Single-cell insights: pioneering an integrated atlas of chromatin accessibility and transcriptomic landscapes in diabetic cardiomyopathy

• Published in: Cardiovascular diabetology 2024-04, Vol.23 (1), p.139-139, Article 139
• Main Authors: Su, Qiang, Huang, Wanzhong, Huang, Yuan, Dai, Rixin, Chang, Chen, Li, Qiu-Yan, Liu, Hao, Li, Zhenhao, Zhao, Yuxiang, Wu, Qiang, Pan, Di-Guang
• Format: Article
• Language: English
• Subjects: Animals; Biomarkers; Cardiac function; Cardiomyocytes; Cardiomyopathy; Cell interactions; Cell proliferation; Cells; Chromatin; Chromatin - genetics; Chromatin - metabolism; Chromatin Assembly and Disassembly; Congestive heart failure; DCM; Diabetes; Diabetes mellitus; Diabetic Cardiomyopathies - genetics; Diabetic Cardiomyopathies - metabolism; Diabetic Cardiomyopathies - pathology; Diabetic Cardiomyopathies - physiopathology; Disease Models, Animal; Endothelial; Endothelial cells; Endothelial Cells - metabolism; Endothelial Cells - pathology; Endothelium; Fibroblasts; Fibroblasts - metabolism; Fibroblasts - pathology; Fibrosis; Gene expression; Gene Expression Profiling; Gene Expression Regulation; Gene Regulatory Networks; Genomics; Heart failure; Immunoassay; Immunofluorescence; Intervention; Macrophages; Male; Mice; Mice, Inbred C57BL; Myocytes, Cardiac - metabolism; Myocytes, Cardiac - pathology; Ontology; Pathology; RNA-Seq; scATAC-seq; scRNA-seq; Single-Cell Analysis; Therapeutic applications; Therapeutic targets; Transcription factors; Transcriptome; Transcriptomics; Vascular endothelial growth factor
• ISSN: 1475-2840; 1475-2840
• DOI: 10.1186/s12933-024-02233-y

Diabetic cardiomyopathy (DCM) poses a growing health threat, elevating heart failure risk in diabetic individuals. Understanding DCM is crucial, with fibroblasts and endothelial cells playing pivotal roles in driving myocardial fibrosis and contributing to cardiac dysfunction. Advances in Multimodal single-cell profiling, such as scRNA-seq and scATAC-seq, provide deeper insights into DCM's unique cell states and molecular landscape for targeted therapeutic interventions. Single-cell RNA and ATAC data from 10x Multiome libraries were processed using Cell Ranger ARC v2.0.1. Gene expression and ATAC data underwent Seurat and Signac filtration. Differential gene expression and accessible chromatin regions were identified. Transcription factor activity was estimated with chromVAR, and Cis-coaccessibility networks were calculated using Cicero. Coaccessibility connections were compared to the GeneHancer database. Gene Ontology analysis, biological process scoring, cell-cell communication analysis, and gene-motif correlation was performed to reveal intricate molecular changes. Immunofluorescent staining utilized various antibodies on paraffin-embedded tissues to verify the findings. This study integrated scRNA-seq and scATAC-seq data obtained from hearts of WT and DCM mice, elucidating molecular changes at the single-cell level throughout the diabetic cardiomyopathy progression. Robust and accurate clustering analysis of the integrated data revealed altered cell proportions, showcasing decreased endothelial cells and macrophages, coupled with increased fibroblasts and myocardial cells in the DCM group, indicating enhanced fibrosis and endothelial damage. Chromatin accessibility analysis unveiled unique patterns in cell types, with heightened transcriptional activity in myocardial cells. Subpopulation analysis highlighted distinct changes in cardiomyocytes and fibroblasts, emphasizing pathways related to fatty acid metabolism and cardiac contraction. Fibroblast-centered communication analysis identified interactions with endothelial cells, implicating VEGF receptors. Endothelial cell subpopulations exhibited altered gene expressions, emphasizing contraction and growth-related pathways. Candidate regulators, including Tcf21, Arnt, Stat5a, and Stat5b, were identified, suggesting their pivotal roles in DCM development. Immunofluorescence staining validated marker genes of cell subpopulations, confirming PDK4, PPARγ and Tpm1 as markers for metabolic pattern-altered car