# Developmental single-cell atlas of coronary vessel growth and cardiomyocyte interaction in zebrafish

**Authors:** Muhammad Abdul Rouf, Gülsüm Kayman Kürekçi, Shaoqiu Zhang, Stéphanie Larrivée Vanier, Sarah M. Kamel, Ann Nee Lee, Ruey-Bing Yang, Shih-Lei Lai, Rubén Marín-Juez

PMC · DOI: 10.1242/dev.205065 · Development (Cambridge, England) · 2026-01-22

## TL;DR

This study maps coronary vessel development in zebrafish, showing how blood vessels and heart muscle cells interact during growth.

## Contribution

The first comprehensive single-cell atlas of coronary vessel development in zebrafish is created, revealing cellular and molecular milestones.

## Key findings

- Coronary vessels act as scaffolds to guide cardiomyocyte growth during development.
- Vegfa signaling is critical for coronary vessel–cardiomyocyte interactions.
- A single-cell RNA sequencing atlas identifies new coronary markers and dynamic cellular interactions.

## Abstract

Cardiac morphogenesis requires the intricate coordination of different cell types and molecular cues. Coronary vessel formation is essential for heart development, yet how coronary vessels grow and contribute to ventricular wall formation remains poorly understood. Here, we combine high-resolution imaging and new genetic tools to systematically analyze coronary vasculature development in zebrafish at each millimeter increment from 7 to 30 mm of body length and identify cellular and molecular milestones defining four distinct coronary network developmental stages. Our data show how coronary vessels expand, pattern, specify and act as vascular scaffolds to guide cardiomyocyte growth throughout development. Manipulating coronary network growth by Vegfa signaling perturbation through gain- and loss-of-function approaches disrupts coronary vessel–cardiomyocyte interactions and cardiomyocyte expansion. To gain further resolution into these processes, we build a single-cell RNA sequencing atlas by profiling 37,554 ventricular cells across the different developmental stages and identify new coronary markers, dynamic cellular interactions, and stage-specific endothelial–cardiomyocyte crosstalk. Overall, we present the first comprehensive roadmap of coronary vessel formation and coordinated cellular and molecular interactions with the developing cardiac muscle in zebrafish.

Summary: The first comprehensive cellular and molecular atlas of coronary vessel development in zebrafish reveals precise spatial and temporal coordination with the growing cardiac muscle.

## Linked entities

- **Proteins:** VEGFA (vascular endothelial growth factor A)
- **Species:** Danio rerio (taxon 7955)

