fibroblast state, whereas PLAGL1 and LUM should be interpreted as candidate regulators or markers that require further spatial, functional, and in vivo validation before causal or translational roles can be established.