PROJECT ID: GSE158099

Data source GEO: GSE158099
Description We used single cell-RNA sequencing to investigate the expression and the heterogeneity of wild type and runx1-mutant cd41-GFPLow cd41GFP hematopoietic stem and progenitor cells at embryonic (2.5 days post fertilization, dpf) and larval stages (6, 10 16 dpf).
Key word stem-cells; definitive hematopoiesis; adult hematopoiesis; cbf-beta; zebrafish; differentiation; gene; generation; leukemia; system
Publication Bresciani E, Carrington B, Yu K, Kim EM et al. Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development. Blood Adv 2021 Dec 14;5(23):4949-4962. PMID: 34492681
Abstract RUNX1 is essential for the generation of hematopoietic stem cells (HSCs). Runx1-null mouse embryos lack definitive hematopoiesis and die in mid-gestation. However, although zebrafish embryos with a runxl W84X mutation have defects in early definitive hematopoiesis, some runx1(W84X/W84X) embryos can develop to fertile adults with blood cells of multilineages, raising the possibility that HSCs can emerge without RUNX1. Here, using 3 new zebrafish runx1(-/-) lines, we uncovered the compensatory mechanism for runx1-independent hematopoiesis. We show that, in the absence of a functional runx1, a cd41-green fluorescent protein (GFP)(+) population of hematopoietic precursors still emerge from the hemogenic endothelium and can colonize the hematopoietic tissues of the mutant embryos. Single-cell RNA sequencing of the cd41-GFP(+) cells identified a set of runx(-/-) -specific signature genes during hematopoiesis. Significantly, gata2b, which normally acts upstream of runxl for the generation of HSCs, was increased in the cd41-GFP(+) cells in runx1(-/-) embryos. Interestingly, genetic inactivation of both gata2b and its paralog gata2a did not affect hematopoiesis. However, knocking out runx1 and any 3 of the 4 alleles of gata2a and gata2b abolished definitive hematopoiesis. Gata2 expression was also upregulated in hematopoietic cells in Runx1(-/-) mice, suggesting the compensatory mechanism is conserved. Our findings indicate that RUNX1 and GATA2 serve redundant roles for HSC production, acting as each other's safeguard.


Dataset Information

Dataset ID Species Tissue / Organ Experiment type Sample Source dataset ID
1. GSE158099 (WT) Danio rerio whole body baseline 2.5dpf, cd41:GFPlow-WT GEO: GSM4792208
2. GSE158099 (runx1 -|-) Danio rerio whole body hematopoietic 2.5dpf, cd41:GFPlow-runx1-/- GEO: GSM4792209
3. GSE158099 (WT) Danio rerio whole body baseline 6dpf, cd41:GFPlow-WT GEO: GSM4792210
4. GSE158099 (runx1 -|-) Danio rerio whole body hematopoietic 6dpf, cd41:GFPlow-runx1-/- GEO: GSM4792211
5. GSE158099 (WT) Danio rerio whole body baseline 10dpf, cd41:GFPlow-WT GEO: GSM4792212
6. GSE158099 (runx1 -|-) Danio rerio whole body hematopoietic 10dpf, cd41:GFPlow-runx1-/- GEO: GSM4792213
7. GSE158099 (WT) Danio rerio whole body baseline 16dpf, cd41:GFPlow-WT GEO: GSM4792214
8. GSE158099 (runx1 -|-) Danio rerio whole body hematopoietic 16dpf, cd41:GFPlow-runx1-/- GEO: GSM4792215
9. GSE158099 (runx1 -|-) Danio rerio whole body hematopoietic 16dpf, cd41:GFPlow-runx1-/- GEO: GSM4792216