## Full-text entities

- **Genes:** gata6 (GATA binding protein 6) [NCBI Gene 58076] {aka GATA-5, cb603}, cav1 (caveolin 1) [NCBI Gene 323695] {aka wu:fc07c04}, DLL4 (delta like canonical Notch ligand 4) [NCBI Gene 54567] {aka AOS6, delta4, hdelta2}, mki67 (marker of proliferation Ki-67) [NCBI Gene 564521] {aka cb31, sb:cb31, si:ch211-250b22.7, wu:fa11g09, wu:fb57a07, wu:fi14e05}, lyve1b (lymphatic vessel endothelial hyaluronic receptor 1b) [NCBI Gene 564249] {aka fj84c10, lyve1, lyve1l, si:dkey-5a9.3, wu:fj84c10}, Pvf1 (PDGF- and VEGF-related factor 1) [NCBI Gene 32876] {aka CG7103, DmVEGF-1, Dmel\CG7103, EP1624, PVF, PVFs}, actn1 (actinin, alpha 1) [NCBI Gene 560400], gata4 (GATA binding protein 4) [NCBI Gene 30483] {aka gata}, kdr (kinase insert domain receptor (a type III receptor tyrosine kinase)) [NCBI Gene 554230] {aka flk1, flk1b, kdrb, si:busm1-205d10.1, si:ch211-254j6.1, si:ch211-278f21.4}, sele (selectin E) [NCBI Gene 558139] {aka E-selectin, si:ch211-260g14.8}, erbb4b (erb-b2 receptor tyrosine kinase 4b) [NCBI Gene 569836] {aka si:dkeyp-52f4.1}, SELE (selectin E) [NCBI Gene 6401] {aka CD62E, ELAM, ELAM1, ESEL, LECAM2, selectin-e}, pcna (proliferating cell nuclear antigen) [NCBI Gene 30678] {aka cb16, fa28e03, fb36g03, wu:fa28e03, wu:fb36g03}, pvrl2l (PVR cell adhesion molecule related 2 like) [NCBI Gene 560933] {aka si:dkey-225e11.1}, scube2 (signal peptide, CUB domain, EGF-like 2) [NCBI Gene 503728] {aka wu:fc27f08, you}, hey2 (hes-related family bHLH transcription factor with YRPW motif 2) [NCBI Gene 58146] {aka grl, zgc:136746}, aurka (aurora kinase A) [NCBI Gene 445246] {aka fb37c10, fc02c02, wu:fb37c10, wu:fc02c02, zgc:100912}, etsrp (ETS1-related protein) [NCBI Gene 555766] {aka ets1b, etv2, grc, wu:fc49b07, zgc:153819}, myl7 (myosin, light chain 7, regulatory) [NCBI Gene 30592] {aka cmlc2, mlc7, mylc2a, zgc:92755}, hbegfb (heparin-binding EGF-like growth factor b) [NCBI Gene 407664] {aka hbegf, zgc:165443}, med20 (mediator complex subunit 20) [NCBI Gene 445191] {aka trfp, zgc:101043}, tbx5a (T-box transcription factor 5a) [NCBI Gene 30071] {aka hst, tbx5, tbx5.1}, flt1 (fms related receptor tyrosine kinase 1) [NCBI Gene 544667] {aka VEGFR1, flt1b, sFlt1}, actb2 (actin, beta 2) [NCBI Gene 57935] {aka actbb, bact2, bactin2}, tnnt2a (troponin T type 2a (cardiac)) [NCBI Gene 58071] {aka cTnT, ctnnt, tnnt2}, fli1 (Fli-1 proto-oncogene, ETS transcription factor) [NCBI Gene 30619] {aka cb855, fli, fli-1, fli1a, wu:fc45b11}, kdrl (kinase insert domain receptor like) [NCBI Gene 796537] {aka flk, flk-1, flk1, kdr, kdra, vegfr-2}, smoc1 (SPARC related modular calcium binding 1) [NCBI Gene 100529120], vegfaa (vascular endothelial growth factor Aa) [NCBI Gene 30682] {aka vegf, vegfa, wu:fj82c06}, actc1a (actin alpha cardiac muscle 1a) [NCBI Gene 408256] {aka actc1c, actc1l, actcl, hm:zewp0073, si:ch73-187m15.4, zewp0073}, mcm5 (minichromosome maintenance complex component 5) [NCBI Gene 286747] {aka wu:fb34a06}, dll4 (delta-like 4 (Drosophila)) [NCBI Gene 563920] {aka si:ch211-244p18.5, zgc:136596}, hbegfa (heparin-binding EGF-like growth factor a) [NCBI Gene 797938] {aka zgc:175091}, mef2d (myocyte enhancer factor 2d) [NCBI Gene 30580] {aka etID309781.16, fk53b11, wu:fc50h03, wu:fk53b11, zgc:109833}, acta2 (actin alpha 2, smooth muscle) [NCBI Gene 322509] {aka wu:fb63d03}
- **Diseases:** LCA (MESH:D000080038), embryonic lethality (MESH:D020964), vascular and developmental defects (MESH:D057772)
- **Chemicals:** heparin (MESH:D006493), calcium (MESH:D002118), agarose (MESH:D012685), magnesium (MESH:D008274), 4-OHT (MESH:C032278), 5-ethynyl-2-deoxyuridine (MESH:C031086), 4',6-diamidino-2-phenylindole (MESH:C007293), Alexa Fluor 568 Goat (-), tamoxifen (MESH:D013629), O-dianisidine (MESH:D003962), PMC (MESH:C008859), EtOH (MESH:D000431), paraformaldehyde (MESH:C003043), STOP (MESH:D014002), PBS (MESH:D007854), Trypan Blue (MESH:D014343), RA (MESH:D014212), water (MESH:D014867), Alexa Fluor  555 (MESH:C000608607)
- **Species:** Danio rerio (leopard danio, species) [taxon 7955], Devario malabaricus (giant danio, species) [taxon 46780], Mus musculus (house mouse, species) [taxon 10090], Homo sapiens (human, species) [taxon 9606]
- **Cell lines:** S2 — Drosophila melanogaster (Fruit fly), Spontaneously immortalized cell line (CVCL_Z232), T8154 — Homo sapiens (Human), Esophageal squamous cell carcinoma, Cancer cell line (CVCL_3174)

## Full text

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## Figures

8 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12863305/full.md

## References

82 references — full list in the complete paper: https://tomesphere.com/paper/PMC12863305/full.md

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Source: https://tomesphere.com/paper/PMC12863305