A genome-wide CRISPR screen identifies BRD4 as a regulator of cardiomyocyte differentiation

Arun Padmanabhan; T Yvanka de Soysa; Angelo Pelonero; Valerie Sapp; Parisha P Shah; Qiaohong Wang; Li Li; Clara Youngna Lee; Nandhini Sadagopan; Tomohiro Nishino; Lin Ye; Rachel Yang; Ashley Karnay; Andrey Poleshko; Nikhita Bolar; Ricardo Linares-Saldana; Sanjeev S Ranade; Michael Alexanian; Sarah U Morton; Mohit Jain; Saptarsi M Haldar; Deepak Srivastava; Rajan Jain

doi:10.1038/s44161-024-00431-1

A genome-wide CRISPR screen identifies BRD4 as a regulator of cardiomyocyte differentiation

Nat Cardiovasc Res. 2024 Mar;3(3):317-331. doi: 10.1038/s44161-024-00431-1. Epub 2024 Feb 23.

Authors

Arun Padmanabhan^{1

2

3}, T Yvanka de Soysa⁴, Angelo Pelonero⁴, Valerie Sapp^{5

6}, Parisha P Shah^{7

8}, Qiaohong Wang^{7

8}, Li Li^{7

8}, Clara Youngna Lee^{4

9}, Nandhini Sadagopan^{4

9}, Tomohiro Nishino⁴, Lin Ye⁴, Rachel Yang^{7

8}, Ashley Karnay^{7

8}, Andrey Poleshko⁸, Nikhita Bolar^{7

8}, Ricardo Linares-Saldana^{7

8}, Sanjeev S Ranade⁴, Michael Alexanian^{4

10}, Sarah U Morton^{11

12}, Mohit Jain^{5

6}, Saptarsi M Haldar^{4

9

13}, Deepak Srivastava^{14

15

16

17}, Rajan Jain^{18

19}

Affiliations

¹ Gladstone Institutes, San Francisco, CA, USA. [email protected].
² Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, CA, USA. [email protected].
³ Chan Zuckerberg Biohub, San Francisco, CA, USA. [email protected].
⁴ Gladstone Institutes, San Francisco, CA, USA.
⁵ Department of Medicine, University of California, San Diego, School of Medicine, San Diego, CA, USA.
⁶ Department of Pharmacology, University of California, San Diego, San Diego, CA, USA.
⁷ Cardiovascular Institute, Epigenetics Institute, and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
⁸ Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA.
⁹ Department of Medicine, University of California, San Francisco, School of Medicine, San Francisco, CA, USA.
¹⁰ Department of Pediatrics, University of California, San Francisco, School of Medicine, San Francisco, CA, USA.
¹¹ Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA.
¹² Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
¹³ Amgen Research, Cardiometabolic Disorders, South San Francisco, CA, USA.
¹⁴ Gladstone Institutes, San Francisco, CA, USA. [email protected].
¹⁵ Department of Pediatrics, University of California, San Francisco, School of Medicine, San Francisco, CA, USA. [email protected].
¹⁶ Roddenberry Center for Stem Cell Biology and Medicine at Gladstone Institutes, San Francisco, CA, USA. [email protected].
¹⁷ Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA. [email protected].
¹⁸ Cardiovascular Institute, Epigenetics Institute, and Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. [email protected].
¹⁹ Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA. [email protected].

Abstract

Human induced pluripotent stem cell (hiPSC) to cardiomyocyte (CM) differentiation has reshaped approaches to studying cardiac development and disease. In this study, we employed a genome-wide CRISPR screen in a hiPSC to CM differentiation system and reveal here that BRD4, a member of the bromodomain and extraterminal (BET) family, regulates CM differentiation. Chemical inhibition of BET proteins in mouse embryonic stem cell (mESC)-derived or hiPSC-derived cardiac progenitor cells (CPCs) results in decreased CM differentiation and persistence of cells expressing progenitor markers. In vivo, BRD4 deletion in second heart field (SHF) CPCs results in embryonic or early postnatal lethality, with mutants demonstrating myocardial hypoplasia and an increase in CPCs. Single-cell transcriptomics identified a subpopulation of SHF CPCs that is sensitive to BRD4 loss and associated with attenuated CM lineage-specific gene programs. These results highlight a previously unrecognized role for BRD4 in CM fate determination during development and a heterogenous requirement for BRD4 among SHF CPCs.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Bromodomain Containing Proteins
CRISPR-Cas Systems* / genetics
Cell Cycle Proteins / genetics
Cell Cycle Proteins / metabolism
Cell Differentiation* / genetics
Cell Lineage / genetics
Cells, Cultured
Gene Expression Regulation, Developmental
Humans
Induced Pluripotent Stem Cells* / cytology
Induced Pluripotent Stem Cells* / metabolism
Mice
Mouse Embryonic Stem Cells / cytology
Mouse Embryonic Stem Cells / metabolism
Myocytes, Cardiac* / cytology
Myocytes, Cardiac* / metabolism
Nuclear Proteins / genetics
Nuclear Proteins / metabolism
Single-Cell Analysis
Transcription Factors* / genetics
Transcription Factors* / metabolism

Substances

Transcription Factors
Brd4 protein, mouse
BRD4 protein, human
Cell Cycle Proteins
Nuclear Proteins
Bromodomain Containing Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding