Transcriptional and Cellular Diversity of the Human Heart

Abstract

Background: The human heart requires a complex ensemble of specialized cell types to perform its essential function. A greater knowledge of the intricate cellular milieu of the heart is critical to increase our understanding of cardiac homeostasis and pathology. As recent advances in low input RNA-sequencing have allowed definitions of cellular transcriptomes at single cell resolution at scale, here we have applied these approaches to assess the cellular and transcriptional diversity of the non-failing human heart. Methods: Microfluidic encapsulation and barcoding was used to perform single nuclear RNA sequencing with samples from seven human donors, selected for their absence of overt cardiac disease. Individual nuclear transcriptomes were then clustered based upon transcriptional profiles of highly variable genes. These clusters were used as the basis for between-chamber and between-sex differential gene expression analyses and intersection with genetic and pharmacologic data. Results: We sequenced the transcriptomes of 287,269 single cardiac nuclei, revealing a total of 9 major cell types and 20 subclusters of cell types within the human heart. Cellular subclasses include two distinct groups of resident macrophages, four endothelial subtypes, and two fibroblasts subsets. Comparisons of cellular transcriptomes by cardiac chamber or sex reveal diversity not only in cardiomyocyte transcriptional programs, but also in subtypes involved in extracellular matrix remodeling and vascularization. Using genetic association data, we identified strong enrichment for the role of cell subtypes in cardiac traits and diseases. Finally, intersection of our dataset with genes on cardiac clinical testing panels and the druggable genome reveals striking patterns of cellular specificity. Conclusions: Using large-scale single nuclei RNA sequencing, we have defined the transcriptional and cellular diversity in the normal human heart. Our identification of discrete cell subtypes and differentially expressed genes within the heart will ultimately facilitate the development of new therapeutics for cardiovascular diseases.

Spatial multi-omic map of human myocardial infarction

“…To establish a consistent map of cell types with snRNA-seq across samples, we first clustered the data for each sample individually and annotated the clusters with curated marker genes from the literature. [9][10][11] To unify cell type annotations between samples, we integrated and batch-corrected data from all samples and clustered them based on the correlation of average gene expression ( Fig. 1d, Extended Data Fig.…”

Vascular Homeostasis and Inflammation in Health and Disease—Lessons from Single Cell Technologies

“…The first large-scale initiative to produce a reference single cell atlas of healthy wild type mice was pioneered by the Tabula Muris Consortium that sequenced more than 100,000 cells from 20 mouse organs [21]. An analogous Human Cell Atlas consortium [22,23], together with other datasets developed by independent laboratories [24][25][26][27][28], is already on the way to producing a comprehensive single cell atlas of all human tissues. While these single cell RNA (scRNA)-seq databases provide an extremely valuable resource, the vascular system remained to be covered in depth, as vascular cells represent only a minor proportion of an organ.…”

Bromodomain and Extraterminal Inhibition Blocks Inflammation-Induced Cardiac Dysfunction and SARS-CoV-2 Infection (Pre-Clinical)

“…A published human cardiac snRNA-seq dataset was then used to identify overlap of marker gene sets for main human heart cell types (e.g. cardiomyocytes, fibroblasts, epicardium, pericytes, etc) with the clusters of our dataset, and were labelled accordingly 17 . Further refined clustering was carried out on specific clusters that showed overlap of more than one of the various heart cell types.…”

“…We used single nuclei RNA sequencing (snRNA-seq) to assess cell specificity in our enhanced hCO (Voges et al, In Revision). Mapping to human heart snRNA-seq 17 revealed the presence of pro-epicardial/epicardial cells, fibroblasts, activated fibroblasts/pericytes and cardiomyocytes ( Extended Data Fig. 2c,d ).…”