Transcriptional and Cellular Diversity of the Human Heart
Nathan R. Tucker,1,2,# Mark Chaffin,1,# Stephen J. Fleming,1,3 Amelia W. Hall, 1,2 Victoria A. Parsons,2 Kenneth Bedi,4 Amer-Denis Akkad,1,5 Caroline N. Herndon,1 Alessandro Arduini,1 Irinna Papangeli,1,5 Carolina Roselli,1,6 François Aguet,7 Seung Hoan Choi,1 Kristin G. Ardlie,7 Mehrtash Babadi,1,3 Kenneth B. Margulies,4 Christian M. Stegmann,1,5 and Patrick T. Ellinor 1,2,*
1. Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142
2. Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA 02114
3. Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA 02142
4. Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA 19104
5. Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA, 02142
6. University Medical Center Groningen, University of Groningen, 9712 CP, Groningen, NL
7. The Broad Institute of MIT and Harvard, Cambridge, MA, USA 02142
# These authors contributed equally
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.