PROJECT ID: GSE123241


Data source GEO: GSE123241
Description Loss of sensory hair cells leads to deafness and balance deficiencies. In contrast to mammalian hair cells, zebrafish ear and lateral line hair cells regenerate from poorly characterized, proliferating support cells. Equally ill-defined is the gene regulatory network underlying the progression of support cells to cycling hair cell progenitors and differentiated hair cells. We used single-cell RNA-Sequencing (scRNA-Seq) of lateral line sensory organs and uncovered five different support cell types, including quiescent and activated stem cells. In silico ordering of support cells along a developmental trajectory identified cells that self-renew and new groups of genes required for hair cell differentiation. scRNA-Seq analyses of fgf3 mutants, in which hair cell regeneration is increased demonstrates that Fgf and Notch signaling inhibit proliferation of support cells in parallel by inhibiting Wnt signaling. Our scRNA-Seq analyses set the foundation for mechanistic studies of sensory organ regeneration and is crucial for identifying factors to trigger hair cell production in mammals.
Key word [1]convergent extension movements; posterior lateral-line; mechanical strain determines; neural-tube closure; pl anar polarity; postembryonic development; gastrulation movements; genes; migration; regeneration; [2]zebrafish lateral-line; postembryonic development; hematopoietic stem; laser-abl ation; fate decisions; enhancer trap; hearing-loss; wnt; proliferation; organ
Publication [1]Navajas Acedo J, Voas MG, Alexander R, Woolley T et al. PCP and Wnt pathway components act in parallel during zebrafish mechanosensory hair cell orientation. Nat Commun 2019 Sep 5;10(1):3993. PMID: 31488837; [2]Lush ME, Diaz DC, Koenecke N, Baek S et al. scRNA-Seq reveals distinct stem cell populations that drive hair cell regeneration after loss of Fgf and Notch signaling. Elife 2019 Jan 25;8. PMID: 30681411
Abstract [1]Planar cell polarity (PCP) plays crucial roles in developmental processes such as gastrulation, neural tube closure and hearing. Wnt pathway mutants are often classified as PCP mutants due to similarities between their phenotypes. Here, we show that in the zebrafish lateral line, disruptions of the PCP and Wnt pathways have differential effects on hair cell orientations. While mutations in the PCP genes vangl2 and scrib cause random orientations of hair cells, mutations in wnt11f1, gpc4 and fzd7a/b induce hair cells to adopt a concentric pattern. This concentric pattern is not caused by defects in PCP but is due to misaligned support cells. The molecular basis of the support cell defect is unknown but we demonstrate that the PCP and Wnt pathways work in parallel to establish proper hair cell orientation. Consequently, hair cell orientation defects are not solely explained by defects in PCP signaling, and some hair cell phenotypes warrant re-evaluation. [2]Loss of sensory hair cells leads to deafness and balance deficiencies. In contrast to mammalian hair cells, zebrafish ear and lateral line hair cells regenerate from poorly characterized support cells. Equally ill-defined is the gene regulatory network underlying the progression of support cells to differentiated hair cells. scRNA-Seq of lateral line organs uncovered five different support cell types, including quiescent and activated stem cells. Ordering of support cells along a developmental trajectory identified self-renewing cells and genes required for hair cell differentiation. scRNA-Seq analyses of fgf3 mutants, in which hair cell regeneration is increased, demonstrates that Fgf and Notch signaling inhibit proliferation of support cells in parallel by inhibiting Wnt signaling. Our scRNA-Seq analyses set the foundation for mechanistic studies of sensory organ regeneration and is crucial for identifying factors to trigger hair cell production in mammals. The data is searchable and publicly accessible via a web-based interface.


Dataset Information


Dataset ID Species Tissue / Organ Experiment type Sample Source dataset ID
1. GSE123241 (wild type) Danio rerio neuromast baseline 5dpf, wild type during sensory hair cell regeneration, lateral line sensory GEO: GSM3498552
2. GSE123241 (fgf3 mutants) Danio rerio neuromast regeneration 5dpf, fgf3 mutants during sensory hair cell regeneration, lateral line sensory GEO: GSM3498553
3. GSE123241 (fgf3 siblings) Danio rerio neuromast regeneration 5dpf, fgf3 siblings during sensory hair cell regeneration, lateral line sensory GEO: GSM3498554

