Spatial transcriptome profiling by MERFISH reveals fetal liver hematopoietic stem cell niche architecture

Yanfang Lu,Samuel G Katz,Siyuan Wang,Xinghua Pan,Jennifer Yang,Miao Liu,Sherman M Weissman

doi:10.1038/s41421-021-00266-1

Abstract

The hematopoietic stem cell (HSC) niche has been extensively studied in bone marrow, yet a more systematic investigation into the microenvironment regulation of hematopoiesis in fetal liver is necessary. Here we investigate the spatial organization and transcriptional profile of individual cells in both wild type (WT) and Tet2−/− fetal livers, by multiplexed error robust fluorescence in situ hybridization. We find that specific pairs of fetal liver cell types are preferentially positioned next to each other. Ligand-receptor signaling molecule pairs such as Kitl and Kit are enriched in neighboring cell types. The majority of HSCs are in direct contact with endothelial cells (ECs) in both WT and Tet2−/− fetal livers. Loss of Tet2 increases the number of HSCs, and upregulates Wnt and Notch signaling genes in the HSC niche. Two subtypes of ECs, arterial ECs and sinusoidal ECs, and other cell types contribute distinct signaling molecules to the HSC niche. Collectively, this study provides a comprehensive picture and bioinformatic foundation for HSC spatial regulation in fetal liver.

Highlights

Hematopoietic stem cells (HSCs) retain the potential to generate all lineages of blood cells throughout the life of the organism
According to a twodimensional representation of the single cell transcriptome and the direction of the arrows in our RNA velocity map, erythroid cells, erythroid progenitors, myeloids, basophils, and neutrophils were connected in a branched development trajectory, while megakaryocytes (MKs) and macrophages were separated from the above mentioned cells; erythroid progenitors differentiated into erythroid cells; and neutrophils were separated into two main subtypes (Neutrophil_Elane and Neutrophil_Ngp) that appear to be differentiated from a common progenitor (Fig. 1b)
We found many known HSC niche genes such as Fgf[1], Icam[1], Cspg[4], Il6, Lepr, Angptl[2], Eng, Nes, Tgfb[2], Nrp[1], Efnb[2], Il7r, Pecam[1], Epcam, Cdh[5], Cxcl[12], and Ephb[4], Wnt genes such as Dkk[2], Fzd[2], Prickle[2], Fzd[4], Vangl[2], Sfrp[1], Fzd[1], and Tcf7l1, and Notch genes such as Notch[1], Dll[1], Jag[2], Dll[4], Notch[4], and Notch[3] were enriched in wild type (WT) arterial ECs (AECs) or sinusoidal ECs (SECs) (Fig. 3a); and niche genes such as Fgf[2], Cspg[4], Angptl[2], Il6, Lepr, Ndn, Meis[1], Il7r, Pecam[1], Eng, Efnb[2], Nes, Nrp[1], Fgf[1], Pdpn, Tgfb[2], Epcam, Cdh[5], Igf[1], Cxcl[12], Ephb[4], and Egfr, Wnt genes such as Tcf7l1, Fzd[3], Prickle[2], Fzd[2], Fzd[4], Sfrp[2], Dkk[2], Vangl[2], Sfrp[1], and Fzd[1], Notch genes such as Jag[2], Jag[1], Dll[1], Notch[4], Dll[4], Notch[1], and Notch[3] were enriched in Tet2−/− AECs or SECs (Fig. 3b)

Summary

Introduction

Hematopoietic stem cells (HSCs) retain the potential to generate all lineages of blood cells throughout the life of the organism. Long-term HSCs arise first in the dorsal aorta of aorta–gonad–mesonephros region of mouse embryos around embryonic day 10.5 (E10.5) through an endothelial-to-hematopoietic transition[1]. On day 12 of gestation, HSCs migrate to the fetal liver through the blood circulation via the umbilical vein from the placenta. HSCs undergo a 38-fold expansion until E162. HSCs migrate from the liver to the bone marrow where they maintain life-long hematopoiesis. Various niches are present in different stages of development given the diversity of tissues where HSCs reside, including the yolk sac, aorta–gonad–mesonephros region, placenta, fetal liver, spleen, and bone marrow[4,5,6]

Methods

Results

Conclusion