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A 3D Atlas of Hematopoietic Stem and Progenitor Cell Expansion by Multi-Dimensional RNA-Seq Analysis

48 Pages Posted: 10 Feb 2019 Sneak Peek Status: Published

See all articles by Yuanyuan Xue

Yuanyuan Xue

Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology; Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration; Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences

Denghui Liu

Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology; Chinese Academy of Sciences (CAS), Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences

Guizhong Cui

Chinese Academy of Sciences (CAS) - Institute of Biochemistry and Cell Biology

Yanyan Ding

Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology; Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration; Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences

Daosheng Ai

Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology; Chinese Academy of Sciences (CAS, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology

Suwei Gao

Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology

Yifan Zhang

Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology; Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration; Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences

Shengbao Suo

Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology; Chinese Academy of Sciences (CAS, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences

Xiaohan Wang

Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology; Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration; Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences

Peng Lv

Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology; Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration; Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences

Chunyu Zhou

Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology; Chinese Academy of Sciences (CAS, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology

Yizhou Li

Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology; Chinese Academy of Sciences (CAS, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology

Xingwei Chen

Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology; Chinese Academy of Sciences (CAS, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology

Guangdun Peng

Chinese Academy of Sciences (CAS), Shanghai Institutes for Biological Sciences, Institute of Biochemistry and Cell Biology, State Key Laboratory of Cell Biology

Naihe Jing

Chinese Academy of Sciences (CAS) - Institute of Biochemistry and Cell Biology

Jing-Dong J. Han

Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology; Chinese Academy of Sciences (CAS), Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology ; Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences

Feng Liu

Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology; Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration; Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences

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Abstract

In vertebrates, hematopoiesis occurring in different niches is orchestrated by intrinsic and extrinsic regulators, which are indispensable for the maintenance of homeostasis in a whole organism. Previous studies have revealed a large number of linear and planar regulatory mechanisms. However, a multi-dimensional transcriptomic atlas of any given hematopoietic organ has not been yet established. Here, we use multiple RNA-seq approaches, including cell type-specific temporal bulk RNA-seq, in vivo GEO-seq, and single-cell RNA-seq (scRNA-seq), to characterize the detailed spatiotemporal transcriptome during hematopoietic stem and progenitor cell (HSPC) expansion in the caudal hematopoietic tissue (CHT) of zebrafish. Combinatorial expression profiling reveals that in the CHT niche, HSPCs and their neighboring supporting cells are co-regulated by shared signaling pathways and intrinsic factors, such as integrin signaling and Smchd1. Moreover, scRNA-seq analysis unveils the strong association between cell cycle status and HSPC differentiation. Taken together, we report a global transcriptome landscape that provides valuable insights and a rich resource for understanding HSPC development, particularly on HSPC expansion in an intact hematopoietic organ. The key signaling pathways and factors identified here would contribute to HSPC expansion in vitro.

Keywords: Hematopoietic stem and progenitor cell, Multi-dimensional RNA-seq, 3D atlas, Signaling, Zebrafish

Suggested Citation

Xue, Yuanyuan and Liu, Denghui and Cui, Guizhong and Ding, Yanyan and Ai, Daosheng and Gao, Suwei and Zhang, Yifan and Suo, Shengbao and Wang, Xiaohan and Lv, Peng and Zhou, Chunyu and Li, Yizhou and Chen, Xingwei and Peng, Guangdun and Jing, Naihe and Han, Jing-Dong J. and Liu, Feng, A 3D Atlas of Hematopoietic Stem and Progenitor Cell Expansion by Multi-Dimensional RNA-Seq Analysis (February 8, 2019). Available at SSRN: https://ssrn.com/abstract=3331363 or http://dx.doi.org/10.2139/ssrn.3331363
This is a paper under consideration at Cell Press and has not been peer-reviewed.

Yuanyuan Xue

Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology

Beijing
China

Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration

Beijing
China

Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences

Building 7, NO. 80 Zhongguancun Road
Beijing, Beijing 100190
China

Denghui Liu

Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology

Shanghai
China

Chinese Academy of Sciences (CAS), Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology

Shanghai
China

Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences

Building 7, NO. 80 Zhongguancun Road
Beijing, Beijing 100190
China

Guizhong Cui

Chinese Academy of Sciences (CAS) - Institute of Biochemistry and Cell Biology

320 Yue Yang Road
Shanghai, 200031
China

Yanyan Ding

Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology

Beijing
China

Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration

Beijing
China

Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences

Building 7, NO. 80 Zhongguancun Road
Beijing, Beijing 100190
China

Daosheng Ai

Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology

Shanghai
China

Chinese Academy of Sciences (CAS, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology

Shanghai
China

Suwei Gao

Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology

Beijing
China

Yifan Zhang

Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology

Beijing
China

Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration

Beijing
China

Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences

Building 7, NO. 80 Zhongguancun Road
Beijing, Beijing 100190
China

Shengbao Suo

Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology

Shanghai
China

Chinese Academy of Sciences (CAS, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology

Shanghai
China

Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences

Building 7, NO. 80 Zhongguancun Road
Beijing, Beijing 100190
China

Xiaohan Wang

Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology

Beijing
China

Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration

Beijing
China

Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences

Building 7, NO. 80 Zhongguancun Road
Beijing, Beijing 100190
China

Peng Lv

Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology

Beijing
China

Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration

Beijing
China

Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences

Building 7, NO. 80 Zhongguancun Road
Beijing, Beijing 100190
China

Chunyu Zhou

Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology

Shanghai
China

Chinese Academy of Sciences (CAS, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology

Shanghai
China

Yizhou Li

Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology

Shanghai
China

Chinese Academy of Sciences (CAS, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology

Shanghai
China

Xingwei Chen

Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology

Shanghai
China

Chinese Academy of Sciences (CAS, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology

Shanghai
China

Guangdun Peng

Chinese Academy of Sciences (CAS), Shanghai Institutes for Biological Sciences, Institute of Biochemistry and Cell Biology, State Key Laboratory of Cell Biology

Shanghai
China

Naihe Jing

Chinese Academy of Sciences (CAS) - Institute of Biochemistry and Cell Biology

320 Yue Yang Road
Shanghai, 200031
China

Jing-Dong J. Han

Chinese Academy of Sciences (CAS), Center for Excellence in Molecular Cell Science, Key Laboratory of Computational Biology ( email )

Shanghai
China

Chinese Academy of Sciences (CAS), Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Collaborative Innovation Center for Genetics and Developmental Biology ( email )

Shanghai
China

Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences ( email )

Building 7, NO. 80 Zhongguancun Road
Beijing, Beijing 100190
China

Feng Liu (Contact Author)

Chinese Academy of Sciences (CAS), Kunming Institute of Zoology, State Key Laboratory of Membrane Biology ( email )

Beijing
China

Chinese Academy of Sciences (CAS) - Institute for Stem Cell and Regeneration ( email )

Beijing
China

Chinese Academy of Sciences (CAS) - University of Chinese Academy of Sciences ( email )

Building 7, NO. 80 Zhongguancun Road
Beijing, Beijing 100190
China

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