Table 1 The PHATE subclusters of the putative MSC-containing subpopulations, along with their characteristic marker genes and putative functions as reported in the literature. These observations provide insights into their transcriptomic identity. Collectively, the subclusters exhibit transcripts and characteristics typically associated with mesenchymal stromal cells
From: Transcriptomic characterization of transitioning cell types in the skin of Atlantic salmon
Cell type | Markers | Comments | Reference |
|---|---|---|---|
0—Undefined | krt5 (ENSSSAG00000120869) krt15 (ENSSSAG000000517492, ENSSSAG00000045107) krt8 (ENSSSAG00000064465) | Epithelial intermediate state cells epithelial marker Basal progenitor markers Mesenchymal progenitor cells marker | [33] [44] [45] |
1—Mesenchymal stromal cells | cd34 (ENSSSAG00000073342, ENSSSAG00000074590) itga5 (ENSSSAG00000098283, ENSSSAG00000120022) klf12b(ENSSSAG00000042459) rapgef1a.1 (ENSSSAG00000053833) klf2 (ENSSSAG00000072786) add3 (ENSSSAG00000000431) fbln2 (ENSSSAG00000008760) loxl1 (ENSSSAG00000004651) cobll1 (ENSSSAG00000080500) ebf1 (ENSSSAG00000070298, ENSSSAG00000079780) | MSC markers MSC marker Adipocyte markers Involved in adipogenic cascade known marker of MSCs in humans Expressed in human mesenchymal stem cells Involved in differentiation of bone cells from mesenchymal stem cells Involved in bone and adipocyte differentiation of bone marrow derived mesenchymal stem cells Highly expressed in adipose derived mesenchymal stem cells in humans Involved in adipocyte formation | [39] [46] [47] [48] [49] [50] [51] [52] [53] [46] |
2—Fibroblasts | flrt2 (ENSSSAG00000118246, ENSSSAG00000116745) bnc2 (ENSSSAG00000121119) Tenascin C (ENSSSAG00000074414) col12a1 (ENSSSAG00000070858, ENSSSAG00000076478) | Fibroblast growth factor Myofibroblasts marker pro-fibrotic stimuli Highly conserved across taxa, very associated with MSC regulating neural and osteocyte differentiation Marker for fibroblasts | [54] [55] [56] [26] |
3—Fibroblasts | Tenascin B (ENSSSAG00000078781) htra1b (ENSSSAG00000051286) add3 (ENSSSAG00000000431) | Induce the epithelial-to-mesenchymal transition Promotes fibroblast differentiation Expressed in human fibroblasts | [57] [35] [50] |
4—Bone precursor | fgfr4 (ENSSSAG00000017777, ENSSSAG00000020292) zeb2b (ENSSSAG00000050763) pth1r (ENSSSAG00000097651) palld (ENSSSAG00000068098 ptprd (ENSSSAG00000096916, ENSSSAG00000111433) runx3 (ENSSSAG00000003444, ENSSSAG00000064246) cbfb (ENSSSAG00000064481) | Osteo marker MSC differentiation Associated with bone cell development Associated with osteoblast differentiation from mesenchymal stem cells Expression is likely involved in bone formation in humans Critically involved in bone development Regulates runx3 in shaping bone development | [58] [22] [59] [12] [60] [61] [61] |
5—Adipocyte precursor | wnt7bb (ENSSSAG00000009090, ENSSSAG00000086070) ebf1 (ENSSSAG00000070298, ENSSSAG00000079780) myh10 (ENSSSAG00000101624) tafa5 (ENSSSAG00000109872, ENSSSAG00000088442) lpl (ENSSSAG00000072070) ptx3.1 (ENSSSAG00000092865) zeb2 (ENSSSAG00000063282, ENSSSAG00000081619) | Highly expressed in adipocytes Involved in adipocyte formation myh10 is involved in driving adipogenesis Also known as FAM19A5 is expressed in adipocytes Involved in adipocyte differentiation Mediator of bone homeostasis in rodents and humans MSC differentiation | [62] [46] [63] [64] [65] [66] [22] |
6—Bone/muscle precursor | pth1r (ENSSSAG00000097651, ENSSSAG00000075121) palld (ENSSSAG00000068098) ptprd (ENSSSAG00000096916, ENSSSAG00000111433) runx3 (ENSSSAG00000003444, ENSSSAG00000064246) cbfb (ENSSSAG00000064481) fgfr4 (ENSSSAG00000017777, ENSSSAG00000020292) slit1 (ENSSSAG00000001168) sox6 (ENSSSAG00000111310, ENSSSAG00000056464) mmp23b (ENSSSAG00000077749) ttn (ENSSSAG00000095939) | Associated with bone cell development Associated with osteoblast differentiation from MSC Expression likely involved in bone formation in humans Critically involved in bone development Regulates runx3 in shaping bone development Marker for bone cells Involved in myoblast movement during development Involved in myogenesis of fast twitch muscle fibres in zebrafish Involved in muscle development in pigs Key component of skeletal muscle and a marker of skeletal muscle in Atlantic Salmon fin/skin samples | [59] [12] [60] [61] [61] [58] [67] [68] [69] [23] |