Integrated molecular analysis identifies a conserved pericyte gene signature in zebrafish

Abstract

Pericytes reside in capillary beds where they share a basement membrane with endothelial cells and regulate their function. However, little is known about embryonic pericyte development, in part, due to lack of specific molecular markers and genetic tools. Here, we applied single cell RNA-sequencing (scRNA-seq) of platelet derived growth factor beta (pdgfrb)-positive cells to molecularly characterize pericytes in zebrafish larvae. scRNA-seq revealed zebrafish cells expressing mouse pericyte gene orthologs while comparison to bulk RNA-seq from wild type and pdgfrb mutant larvae further refined a pericyte geneset. Subsequent integration with mouse pericyte scRNA-seq profiles revealed a core set of conserved pericyte genes. Using transgenic reporter lines, we validated pericyte expression of two genes identified in our analysis: NDUFA4 mitochondrial complex associated like 2a (ndufa4l2a), and potassium voltage-gated channel, Isk-related family, member 4 (kcne4). Both reporter lines exhibited pericyte expression in multiple anatomical locations, while kcne4 was also detected in a subset of vascular smooth muscle cells. Thus, our integrated molecular analysis revealed a molecular profile for zebrafish pericytes and allowed us to develop new tools to observe these cells in vivo.

Activation of a transient progenitor state in the epicardium is required for zebrafish heart regeneration

“…2c) 30,31 . Further analysis of the mural cells demonstrated enriched transcripts for known pericyte and vascular smooth muscle cell markers, including tropomyosin 1 (tpm1), notch receptor 3 (notch3), regulator of G protein signaling 5a (rgs5a), myosin heavy chain 11a (myh11a), actin alpha 2 smooth muscle (acta2), transgelin (tagln), ATP-binding cassette sub-family C member 9 (abcc9), and chemokine C-X-C motif ligand 12b (cxcl12b), as well as two recently identified mural cell markers NDUFA4 mitochondrial complex associated like 2a (ndufa4l2a) and potassium voltage-gated channel Iskrelated family member 4 (kcne4) 32,33 (Supplementary Fig. 2c).…”

Activation of an injury-associated transient progenitor state in the epicardium is required for zebrafish heart regeneration

“…Besides these contaminating clusters, cluster 6 was identified as mural cells expressing platelet-derived growth factor receptor beta pdgfrb (Figure 2C) 29, 30 . Further analysis of the mural cells demonstrated enriched transcripts for known pericyte and vascular smooth muscle cell markers, including tropomyosin 1 ( tpm1 ), notch receptor 3 ( notch3 ), regulator of G protein signaling 5a ( rgs5a ), myosin heavy chain 11a ( myh11a ), actin alpha 2 smooth muscle ( acta2 ), transgelin ( tagln ), ATP-binding cassette sub-family C member 9 ( abcc9 ), and chemokine C-X-C motif ligand 12b ( cxcl12b ), as well as two recently identified mural cell markers NDUFA4 mitochondrial complex associated like 2a ( ndufa4l2a ) and potassium voltage-gated channel Isk-related family member 4 ( kcne4 ) 31, 32 (Figure S2C). While ndufa4l2a is restricted to a subset of mural cells, kcne4 is highly expressed in mural cells and also present in the core epicardial clusters at lower levels.…”

Defining the cellular complexity of the zebrafish bipotential gonad

“…and Shih et al (21,37). Briefly, both publications included lists of highly expressed genes identified in all cell type.…”

“…Similarly, using publicly available data from Shih et al (37), we downloaded the highly expressed genes identified in all pdgfrb-expressing cells (from Supplemental Table S2.1). As described in the publication we filtered for expression level log2>1, this list of genes was defined (which was not certified by peer review) is the author/funder.…”

“…To generate the pericyte Venn diagram, we used publicly available data from Liu et al and Shih et al (21,37). Briefly, both publications included lists of highly expressed genes identified in all cell type.…”