Clustering Result

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Multipotent cells ENSDARG00000078781 (si:ch211-161c3.6) marker DOI:10.1182/bloodadvances.2020003969
2 HSPCs ENSDARG00000043126 (blf) marker DOI:10.1182/bloodadvances.2020003969
2 HSPCs ENSDARG00000004392 (hdr) marker DOI:10.1182/bloodadvances.2020003969
2 HSPCs ENSDARG00000019930 (tal1) marker DOI:10.1182/bloodadvances.2020003969
3 Chondrocytes ENSDARG00000073699 (col9a1a) marker DOI:10.1182/bloodadvances.2020003969
4 Epithelial cells ENSDARG00000040534 (epcam) marker DOI:10.1182/bloodadvances.2020003969
5 Multipotent cells ENSDARG00000078781 (si:ch211-161c3.6) marker DOI:10.1182/bloodadvances.2020003969
6 Multipotent cells ENSDARG00000078781 (si:ch211-161c3.6) marker DOI:10.1182/bloodadvances.2020003969
7 Erythroid cells ENSDARG00000113599 (hbbe1.1) marker DOI:10.1182/bloodadvances.2020003969
8 HSPCs ENSDARG00000043126 (blf) marker DOI:10.1182/bloodadvances.2020003969
8 HSPCs ENSDARG00000004392 (hdr) marker DOI:10.1182/bloodadvances.2020003969
8 HSPCs ENSDARG00000019930 (tal1) marker DOI:10.1182/bloodadvances.2020003969
9 Neutrophils ENSDARG00000019521 (mpx) marker DOI:10.1182/bloodadvances.2020003969
10 Neuron ENSDARG00000021143 (rtn1b) marker DOI:10.1182/bloodadvances.2020003969
12 Epidermal cells ENSDARG00000032849 (ndrg1a) marker DOI:10.1182/bloodadvances.2020003969
13 Macrophages ENSDARG00000055290 (mpeg1.1) marker DOI:10.1182/bloodadvances.2020003969

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Epithelial cells ENSDARG00000040534 (epcam) marker DOI:10.1182/bloodadvances.2020003969
2 Chondrocytes ENSDARG00000073699 (col9a1a) marker DOI:10.1182/bloodadvances.2020003969
3 Erythroid cells ENSDARG00000113599 (hbbe1.1) marker DOI:10.1182/bloodadvances.2020003969
4 Neuron ENSDARG00000021143 (rtn1b) marker DOI:10.1182/bloodadvances.2020003969
5 HSPCs ENSDARG00000019930 (tal1) marker DOI:10.1182/bloodadvances.2020003969
6 Epithelial cells ENSDARG00000040534 (epcam) marker DOI:10.1182/bloodadvances.2020003969
7 Epidermal cells ENSDARG00000032849 (ndrg1a) marker DOI:10.1182/bloodadvances.2020003969
8 Macrophages ENSDARG00000055290 (mpeg1.1) marker DOI:10.1182/bloodadvances.2020003969
9 Multipotent cells ENSDARG00000038066 (kpna2) marker DOI:10.1182/bloodadvances.2020003969
10 Epidermal cells ENSDARG00000075714 (si:dkey-27p23.3) marker DOI:10.1182/bloodadvances.2020003969

Cluster Cell type Gene id (symbol) Marker class Evidence
1 HSPCs ENSDARG00000043126 (blf) marker DOI:10.1182/bloodadvances.2020003969
1 HSPCs ENSDARG00000004392 (hdr) marker DOI:10.1182/bloodadvances.2020003969
1 HSPCs ENSDARG00000019930 (tal1) marker DOI:10.1182/bloodadvances.2020003969
2 Multipotent cells ENSDARG00000078781 (si:ch211-161c3.6) marker DOI:10.1182/bloodadvances.2020003969
3 Erythroid cells ENSDARG00000113599 (hbbe1.1) marker DOI:10.1182/bloodadvances.202000396
4 Multipotent cells ENSDARG00000055186 (ccr9a) marker DOI:10.1182/bloodadvances.202000396
5 HSPCs ENSDARG00000043126 (blf) marker DOI:10.1182/bloodadvances.2020003969
5 HSPCs ENSDARG00000004392 (hdr) marker DOI:10.1182/bloodadvances.2020003969
5 HSPCs ENSDARG00000019930 (tal1) marker DOI:10.1182/bloodadvances.2020003969
6 Macrophages ENSDARG00000013771 (ctss2.2) marker DOI:10.1182/bloodadvances.2020003969
7 Epithelial cells ENSDARG00000040534 (epcam) marker DOI:10.1182/bloodadvances.2020003969
8 Multipotent cells ENSDARG00000058471 (plk1) marker DOI:10.1182/bloodadvances.2020003969
9 Neutrophils ENSDARG00000019521 (mpx) marker DOI:10.1182/bloodadvances.2020003969
10 T cells ENSDARG00000030297 (sox13) marker DOI:10.1182/bloodadvances.2020003969
10 T cells ENSDARG00000016526 (gata3) marker DOI:10.1182/bloodadvances.2020003969
10 T cells ENSDARG00000059327 (gata2a) marker DOI:10.1182/bloodadvances.2020003969
11 Epidermal cells ENSDARG00000032849 (ndrg1a) marker DOI:10.1182/bloodadvances.2020003969
12 Neuron ENSDARG00000004621 (gpm6ab) marker DOI:10.1182/bloodadvances.2020003969

