Xiaoping Han: Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.
Haide Chen: Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China. hyde@zju.edu.cn.
Daosheng Huang: Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.
Huidong Chen: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Chan School of Public Health, Boston, MA, 02115, USA.
Lijiang Fei: Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China.
Chen Cheng: College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
He Huang: Institute of Hematology, The 1st Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
Guo-Cheng Yuan: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Chan School of Public Health, Boston, MA, 02115, USA. gcyuan@jimmy.harvard.edu.
Guoji Guo: Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, 310058, China. ggj@zju.edu.cn.
BACKGROUND: Human pluripotent stem cells (hPSCs) provide powerful models for studying cellular differentiations and unlimited sources of cells for regenerative medicine. However, a comprehensive single-cell level differentiation roadmap for hPSCs has not been achieved. RESULTS: We use high throughput single-cell RNA-sequencing (scRNA-seq), based on optimized microfluidic circuits, to profile early differentiation lineages in the human embryoid body system. We present a cellular-state landscape for hPSC early differentiation that covers multiple cellular lineages, including neural, muscle, endothelial, stromal, liver, and epithelial cells. Through pseudotime analysis, we construct the developmental trajectories of these progenitor cells and reveal the gene expression dynamics in the process of cell differentiation. We further reprogram primed H9 cells into naïve-like H9 cells to study the cellular-state transition process. We find that genes related to hemogenic endothelium development are enriched in naïve-like H9. Functionally, naïve-like H9 show higher potency for differentiation into hematopoietic lineages than primed cells. CONCLUSIONS: Our single-cell analysis reveals the cellular-state landscape of hPSC early differentiation, offering new insights that can be harnessed for optimization of differentiation protocols.
