Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing

被引:71
作者
Han, Xiaoping [1 ,2 ,8 ]
Chen, Haide [1 ,3 ,5 ]
Huang, Daosheng [1 ,8 ]
Chen, Huidong [4 ,6 ]
Fei, Lijiang [1 ,8 ]
Cheng, Chen [7 ]
Huang, He [2 ,8 ]
Yuan, Guo-Cheng [4 ]
Guo, Guoji [1 ,2 ,3 ,8 ]
机构
[1] Zhejiang Univ, Sch Med, Ctr Stem Cell & Regenerat Med, Hangzhou 310058, Zhejiang, Peoples R China
[2] Zhejiang Univ, Sch Med, Inst Hematol, Affiliated Hosp 1, Hangzhou 310003, Zhejiang, Peoples R China
[3] Dr Li Dak Sum & Yip Yio Chin Ctr Stem Cell & Rege, Zhejiang Prov Key Lab Tissue Engn & Regenerat Med, Hangzhou 310058, Zhejiang, Peoples R China
[4] Harvard Chan Sch Publ Hlth, Dana Farber Canc Inst, Dept Biostat & Computat Biol, Boston, MA 02115 USA
[5] Zhejiang Univ, Coll Anim Sci, Hangzhou 310058, Zhejiang, Peoples R China
[6] Tongji Univ, Dept Comp Sci & Technol, Shanghai 201804, Peoples R China
[7] Zhejiang Univ, Coll Life Sci, Hangzhou 310058, Zhejiang, Peoples R China
[8] Zhejiang Univ, Stem Cell Inst, Hangzhou 310058, Zhejiang, Peoples R China
来源
GENOME BIOLOGY | 2018年 / 19卷
基金
中国国家自然科学基金;
关键词
Single-cell RNA-sequencing; Primed human pluripotent stem cell; Embryoid body; Naive human pluripotent stem cell; MESSENGER-RNA; SIGNALING PATHWAYS; CULTURE-CONDITIONS; STROMAL CELLS; HUMAN ES; GENE; EXPRESSION; NAIVE; MUSCLE; MOUSE;
D O I
10.1186/s13059-018-1426-0
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
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 naive-like H9 cells to study the cellular-state transition process. We find that genes related to hemogenic endothelium development are enriched in naive-like H9. Functionally, naive-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.
引用
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页数:19
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