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Compartmentalization and synergy of osteoblasts drive bone formation in the regenerating fin

ABSTRACT: This study investigated the cell composition and lineage relationships of FACS (fluorescence activated cell sorting)-enriched epidermal, bone forming (osteoblast) and (non-osteoblast) blastemal fin regenerate cells by single cell (sc) RNA sequencing. The repetitive cell harvesting in four-week intervals revealed a constant gene regulation over four successive regeneration rounds in the early outgrowth stage. In addition, the sc RNA dataset uncovered a potential lineage relationship between distal blastema cells and osteoblasts during fin regeneration. These findings, together with the identification of novel fin regenerate markers, advance our understanding of complex tissue regeneration in zebrafish.

ORGANISM(S): Danio rerio

PROVIDER: GSE251828 | GEO | 2023/12/22

REPOSITORIES: GEO

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Calcineurin Controls Proximodistal Blastema Polarity in Zebrafish Fin Regeneration

Project description:Planarian flatworms regenerate their heads and tails from anterior or posterior wounds and this blastema regeneration polarity is controlled by Wnt/β-catenin signaling. It is well known that a regeneration blastema of appendages of vertebrates such as fish and amphibians grows distally. However, it remains unclear whether a regeneration blastema in vertebrate appendages can grow proximally. Here, we show that a regeneration blastema in zebrafish fins can grow proximally along the proximodistal axis by calcineurin inhibition. We used fin excavation in adult zebrafish to observe the unidirectional regeneration, from the anterior cut edge (ACE) to the posterior cut edge (PCE) of the cavity and this unidirectional regeneration polarity occurs as the PCE fails to build blastemas. Furthermore, we found that calcineurin activities in the ACE were greater than in the PCE. Calcineurin inhibition induced the PCE blastemas, and calcineurin hyperactivation suppressed fin regeneration. Collectively, these findings identify calcineurin as a molecular switch to specify the PCE blastema of the proximodistal axis and regeneration polarity in zebrafish fin.

2020-10-20 | GSE159560 | GEO

Single-cell RNA sequencing of the cut and uncut caudal fin of zebrafish larvae

Project description:Purpose: The goal of this study was to establish the first detailed cell atlas of the regenerating caudal fin of zebrafish larvae. Intact and regenerating caudal fin were used for single-cell RNA-sequencing with the aim to provide the first integrated model of epimorphic regeneration in zebrafish larvae and demonstrate the diversity of the cells required for blastema formation. Methods: 150 of regenerating caudal fin (cut) and intact caudal fine (uncut) samples were dissociated and loaded into the 10x Genomics Chromium Platform, and sequenced using Illumina NovaSeq 6000. Conclusion: Our study constitutes a resource of the gene expression profile in intact and regenerating caudal fin of zebrafish larvae. We report the application of single-molecule-based sequencing technology for high-throughput profiling of both intact (uncut) and regenerating caudal fin samples (cut) at 24hpA. We confirmed the presence of macrophage subsets, previously described by our group to govern zebrafish fin regeneration, and identified a novel blastemal cell population.

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Regenerating zebrafish fin fold vs. uncut control