Clustering Result


Cluster Cell type Gene id (symbol) Marker class Evidence
1 Dorsal-ventral cells ENSDARG00000027740 (adcyap1b) marker DOI:10.7554/eLife.44431
2 Central support cells ENSDARG00000100244 (ebf3a) marker DOI:10.7554/eLife.44431
2 Central support cells ENSDARG00000037879 (lfng) marker DOI:10.1371/journal.pone.0167286
2 Central support cells ENSDARG00000009094 (gata2b) marker DOI:10.1016/bs.ctdb.2016.01.002
2 Central support cells ENSDARG00000104431 (slc1a3a) marker DOI:10.1016/j.stem.2015.07.002
2 Central support cells ENSDARG00000073978 (crabp2a) marker DOI:10.7554/eLife.44431
3 Anterior-posterior cells ENSDARG00000105061 (si:ch73-261i21.5) marker DOI:10.7554/eLife.44431
4 Central support cells ENSDARG00000100244 (ebf3a) marker DOI:10.7554/eLife.44431
4 Central support cells ENSDARG00000037879 (lfng) marker DOI:10.1371/journal.pone.0167286
4 Central support cells ENSDARG00000009094 (gata2b) marker DOI:10.1016/bs.ctdb.2016.01.002
4 Central support cells ENSDARG00000104431 (slc1a3a) marker DOI:10.1016/j.stem.2015.07.002
5 Hair cells ENSDARG00000055294 (atoh1a) marker DOI:10.7554/eLife.44431
5 Hair cells ENSDARG00000056732 (her4.1) marker DOI:10.7554/eLife.44431
6 Mantle cells ENSDARG00000059279 (tfap2a) marker DOI:10.7554/eLife.44431
6 Mantle cells ENSDARG00000053858 (crip1) marker DOI:10.7554/eLife.44431
6 Mantle cells ENSDARG00000089368 (hopx) marker DOI:10.7554/eLife.44431
7 Hair cells ENSDARG00000055294 (atoh1a) marker DOI:10.7554/eLife.44431

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Dorsal-ventral cells ENSDARG00000027740 (adcyap1b) marker DOI:10.7554/eLife.44431
2 Central support cells ENSDARG00000100244 (ebf3a) marker DOI:10.7554/eLife.44431
2 Central support cells ENSDARG00000037879 (lfng) marker DOI:10.1371/journal.pone.0167286
2 Central support cells ENSDARG00000009094 (gata2b) marker DOI:10.1016/bs.ctdb.2016.01.002
2 Central support cells ENSDARG00000104431 (slc1a3a) marker DOI:10.1016/j.stem.2015.07.002
2 Central support cells ENSDARG00000073978 (crabp2a) marker DOI:10.7554/eLife.44431
3 Anterior-posterior cells ENSDARG00000105061 (si:ch73-261i21.5) marker DOI:10.7554/eLife.44431
4 Hair cells ENSDARG00000056732 (her4.1) marker DOI:10.7554/eLife.44431
5 Mantle cells ENSDARG00000059279 (tfap2a) marker DOI:10.7554/eLife.44431
5 Mantle cells ENSDARG00000053858 (crip1) marker DOI:10.7554/eLife.44431
5 Mantle cells ENSDARG00000089368 (hopx) marker DOI:10.7554/eLife.44431
6 Hair cells ENSDARG00000055294 (atoh1a) marker DOI:10.7554/eLife.44431

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Dorsal-ventral cells ENSDARG00000061259 (sost) marker DOI:10.7554/eLife.44431
1 Dorsal-ventral cells ENSDARG00000041117 (wnt2) marker DOI:10.1016/j.devcel.2015.05.025
1 Dorsal-ventral cells ENSDARG00000054878 (six2b) marker DOI:10.7554/eLife.44431
2 Central support cells ENSDARG00000100244 (ebf3a) marker DOI:10.7554/eLife.44431
2 Central support cells ENSDARG00000037879 (lfng) marker DOI:10.1371/journal.pone.0167286
2 Central support cells ENSDARG00000009094 (gata2b) marker DOI:10.1016/bs.ctdb.2016.01.002
2 Central support cells ENSDARG00000104431 (slc1a3a) marker DOI:10.1016/j.stem.2015.07.002
2 Central support cells ENSDARG00000073978 (crabp2a) marker DOI:10.7554/eLife.44431
3 Anterior-posterior cells ENSDARG00000105061 (si:ch73-261i21.5) marker DOI:10.7554/eLife.44431
4 Hair cells ENSDARG00000055294 (atoh1a) marker DOI:10.7554/eLife.44431
5 Mantle cells ENSDARG00000059279 (tfap2a) marker DOI:10.7554/eLife.44431
5 Mantle cells ENSDARG00000053858 (crip1) marker DOI:10.7554/eLife.44431
5 Mantle cells ENSDARG00000089368 (hopx) marker DOI:10.7554/eLife.44431
6 Hair cells ENSDARG00000055294 (atoh1a) marker DOI:10.7554/eLife.44431