Single-nuclei profiling of human dilated and hypertrophic cardiomyopathy

Mark Chaffin,1 Irinna Papangeli,2 Bridget Simonson,1 Amer-Denis Akkad,2 Matthew C. Hill,1,3 Alessandro Arduini,1 Stephen J. Fleming,1,4 Michelle Melanson,5 Sikander Hayat,2 Maria Kost-Alimova,5 Ondine Atwa,1 Jiangchuan Ye,1 Kenneth C. Bedi Jr.,6 Matthias Nahrendorf,3,7 Virendar K. Kaushik,5 Christian M. Stegmann,2 Kenneth B. Margulies,6 Nathan R. Tucker,8 and Patrick T. Ellinor1,3,9*

1. Precision Cardiology Laboratory and the Cardiovascular Disease Initiative, The Broad Institute, Cambridge, MA, USA 02142

2. Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA, USA 02142

3. Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA 02114

4. Data Sciences Platform, The Broad Institute, Cambridge, MA, USA 02142

5. Center for the Development of Therapeutics, The Broad Institute, Cambridge, MA USA 02142

6. Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA 19104

7. Center for Systems Biology, Department of Radiology, Massachusetts General Hospital, Boston, MA USA 02114

8. Masonic Medical Research Institute, Utica, NY, USA 13501

9. Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA 02114

Heart failure is a growing public health concern which encompasses a heterogenous set of clinical features, converging on impaired cardiac contractile function.1,2 Previous work has highlighted changes in both transcription and protein expression in failing hearts,3,4 but may overlook molecular changes in less prevalent cell types. Here, we identify extensive molecular alterations present in failing hearts at single-cell resolution by performing single-nuclei RNA sequencing of nearly 600,000 nuclei in left ventricle samples from 11 dilated cardiomyopathy, 15 hypertrophic cardiomyopathy and 16 non-failing hearts. Broadly, the transcriptional profiles of dilated and hypertrophic cardiomyopathy patients converged at the tissue and cell type level. Further, a subset of cardiomyopathy patients harbor a unique population of activated fibroblasts nearly entirely absent from non-failing samples. A CRISPR knockout screen was performed in primary human cardiac fibroblasts to evaluate this fibrotic cell state transition. After knocking out genes associated with fibroblast transition in vivo, we observed a reduction in myofibroblast cell-state transition upon TGFβ1 stimulation for a subset of genes. Our results provide novel insights into the transcriptional diversity of the human heart in health and disease as well as new potential therapeutic targets and biomarkers for heart failure.