Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation

Clayton E Friedman; Quan Nguyen; Samuel W Lukowski; Abbigail Helfer; Han Sheng Chiu; Jason Miklas; Shiri Levy; Shengbao Suo; Jing-Dong Jackie Han; Pierre Osteil; Guangdun Peng; Naihe Jing; Greg J Baillie; Anne Senabouth; Angelika N Christ; Timothy J Bruxner; Charles E Murry; Emily S Wong; Jun Ding; Yuliang Wang; James Hudson; Hannele Ruohola-Baker; Ziv Bar-Joseph; Patrick P L Tam; Joseph E Powell; Nathan J Palpant

doi:10.1016/j.stem.2018.09.009

Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation

Cell Stem Cell. 2018 Oct 4;23(4):586-598.e8. doi: 10.1016/j.stem.2018.09.009.

Authors

Clayton E Friedman¹, Quan Nguyen², Samuel W Lukowski², Abbigail Helfer¹, Han Sheng Chiu¹, Jason Miklas³, Shiri Levy³, Shengbao Suo⁴, Jing-Dong Jackie Han⁴, Pierre Osteil⁵, Guangdun Peng⁶, Naihe Jing⁷, Greg J Baillie², Anne Senabouth², Angelika N Christ², Timothy J Bruxner², Charles E Murry³, Emily S Wong⁸, Jun Ding⁹, Yuliang Wang¹⁰, James Hudson¹¹, Hannele Ruohola-Baker³, Ziv Bar-Joseph⁹, Patrick P L Tam¹², Joseph E Powell¹³, Nathan J Palpant¹⁴

Affiliations

¹ Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Centre for Cardiac and Vascular Biology, The University of Queensland, Brisbane, QLD 4072, Australia.
² Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
³ Departments of Pathology, Biochemistry, Bioengineering and Medicine/Cardiology, Institute for Stem Cell and Regenerative Medicine, The University of Washington, Seattle, WA 98195, USA.
⁴ Key Laboratory of Computational Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China.
⁵ Embryology Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia.
⁶ State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China.
⁷ State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China.
⁸ School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia.
⁹ Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
¹⁰ Departments of Pathology, Biochemistry, Bioengineering and Medicine/Cardiology, Institute for Stem Cell and Regenerative Medicine, The University of Washington, Seattle, WA 98195, USA; Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA.
¹¹ Queensland Institute for Medical Research, Brisbane, QLD 4006, Australia.
¹² Embryology Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Sydney Medical School, University of Sydney, NSW 2006, Australia.
¹³ Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute for Medical Research, Sydney, NSW 2010, Australia. Electronic address: [email protected].
¹⁴ Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Centre for Cardiac and Vascular Biology, The University of Queensland, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia. Electronic address: [email protected].

Abstract

Cardiac differentiation of human pluripotent stem cells (hPSCs) requires orchestration of dynamic gene regulatory networks during stepwise fate transitions but often generates immature cell types that do not fully recapitulate properties of their adult counterparts, suggesting incomplete activation of key transcriptional networks. We performed extensive single-cell transcriptomic analyses to map fate choices and gene expression programs during cardiac differentiation of hPSCs and identified strategies to improve in vitro cardiomyocyte differentiation. Utilizing genetic gain- and loss-of-function approaches, we found that hypertrophic signaling is not effectively activated during monolayer-based cardiac differentiation, thereby preventing expression of HOPX and its activation of downstream genes that govern late stages of cardiomyocyte maturation. This study therefore provides a key transcriptional roadmap of in vitro cardiac differentiation at single-cell resolution, revealing fundamental mechanisms underlying heart development and differentiation of hPSC-derived cardiomyocytes.

Keywords: CRISPRi; HOPX; cardiomyocytes; development; heart; human pluripotent stem cells; hypertrophy; in silico lineage tracing; scdiff; single-cell RNA-seq.

Publication types

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

MeSH terms

Animals
Cell Differentiation / genetics*
Cells, Cultured
Female
Homeodomain Proteins / genetics*
Homeodomain Proteins / metabolism
Humans
Male
Mice
Mice, Inbred C3H
Mice, Inbred C57BL
Mice, Inbred NOD
Mice, Knockout
Mice, Transgenic
Myocytes, Cardiac / cytology*
Myocytes, Cardiac / metabolism
Pluripotent Stem Cells / cytology*
Pluripotent Stem Cells / metabolism
Single-Cell Analysis*
Transcriptome*
Tumor Suppressor Proteins / genetics*
Tumor Suppressor Proteins / metabolism

Substances

HOPX protein, human
Homeodomain Proteins
Tumor Suppressor Proteins

Grants and funding

R01 GM122096/GM/NIGMS NIH HHS/United States