PROJECT ID: GSE151354


Data source GEO: GSE151354
Description The specification and maintenance of distinct zones of chondrocytes within growth plates and joints ensures proper skeletal development through adulthood. Rare mutations in the transcription factor NKX3.2 underlie Spondylo-megaepiphyseal-metaphyseal dysplasia (SMMD), which is characterized by skeletal defects including scoliosis, large epiphyses, wide growth plates, and supernumerary joints in the distal limbs. Embryonic knockdown of nkx3.2 function in zebrafish had revealed a requirement in jaw joint specification, yet embryonic lethality of nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants had precluded an analysis of post-embryonic functions. Here we report adult viable nkx3.2 zebrafish mutants that display ectopic cartilage overgrowth in place of a missing jaw joint, as well as severe dysmorphologies of the facial skeleton, skullcap, and spine. We also isolate rare viable nkx3.2 knockdown animals that lack the jaw joint but fail to display ectopic cartilage growth and scoliosis, indicating post-embryonic roles for Nkx3.2 beyond jaw joint specification. Consistently, we observe nkx3.2 expression in the subarticular zone of the adult jaw joint and in pre-hypertrophic growth plate chondrocytes. Single-cell RNA sequencing reveals an upregulation of stress-induced pathways in mutants, including the prostaglandin D2 synthase ptgdsb.1 and the mTOR regulator sestrin1, which we confirm by in situ RNA analysis of the defective jaw joint region. Our data reveal a zebrafish model for the joint and spine defects of SMMD and point to post-embryonic roles for Nkx3.2 in buffering the stress response and dampening proliferation in joint-adjacent chondrocytes.
Key word nkx3.2; chondrocyte; proliferation; joint; spine; zebrafish;gene-expression; articular-cartil age; homeobox gene; danio-rerio; bmp signals; bapx1; growth; sox9; jaw
Publication Smeeton J, Natarajan N, Naveen Kumar A, Miyashita T et al. Zebrafish model for spondylo-megaepiphyseal-metaphyseal dysplasia reveals post-embryonic roles of Nkx3.2 in the skeleton. Development 2021 Jan 25;148(2). PMID: 33462117
Abstract The regulated expansion of chondrocytes within growth plates and joints ensures proper skeletal development through adulthood. Mutations in the transcription factor NKX3.2 underlie spondylo-megaepiphyseal-metaphyseal dysplasia (SMMD), which is characterized by skeletal defects including scoliosis, large epiphyses, wide growth plates and supernumerary distal limb joints. Whereas nkx3.2 knockdown zebrafish and mouse Nkx3.2 mutants display embryonic lethal jaw joint fusions and skeletal reductions, respectively, they lack the skeletal overgrowth seen in SMMD patients. Here, we report adult viable nkx3.2 mutant zebrafish displaying cartilage overgrowth in place of a missing jaw joint, as well as severe dysmorphologies of the facial skeleton, skullcap and spine. In contrast, cartilage overgrowth and scoliosis are absent in rare viable nkx3.2 knockdown animals that lack jaw joints, supporting post-embryonic roles for Nkx3.2. Single-cell RNA-sequencing and in vivo validation reveal increased proliferation and upregulation of stress-induced pathways, including prostaglandin synthases, in mutant chondrocytes. By generating a zebrafish model for the skeletal overgrowth defects of SMMD, we reveal post-embryonic roles for Nkx3.2 in dampening proliferation and buffering the stress response in joint-associated chondrocytes.


Dataset Information


Dataset ID Species Tissue / Organ Experiment type Sample Source dataset ID
1. GSE151354 (wild type) Danio rerio cartilage baseline 21dpf, wild type GEO: GSM4575942
2. GSE151354 (nkx3.2 mutant) Danio rerio cartilage growth 21dpf, nkx3.2 mutant GEO: GSM4575943