Cluster Cell type Gene id (symbol) Marker class Evidence
1 HSPCs ENSDARG00000019930 (tal1) marker DOI:10.1182/bloodadvances.2020003969
2 HSPCs ENSDARG00000019930 (tal1) marker DOI:10.1182/bloodadvances.2020003969
3 Epithelial cells ENSDARG00000040534 (epcam) marker DOI:10.1182/bloodadvances.2020003969
4 Epidermal cells ENSDARG00000032849 (ndrg1a) marker DOI:10.1182/bloodadvances.2020003969
5 Neuron ENSDARG00000004621 (gpm6ab) marker DOI:10.1182/bloodadvances.2020003969
6 Dividing HSPCs ENSDARG00000051923 (ccnb1) marker DOI:10.1182/bloodadvances.2020003969

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Multipotent cells ENSDARG00000055186 (ccr9a) marker DOI:10.1182/bloodadvances.2020003969
2 HSPCs ENSDARG00000043126 (blf) marker DOI:10.1182/bloodadvances.2020003969
2 HSPCs ENSDARG00000004392 (hdr) marker DOI:10.1182/bloodadvances.2020003969
2 HSPCs ENSDARG00000019930 (tal1) marker DOI:10.1182/bloodadvances.2020003969
3 Multipotent cells ENSDARG00000078781 (si:ch211-161c3.6) marker DOI:10.1182/bloodadvances.2020003969
4 Multipotent cells ENSDARG00000058471 (plk1) marker DOI:10.1182/bloodadvances.2020003969
5 HSPCs ENSDARG00000043126 (blf) marker DOI:10.1182/bloodadvances.2020003969
5 HSPCs ENSDARG00000004392 (hdr) marker DOI:10.1182/bloodadvances.2020003969
5 HSPCs ENSDARG00000019930 (tal1) marker DOI:10.1182/bloodadvances.2020003969
6 Neutrophils ENSDARG00000019521 (mpx) marker DOI:10.1182/bloodadvances.2020003969
7 Macrophages ENSDARG00000013771 (ctss2.2) marker DOI:10.1182/bloodadvances.2020003969
8 Erythroid cells ENSDARG00000113599 (hbbe1.1) marker DOI:10.1182/bloodadvances.202000396
10 Epidermal cells ENSDARG00000016691 (cd9b) marker DOI:10.1182/bloodadvances.2020003969

Cluster Cell type Gene id (symbol) Marker class Evidence
2 Multipotent cells ENSDARG00000058471 (plk1) marker DOI:10.1182/bloodadvances.2020003969
3 Multipotent cells ENSDARG00000078781 (si:ch211-161c3.6) marker DOI:10.1182/bloodadvances.2020003969
4 Erythroid cells ENSDARG00000113599 (hbbe1.1) marker DOI:10.1182/bloodadvances.2020003969
6 HSPCs ENSDARG00000004392 (hdr) marker DOI:10.1182/bloodadvances.2020003969
6 HSPCs ENSDARG00000043126 (blf) marker DOI:10.1182/bloodadvances.2020003969
6 HSPCs ENSDARG00000019930 (tal1) marker DOI:10.1182/bloodadvances.2020003969
7 Neutrophils ENSDARG00000019521 (mpx) marker DOI:10.1182/bloodadvances.2020003969
8 Epidermal cells ENSDARG00000016691 (cd9b) marker DOI:10.1182/bloodadvances.2020003969

Cluster Cell type Gene id (symbol) Marker class Evidence
1 HSPCs ENSDARG00000043126 (blf) marker DOI:10.1182/bloodadvances.2020003969
1 HSPCs ENSDARG00000004392 (hdr) marker DOI:10.1182/bloodadvances.2020003969
1 HSPCs ENSDARG00000019930 (tal1) marker DOI:10.1182/bloodadvances.2020003969
2 Multipotent cells ENSDARG00000078781 (si:ch211-161c3.6) marker DOI:10.1182/bloodadvances.2020003969
3 Multipotent cells ENSDARG00000055186 (ccr9a) marker DOI:10.1182/bloodadvances.2020003969
5 Neutrophils ENSDARG00000019521 (mpx) marker DOI:10.1182/bloodadvances.2020003969
6 Multipotent cells ENSDARG00000058471 (plk1) marker DOI:10.1182/bloodadvances.2020003969
7 Macrophages ENSDARG00000013771 (ctss2.2) marker DOI:10.1182/bloodadvances.2020003969
8 Neuron ENSDARG00000036577 (atp6v0cb) marker DOI:10.1182/bloodadvances.2020003969
9 Neutrophils ENSDARG00000102119 (si:ch73-359m17.2) marker DOI:10.1182/bloodadvances.2020003969
11 Macrophages ENSDARG00000077809 (il13) marker DOI:10.1182/bloodadvances.2020003969
13 Epidermal cells ENSDARG00000016691 (cd9b) marker DOI:10.1182/bloodadvances.2020003969
14 Epidermal cells ENSDARG00000102750 (cdh1) marker DOI:10.1182/bloodadvances.2020003969

