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Identification of Key Factors in Cardiomyocyte Development by Single‐Cell Transcriptome Analysis
Author(s) -
Zhu Jun,
Wu Dingfeng,
Gao Wenxing,
Chen Wanning,
Fu Qianzheng,
Jiao Na,
Zhu Lixin,
Zhu Ruixin
Publication year - 2020
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.2020.34.s1.05306
Subject(s) - biology , induced pluripotent stem cell , transcriptome , progenitor cell , embryonic stem cell , microbiology and biotechnology , stem cell , mesoderm , cellular differentiation , cell type , computational biology , cell , genetics , gene expression , gene
Background A promising intervention for heart diseases is the application of cardiomyocytes differentiated from pluripotent stem cells. However, the driving factors of the differentiation process still remain unclear. This study aims to map the transcriptional landscapes of directional differentiation of pluripotent stem cells at multiple stages, using single‐cell sequencing data, in order to identify the key drivers of the differentiation process. Method Single‐cell sequencing data from pluripotent stem cell‐derived cardiomyocytes at age day 0, day 2, day 5, day 15 and day 30 were included and normalized. UMAP algorithm was then used to reduce the dimensionality of the transcriptome profiles, followed by community detection to group the cells and cell type identification using marker genes. Graph‐autocorrelation analysis was implemented to identify differentially expressed genes among cell groups with Gene Ontology term enrichment. Next, we calculated the pseudotimes of each cardiomyocyte to construct the pseudotime trajectories. Finally, knowledge based dynamic changes in gene expression were analyzed to identify the key factors driving the cardiomyocyte development. Result We identified 9 different cell types in the process of cardiomyocyte development, including cardiomyocytes, induced pluripotent stem cells, cardiogenic mesoderm cells, cardiovascular progenitor cells, embryonic stem cells, endoderm cells, epithelial progenitor cells, cardiomyocyte progenitor cells and multipotent progenitor cells. Identification of cardiomyocyte was confirmed with specific gene expression profiles such as significant enrichment in the biological processes of cell adhesion and supramolecular fiber organization. The expression of NKX2‐5, which encodes a homeobox‐containing transcription factor, was found to be at a lower level in the early stages and continually increased as cardiomyocyte develop, suggesting that NKX2‐5 was one of the driving factors of cardiac development, acting through promoting myocardial maturation and development. Conclusion Single cell sequencing data revealed the dynamic changes of gene expression during cardiomyocyte development differentiation. NKX2‐5 was identified as a key factor in cardiac development. Our finding contributes to the understanding of the mechanism behind the cardiomyocyte development, and may serve as the basis for stem cell based therapies. Support or Funding Information This work was supported by National Natural Science Foundation of China 81774152 (to RZ) and 81770571 (to LZ).