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RNA-seq experiments on heart regeneration in WT, foxm1 and dusp6 mutants.

ABSTRACT: The study compares gene expression profile at several stages post amputation of the adult zebrafish ventricular heart between zebrafish mutants and WT siblings. The first experiment was to identify genes that are activated in response to cardiac injury at 3 and 7 days post amputation (dpa). Dusp6 mutant hearts were reported to show an enhanced regenerative response. For this experiment, bulk RNA seq was obtained from WT and Dusp6 mutant hearts and genes increased at 3 and 7 dpa were identified. The forkhead transcription factor, foxm1, showed increased expression in cardiomyocytes and follow up studies show that it is required to regulate cardiomyocyte proliferation. This was further explored with RNA-seq experiments comparing WT and foxm1 mutant hearts at 3dpa. We identified genes normally expressed in proliferating cells to be decreased in the foxm1 mutants.

ORGANISM(S): Danio rerio

PROVIDER: GSE201139 | GEO | 2022/06/22

REPOSITORIES: GEO

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Project description:Adult zebrafish can completely regenerate their caudal fin following amputation. This complex process is initiated by the formation of an epithelial would cap over the amputation site by 12 hours post amputation (hpa). Once the cap is formed, mesenchymal cells proliferate and migrate from sites distal to the wound plane and accumulate under the epithelial cap forming the blastemal structure within 48 hpa. Blastemal cells proliferate and differentiate, replacing the amputated tissues, which are populated with angiogenic vessels and innervating nerves during the regenerative outgrowth phase which is completed around 14 days post amputation (dpa). Regenerative outgrowth does not occur in TCDD-exposed zebrafish. To identify the molecular pathways that are perturbed by TCDD exposure, male zebrafish were i.p. injected with 50 ng/g TCDD or vehicle and caudal fins were amputated. Regenerating fin tissue was collected at 1, 3 and 5 dpa for mRNA abundance analysis. Microarray analysis and quantitative real time PCR revealed that wound healing and regeneration alone altered the expression of nearly 900 genes by at least two fold between 1 and 5 dpa. TCDD altered the abundance of 370 genes at least two fold. Among these, several known aryl hydrocarbon responsive genes were identified in addition to several genes involved in extracellular matrix composition and metabolism. The profile of misexpressed genes is suggestive of impaired cellular differentiation and extracellular matrix composition potentially regulated by Sox9b. Experiment Overall Design: Regenerating fins were isolated at 1, 3 and 5 days post amputation. Three replicates were collected at each time point. 10 fins were pooled to comprise one replicate. Fish were dosed at 0 days post amputation with vehicle control alone or 50 ng/g TCDD. Experiment Overall Design: 1 Day Post Amputation Vehicle Exposed: GSM85187, GSM85188, and GSM85189 Experiment Overall Design: 1 Day Post Amputation TCDD Exposed: GSM85190, GSM85191, and GSM85192 Experiment Overall Design: 3 Days Post Amputation Vehicle Exposed: GSM85193, GSM85194, and GSM85195 Experiment Overall Design: 3 Day Post Amputation TCDD Exposed: GSM85196, GSM85197, and GSM85198 Experiment Overall Design: 5 Days Post Amputation Vehicle Exposed: GSM85199, GSM85200, and GSM85201 Experiment Overall Design: 5 Days Post Amputation TCDD Exposed: GSM85202, GSM85203, and GSM85204

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RNA-seq experiments on heart regeneration in WT, foxm1 and dusp6 mutants.

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