Cluster Cell type Gene id (symbol) Marker class Evidence
2 HSPCs ENSDARG00000004392 (hdr) marker DOI:10.1182/bloodadvances.2020003969
2 HSPCs ENSDARG00000043126 (blf) marker DOI:10.1182/bloodadvances.2020003969
2 HSPCs ENSDARG00000077504 (si:ch211-103n10.5) marker DOI:10.1182/bloodadvances.2020003969
3 Neutrophils ENSDARG00000078781 (si:ch211-161c3.6) marker DOI:10.1182/bloodadvances.2020003969
5 HSPCs ENSDARG00000077504 (si:ch211-103n10.5) marker DOI:10.1182/bloodadvances.2020003969
6 Multipotent cells ENSDARG00000078781 (si:ch211-161c3.6) marker DOI:10.1182/bloodadvances.2020003969
7 Macrophages ENSDARG00000013771 (ctss2.2) marker DOI:10.1182/bloodadvances.2020003969
8 Epidermal cells ENSDARG00000102750 (cdh1) marker DOI:10.1182/bloodadvances.2020003969
9 Neuron ENSDARG00000006497 (rtn1a) marker DOI:10.1182/bloodadvances.2020003969
10 Epidermal cells ENSDARG00000016691 (cd9b) marker DOI:10.1182/bloodadvances.2020003969
10 Epidermal cells ENSDARG00000077570 (cdh16) marker DOI:10.1182/bloodadvances.2020003969
11 Neutrophils ENSDARG00000019521 (mpx) marker DOI:10.1182/bloodadvances.2020003969
12 Epidermal cells ENSDARG00000077570 (cdh16) marker DOI:10.1182/bloodadvances.2020003969
13 Epidermal cells ENSDARG00000013453 (tdrd9) marker DOI:10.1182/bloodadvances.2020003969

Cluster Cell type Gene id (symbol) Marker class Evidence
1 HSPCs ENSDARG00000043126 (blf) marker DOI:10.1182/bloodadvances.2020003969
1 HSPCs ENSDARG00000004392 (hdr) marker DOI:10.1182/bloodadvances.2020003969
1 HSPCs ENSDARG00000019930 (tal1) marker DOI:10.1182/bloodadvances.2020003969
2 HSPCs ENSDARG00000043126 (blf) marker DOI:10.1182/bloodadvances.2020003969
2 HSPCs ENSDARG00000004392 (hdr) marker DOI:10.1182/bloodadvances.2020003969
2 HSPCs ENSDARG00000019930 (tal1) marker DOI:10.1182/bloodadvances.2020003969
3 Multipotent cells ENSDARG00000078781 (si:ch211-161c3.6) marker DOI:10.1182/bloodadvances.2020003969
5 HSPCs ENSDARG00000043126 (blf) marker DOI:10.1182/bloodadvances.2020003969
5 HSPCs ENSDARG00000004392 (hdr) marker DOI:10.1182/bloodadvances.2020003969
5 HSPCs ENSDARG00000019930 (tal1) marker DOI:10.1182/bloodadvances.2020003969
6 Neutrophils ENSDARG00000019521 (mpx) marker DOI:10.1182/bloodadvances.2020003969
7 Multipotent cells ENSDARG00000078781 (si:ch211-161c3.6) marker DOI:10.1182/bloodadvances.2020003969
8 HSPCs ENSDARG00000034852 (nt5c2l1) marker DOI:10.1182/bloodadvances.2020003969
9 Epidermal cells ENSDARG00000016691 (cd9b) marker DOI:10.1182/bloodadvances.2020003969
9 Epidermal cells ENSDARG00000102750 (cdh1) marker DOI:10.1182/bloodadvances.2020003969
10 Macrophages ENSDARG00000013771 (ctss2.2) marker DOI:10.1182/bloodadvances.2020003969
11 Neuron ENSDARG00000006497 (rtn1a) marker DOI:10.1182/bloodadvances.2020003969
12 Epidermal cells ENSDARG00000016691 (cd9b) marker DOI:10.1182/bloodadvances.2020003969
13 Epidermal cells ENSDARG00000102750 (cdh1) marker DOI:10.1182/bloodadvances.2020003969
14 Epidermal cells ENSDARG00000032849 (ndrg1a) marker DOI:10.1182/bloodadvances.2020003969