ZFIN ID: ZDB-PUB-190507-6
A 3D Atlas of Hematopoietic Stem and Progenitor Cell Expansion by Multi-dimensional RNA-Seq Analysis
Xue, Y., Liu, D., Cui, G., Ding, Y., Ai, D., Gao, S., Zhang, Y., Suo, S., Wang, X., Lv, P., Zhou, C., Li, Y., Chen, X., Peng, G., Jing, N., Han, J.J., Liu, F.
Date: 2019
Source: Cell Reports   27: 1567-1578.e5 (Journal)
Registered Authors: Liu, Feng, Lv, Peng, Zhang, Yifan
Keywords: 3D atlas, hematopoietic stem and progenitor cell, multi-dimensional RNA-seq, signaling, zebrafish
Microarrays: GEO:GSE120503, GEO:GSE120509, GEO:GSE120578, GEO:GSE120581
MeSH Terms:
  • Animals
  • Hematopoiesis*
  • Hematopoietic Stem Cells/classification
  • Hematopoietic Stem Cells/cytology*
  • Hematopoietic Stem Cells/metabolism
  • RNA-Seq
  • Signal Transduction
  • Single-Cell Analysis
  • Stem Cell Niche
  • Transcriptome*
  • Zebrafish
PubMed: 31042481 Full text @ Cell Rep.
In vertebrates, hematopoiesis occurring in different niches is orchestrated by intrinsic and extrinsic regulators. Previous studies have revealed numerous linear and planar regulatory mechanisms. However, a multi-dimensional transcriptomic atlas of any given hematopoietic organ has not yet been established. Here, we use multiple RNA sequencing (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 to understand HSPC expansion in an intact vertebrate hematopoietic organ.