2008-10-01 | GSE11391 | GEO

Regenerating zebrafish fin fold vs. uncut control

Project description:Teleost fish have the remarkable ability to regenerate their body parts including heart, spinal cord, and the caudal fin, while many higher vertebrates including us humans have only a limited ability. To facilitate molecular and genetic approaches for regeneration, we previously established an assay using the fin fold of early stage larvae, which regenerate their caudal fin folds as in adult regeneration. Here, we performed transcriptional profiling of regenerating larval fin folds and identified genes with differential expression during regeneration. Gene expression profiling of zebrafish larval fin-fold regeneration was performed by comparing amputated fin fold and uncut control. Keywords: Stress response, injury response. Two time points, 18-24 hours post amputation (hpa) and 48 hpa, of regenerating fin fold were analyzed. We performed one replicate per each time point. For microarray expression profiling, total RNA was extracted from regenerating and uncut caudal fin folds of AB strain larvae. Tail tissues of 16-24 hpa, 48 hpa, and uncut siblings of the respective stages including 3-5 posterior somite segments were collected on ice. Total RNA was extracted by using TRIzol reagent (Invitrogen, Carlsbad, California, United States) according to the manufacturerâs instruction. The quantity and quality of total RNA were assessed by absorbance at 260 nm and 280 nm and by gel electrophoresis. Approx. 9 Î¼g of total RNA was recovered from ~250 tail tissues at 16-24 hpa or uncut control tissues; and approx. 5 Î¼g, from ~130 tail tissues at 48 hpa or uncut control tissues. Probes for microarray analysis were labeled with cy3 (amputated fin fold at 16-24 hpa and uncut control at 48 hpa) or cy5 (uncut control at 16-24 hpa and amputated fin fold at 48 hpa), and used for hybridization.

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Zebrafish caudal fin amputation induces a metabolic switch necessary for cell identity transitions and cell cycle re-entry to support blastema formation and bone regeneration

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RNA-seq data from adult zebrafish caudal fin regeneration

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Transcription profiling of zebrafish adult and larval fin to investigate mechanisms of regeneration

Project description:Zebrafish have the remarkable ability to regenerate body parts including the heart, spinal cord and fins by a process referred to as epimorphic regeneration. Recent studies have illustrated that similar to adult zebrafish, early life stage-larvae also possess the ability to regenerate the caudal fin. A comparative genomic analysis was used to determine the degree of conservation in gene expression among the regenerating adult caudal fin, adult heart and larval fin. Results indicate that these tissues respond to amputation/injury with strikingly similar genomic responses. Comparative analysis revealed raldh2, a rate-limiting enzyme for the synthesis of Retinoic acid (RA), as one of the highly induced genes across the three regeneration platforms. Experiment Overall Design: The caudal fin of zebrafish larvae at 2days post fertilization were amputated. Caudal fin tissue at 2dpf and regenerating fins were isolated at 1, 2and 3 days post amputation. Three replicates were collected at each time point. 150 fins were pooled to comprise one replicate.

2008-04-07 | E-GEOD-10188 | biostudies-arrayexpress

Research on Molecular Mechanism of Zebrafish Caudal Fin Regeneration Based on Whole Transcriptome Technology

Project description:Background/Aims:The ability of regeneration varies widely from invertebrates to vertebrates. Some animals, for example, flatworms, newts, salamanders, and lower vertebrates have the outstanding ability to regenerate all the organs even the whole individual. Unfortunately, the regenerative capacity of humans extremely attenuates along with the biological evolution and this makes it difficult for humans to recover from damaged or missing organs or tissues, and even cause serious loss of function or death. However, the research on regeneration mechanisms is limited and incomplete so far. Here, we investigated the biological mechanisms of zebrafish caudal fin regeneration. Methods:The zebrafish was used as the research object to analyze the differences of mRNA and ncRNA expressed in new tissues at 0d, 3d, and 7d after caudal fin removal, and analyzed the molecular mechanism of caudal fin regeneration from the perspective of the whole transcriptome. Results: We observed that the amputated caudal fin went through a complex genetic change, especially at 3 dpa. This result showed that genes related to response to cell cycle and wounding might play a role in caudal fin regeneration.The up regulated DEGs at 3 dpa (blastema outgrowth stage) were dramatically enriched in 20 Biological Processes (FDR < 0.05), three of which were cell cycle (GO:0007049), mitotic cell cycle (GO:0000278), and cell cycle process (GO:0022402), one was response to wounding (GO:0009611), etc. Conclusion: Taken together, the results revealed that the DEGs were enriched in numerous biological processes, molecular function, cellular component, and signaling pathways, suggesting that the caudal fin regeneration is a highly complicated process of the molecular mechanism.

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Comparative genomic analysis between adult and larval fin regeneration

2008-02-29 | GSE10188 | GEO