Clustering Result


Cluster Cell type Gene id (symbol) Marker class Evidence
1 Chondrocytes ENSDARG00000069093 (col2a1a) marker DOI:10.7554/eLife.16415
1 Chondrocytes ENSDARG00000073699 (col9a1a) marker DOI:10.7554/eLife.16415
2 Perichondrium ENSDARG00000076120 (foxp4) marker DOI:10.1016/j.ydbio.2014.12.007
3 Chondrocytes ENSDARG00000069093 (col2a1a) marker DOI:10.7554/eLife.16415
3 Chondrocytes ENSDARG00000073699 (col9a1a) marker DOI:10.7554/eLife.16415
4 Articular chondrocyte ENSDARG00000036893 (f13a1b) marker DOI:10.1242/dev.193409
5 Hypertrophic chondrocyte ENSDARG00000054753 (col10a1a) marker DOI:10.7554/eLife.16415
6 Articular chondrocyte ENSDARG00000036893 (f13a1b) marker DOI:10.1242/dev.193409
7 Hypertrophic chondrocyte ENSDARG00000054753 (col10a1a) marker DOI:10.7554/eLife.16415
7 Hypertrophic chondrocyte ENSDARG00000044276 (spp1) marker DOI:10.1242/dev.193409
8 Chondrocyte-S-phase ENSDARG00000069093 (col2a1a) marker DOI:10.7554/eLife.16415
8 Chondrocyte-S-phase ENSDARG00000073699 (col9a1a) marker DOI:10.7554/eLife.16415
8 Chondrocyte-S-phase ENSDARG00000054155 (pcna) marker DOI:10.1242/dev.193409
9 Melanoma cells ENSDARG00000093303 (ifitm1) marker DOI:10.1359/JBMR.080412
9 Melanoma cells ENSDARG00000012593 (col5a1) marker DOI:10.7554/eLife.16415
10 Chondrocyte-S-phase ENSDARG00000054155 (pcna) marker DOI:10.1242/dev.193409
11 Melanoma cells ENSDARG00000093303 (ifitm1) marker DOI:10.1359/JBMR.080412
11 Melanoma cells ENSDARG00000012593 (col5a1) marker DOI:10.7554/eLife.16415
12 Osteoblast ENSDARG00000012405 (col1a1a) marker DOI:10.7554/eLife.16415
12 Osteoblast ENSDARG00000105153 (ifitm5) marker DOI:10.1359/JBMR.080412

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Chondrocytes ENSDARG00000069093 (col2a1a) marker DOI:10.7554/eLife.16415
1 Chondrocytes ENSDARG00000073699 (col9a1a) marker DOI:10.7554/eLife.16415
2 Chondrocytes ENSDARG00000073699 (col9a1a) marker DOI:10.7554/eLife.16415
3 Perichondrium ENSDARG00000076120 (foxp4) marker DOI:10.1016/j.ydbio.2014.12.007
4 Articular chondrocyte ENSDARG00000036893 (f13a1b) marker DOI:10.1242/dev.193409
5 Chondrocyte-mitosis ENSDARG00000054155 (pcna) marker DOI:10.1242/dev.193409
6 Melanoma cells ENSDARG00000093303 (ifitm1) marker DOI:10.1359/JBMR.080412
6 Melanoma cells ENSDARG00000012593 (col5a1) marker DOI:10.7554/eLife.16415
7 Melanoma cells ENSDARG00000093303 (ifitm1) marker DOI:10.1359/JBMR.080412
8 Chondrocyte-mitosis ENSDARG00000069093 (col2a1a) marker DOI:10.7554/eLife.16415
8 Chondrocyte-mitosis ENSDARG00000114670 (ube2c) marker DOI:10.1242/dev.193409
8 Chondrocyte-mitosis ENSDARG00000054155 (pcna) marker DOI:10.1242/dev.193409
9 Chondrocyte-S-phase ENSDARG00000069093 (col2a1a) marker DOI:10.7554/eLife.16415
9 Chondrocyte-S-phase ENSDARG00000073699 (col9a1a) marker DOI:10.7554/eLife.16415
9 Chondrocyte-S-phase ENSDARG00000054155 (pcna) marker DOI:10.1242/dev.193409
10 Hypertrophic chondrocyte ENSDARG00000054753 (col10a1a) marker DOI:10.7554/eLife.16415
10 Hypertrophic chondrocyte ENSDARG00000044276 (spp1) marker DOI:10.1242/dev.193409