Defining Cardiac Recovery at Single Cell Resolution

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract Recovery of cardiac function is the ultimate goal of heart failure therapy. Unfortunately, cardiac recovery remains a rare and poorly understood phemomenon. Herein, we performed single nucleus RNA-sequencing (snRNA-seq) from non-diseased donors and heart failure patients. By comparing patients who recovered LV systolic function following LV assist device implantation to those who did not recover and donors, we defined the cellular and transcriptional landscape and predictors of cardiac recovery. We sequenced 40 hearts and recovered 185,881 nuclei with 13 distinct cell types. Using pseudobulk differential expression analysis to explicate cell specific signatures of cardiac recovery, we observed that recovered cardiomyocytes do not revert to a normal state, and instead, retain transcriptional signatures observed in heart failure. Macrophages and fibroblasts displayed the strongest signatures of recovery. While some evidence of reversion to a normal state was observed, many heart failure associated genes remained elevated and recovery signatures were predominately indicative of a biological state that was unique from donor and heart failure conditions. Acquisition of recovery states was associated with improved LV systolic function. Pro-inflammatory macrophages and inflammatory signaling in fibroblasts were identified as negative predictors of recovery. We identified downregulation of RUNX1 transcriptional activity in macrophages and fibroblasts as a central event associated with and predictive of cardiac recovery. In silico perturbation of RUNX1 in macrophages and fibroblasts recapitulated the transcriptional state of cardiac recovery. This prediction was corroborated in a mouse model of cardiac recovery mediated by BRD4 inhibition where we observed a decrease in macrophage and fibroblast Runx1 expression, diminished chromatin accessibility within peaks linked to the Runx1 locus, and acquisition of recovery signatures. These findings suggest that cardiac recovery is a unique biological state and identify RUNX1 as a possible therapeutic target to facilitate cardiac recovery.

Authors 20

1. Junedh Amrute

   Washington University in St. Louis

   Affiliation as printed

   Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA

2. Lulu Lai

   Washington University in St. Louis

   Affiliation as printed

   Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA

3. Pan Ma

   Washington University in St. Louis

   Affiliation as printed

   Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA

4. Andrew L. Koenig

   Washington University in St. Louis

   Affiliation as printed

   Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA

5. Kenji Kamimoto

   Washington University in St. Louis

   Affiliation as printed

   Center for Regenerative Medicine, Washington University School of Medicine, Saint Louis, Missouri, USA

   Department of Developmental Biology, Washington University School of Medicine, Saint Louis, Missouri, USA

   Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, USA

6. Andrea L. Bredemeyer

   Washington University in St. Louis

   Affiliation as printed

   Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA

7. Thirupura Sundari Shankar

   University of Utah · University of Utah Health Care

   Affiliation as printed

   Division of Cardiovascular Medicine & Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah Health & School of Medicine, Salt Lake City, UT

8. Christoph Kuppe Aachen Institute of Experimental Medicine and Systems Biology Division of Nephrology

   RWTH Aachen University

   Affiliation as printed

   Institute of Experimental Medicine and Systems Biology and Division of Nephrology, RWTH Aachen University, Aachen, Germany

9. Farid F. Kadyrov

   Washington University in St. Louis

   Affiliation as printed

   Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA

10. Linda Schulte

    Washington University in St. Louis

    Affiliation as printed

    Division of Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, Saint Louis, MO, 63110, USA

11. Dylan Stoutenburg

    Washington University in St. Louis

    Affiliation as printed

    Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA

12. Benjamin J. Kopecky

    Washington University in St. Louis

    Affiliation as printed

    Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA

13. Sutip Navankasattusas

    University of Utah · University of Utah Health Care

    Affiliation as printed

    Division of Cardiovascular Medicine & Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah Health & School of Medicine, Salt Lake City, UT

14. Joseph R. Visker

    University of Utah · University of Utah Health Care

    Affiliation as printed

    Division of Cardiovascular Medicine & Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah Health & School of Medicine, Salt Lake City, UT

15. Samantha A. Morris

    Washington University in St. Louis

    Affiliation as printed

    Center for Regenerative Medicine, Washington University School of Medicine, Saint Louis, Missouri, USA

    Department of Developmental Biology, Washington University School of Medicine, Saint Louis, Missouri, USA

    Department of Genetics, Washington University School of Medicine, Saint Louis, Missouri, USA

16. Rafael Kramann Aachen Institute of Experimental Medicine and Systems Biology Division of Nephrology

    Erasmus MC · RWTH Aachen University

    Affiliation as printed

    Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands

    Institute of Experimental Medicine and Systems Biology and Division of Nephrology, RWTH Aachen University, Aachen, Germany

17. Florian Leuschner

    University Hospital Heidelberg · German Centre for Cardiovascular Research

    Affiliation as printed

    Department of Cardiology, University Hospital Heidelberg, Heidelberg, Germany

    German Centre for Cardiovascular Research (DZHK), Partner Site Heidelberg, Heidelberg, Germany

18. Douglas L. Mann

    Washington University in St. Louis

    Affiliation as printed

    Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA

19. Stavros George Drakos

    University of Utah · University of Utah Health Care

    Affiliation as printed

    Division of Cardiovascular Medicine & Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah Health & School of Medicine, Salt Lake City, UT

20. Kory J. Lavine corresponding

    Washington University in St. Louis

    Affiliation as printed

    Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA

    Center for Regenerative Medicine, Washington University School of Medicine, Saint Louis, Missouri, USA

    Department of Developmental Biology, Washington University School of Medicine, Saint Louis, Missouri, USA

    Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA