Comprehensive Integration of Single-Cell Transcriptional Profiling Reveals the Heterogeneities of Non-cardiomyocytes in Healthy and Ischemic Hearts

Abstract

Advances in single-cell RNA sequencing (scRNA-seq) technology have recently shed light on the molecular mechanisms of the spatial and temporal changes of thousands of cells simultaneously under homeostatic and ischemic conditions. The aim of this study is to investigate whether it is possible to integrate multiple similar scRNA-seq datasets for a more comprehensive understanding of diseases. In this study, we integrated three representative scRNA-seq datasets of 27,349 non-cardiomyocytes isolated at 3 and 7 days after myocardial infarction or sham surgery. In total, seven lineages, including macrophages, fibroblasts, endothelia, and lymphocytes, were identified in this analysis with distinct dynamic and functional properties in healthy and nonhealthy hearts. Myofibroblasts and endothelia were recognized as the central hubs of cellular communication via ligand-receptor interactions. Additionally, we showed that macrophages from different origins exhibited divergent transcriptional signatures, pathways, developmental trajectories, and transcriptional regulons. It was found that myofibroblasts predominantly expand at 7 days after myocardial infarction with pro-reparative characteristics. We identified signature genes of myofibroblasts, such as Postn, Cthrc1, and Ddah1, among which Ddah1 was exclusively expressed on activated fibroblasts and exhibited concordant upregulation in bulk RNA sequencing data and in vivo and in vitro experiments. Collectively, this compendium of scRNA-seq data provides a valuable entry point for understanding the transcriptional and dynamic changes of non-cardiomyocytes in healthy and nonhealthy hearts by integrating multiple datasets.

High Proteoglycan Decorin Levels Are Associated With Acute Coronary Syndrome and Provoke an Imbalanced Inflammatory Response

“…To determine which cell type expressed DCN in the heart, we investigated the level of DCN in our integrated single-cell RNA-sequencing data, which were consisted of fibroblasts, macrophages, neutrophils, endothelial cells, and pericytes ( Zhuang et al, 2020 ). We found that DCN was virtually expressed in fibroblasts ( Supplementary Figure 1A ).…”

Progress of Single-Cell RNA Sequencing Technology in Myocardial Infarction Research

“…They are the most abundant immune cells in the heart and undergo significant cell flux in injured hearts ( 45 ). Zhuang et al ( 22 ) identified seven macrophage subsets by integrating 27,349 non-myocardial cells after MI and performing single-cell sequencing. Tissue-resident macrophages were selected for the subsequent analyses, and they expressed the repair genes CD163 and Mrc1.…”

“…Bone marrow-derived, Rel-mediated CD72 hi macrophages play a proinflammatory role in heart injury induction and are, therefore, potential therapeutic targets for various cardiovascular diseases. Zhuang et al found through single-cell sequencing that macrophages from various sources have different transcriptional characteristics, pathways, developmental tracks, and transcriptional regulators ( 22 ). Using single-cell sequencing, Ren et al ( 48 ) found that macrophage activation and subtype conversion are key events in cardiac hypertrophy metaphase.…”

“…Abnormal, persistent fibroblast activation contributes to heart failure progression. Recent advances in this field have shown that various fibroblast subsets occur in diseased tissue and undergo temporal variation at the time of injury ( 19 , 22 ). Fibroblast states are highly complex; hence, dynamic state-space models may more accurately describe fibroblast trans-differentiation than traditional models.…”

“…In addition, the study myofibroblasts and endothelial cells are central hubs for cell communication mediated by ligand-receptor interactions. Zhuang et al ( 22 ) found that myofibroblasts significantly increased by 7 d after MI. They promoted repair and expressed Postn, Cthrc1, and Ddah1.…”