Transcriptional Profiling of Individual Cells from the Human Heart

Abstract

Global transcriptional profiling of individual cells represents a powerful approach to systematically survey contributions from specific cellular phenotypes to human disease states. Heart diseases are the leading causes of death globally, yet no protocols for robust single cell isolation from adult human hearts have been published. Here, we found that enzymatic dissociation of human heart resulted in low-quality cell suspensions across a range of protocols. We show that isolation of cardiac nuclei provides a robust alternative, and that nuclear transcriptomes reliably represent the cytoplasmic and whole-cell transcriptomes of major cardiac cell types. Furthermore, coupling of nuclear isolation to PCM1-gated flow cytometry facilitated specific cardiomyocyte depletion, expanding the cardiac transcriptome beyond bulk tissue transcriptomes which were strongly correlated with PCM1+ transcriptomes (r=0.8). We applied these methods to generate a transcriptional catalogue of human cardiac cells by droplet-based RNA-sequencing of 8,460 nuclei from which cellular identities were inferred. Reproducibility was explored in an independent biopsy (4,760 additional nuclei) from the same human heart. Our results provide a perspective of the cellular composition of the adult human heart and validate a framework for assessment of cellular individuality across cardiac disease states.