Single-cell reconstruction of differentiation trajectory reveals a critical role of ETS1 in human cardiac lineage commitment
Authors: Youqiong Ye
Hanshi Xu
Leng Han
Peng Yu
Fang Yao
Bingying Zhou
Zongna Ren
Jiewei Liu
Lixia Diao
Hang Ruan
Shengli Li
Zhao Zhang
Yingnan Liao
Li Wang
Lin Mao
Journal: BMC biology (2019)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: Cardiac lineage commitment; Cell-cell crosstalk; ETS1; Human pluripotent stem cells; Single-cell RNA sequencing
Affiliations: State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 North Lishi Road, Beijing, 100037, People's Republic of China., Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, 6431 Fannin St, MSB6.166, Houston, TX, 77030, USA., Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA., Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, 6431 Fannin St, MSB6.166, Houston, TX, 77030, USA. ., State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167 North Lishi Road, Beijing, 100037, People's Republic of China. .

Abstract:  Background: Cardiac differentiation from human pluripotent stem cells provides a unique opportunity to study human heart development in vitro and offers a potential cell source for cardiac regeneration. Compared to the large body of studies investigating cardiac maturation and cardiomyocyte subtype-specific induction, molecular events underlying cardiac lineage commitment from pluripotent stem cells at early stage remain poorly characterized. Results: In order to uncover key molecular events and regulators controlling cardiac lineage commitment from a pluripotent state during differentiation, we performed single-cell RNA-Seq sequencing and obtained high-quality data for 6879 cells collected from 6 stages during cardiac differentiation from human embryonic stem cells and identified multiple cell subpopulations with distinct molecular features. Through constructing developmental trajectory of cardiac differentiation and putative ligand-receptor interactions, we revealed crosstalk between cardiac progenitor cells and endoderm cells, which could potentially provide a cellular microenvironment supporting cardiac lineage commitment at day 5. In addition, computational analyses of single-cell RNA-Seq data unveiled ETS1 (ETS Proto-Oncogene 1) activation as an important downstream event induced by crosstalk between cardiac progenitor cells and endoderm cells. Consistent with the findings from single-cell analysis, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) against ETS1 revealed genomic occupancy of ETS1 at cardiac structural genes at day 9 and day 14, whereas ETS1 depletion dramatically compromised cardiac differentiation. Conclusion: Together, our study not only characterized the molecular features of different cell types and identified ETS1 as a crucial factor induced by cell-cell crosstalk contributing to cardiac lineage commitment from a pluripotent state, but may also have important implications for understanding human heart development at early embryonic stage, as well as directed manipulation of cardiac differentiation in regenerative medicine. 

Retracted: No

PubPeer comments:
 Hi! Can you tell me why Series Matrix File(s) of GSE129986 contains no information of gene expression? ![file] , 
 #1 The data deposited under GSE129986 is ChIP-seq data. The single cell expression data are deposited under another accession number GSE129987. The format of scRNA-seq data is different from traditional RNA-seq data. Please refer to supplementary file  GSE129987_RAW.tar for the expression matrix. ,