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Transcriptional Profiling of Individual Cells from the Human Heart

39 Pages Posted: 29 Apr 2020 Sneak Peek Status: Review Complete

See all articles by Neha Pimpalwar

Neha Pimpalwar

Lund University - Department of Cardiology

Tomasz Czuba

Lund University - Department of Cardiology

Maya Landenhed Smith

Lund University - Skåne University Hospital

Johan Nilsson

Lund University - Skåne University Hospital

Olof Gidlöf

Lund University - Department of Cardiology

J. Gustav Smith

Lund University - Department of Cardiology

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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.

Keywords: heart, human, RNA sequencing, single cell

Suggested Citation

Pimpalwar, Neha and Czuba, Tomasz and Landenhed Smith, Maya and Nilsson, Johan and Gidlöf, Olof and Smith, J. Gustav, Transcriptional Profiling of Individual Cells from the Human Heart. Available at SSRN: https://ssrn.com/abstract=3578146 or http://dx.doi.org/10.2139/ssrn.3578146
This is a paper under consideration at Cell Press and has not been peer-reviewed.

Neha Pimpalwar

Lund University - Department of Cardiology

Sweden

Tomasz Czuba

Lund University - Department of Cardiology

Sweden

Maya Landenhed Smith

Lund University - Skåne University Hospital

Malmö
Sweden

Johan Nilsson

Lund University - Skåne University Hospital

Malmö
Sweden

Olof Gidlöf

Lund University - Department of Cardiology

Sweden

J. Gustav Smith (Contact Author)

Lund University - Department of Cardiology ( email )

Sweden

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