Identification of regenerative roadblocks via repeat deployment of limb regeneration in axolotls
Ontology highlight
ABSTRACT:
ORGANISM(S): Ambystoma mexicanum
PROVIDER: GSE103087 | GEO | 2017/09/30
SECONDARY ACCESSION(S): PRJNA400170
REPOSITORIES: GEO
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Project description:Salamanders completely regenerate their limbs after amputation. Thus, these animals are unique models to investigate the mechanisms modulating the regeneration in vertebrates. To investigate the influence of microRNAs on the newt limb regeneration, an integrative analysis of microRNAome, transcriptome, and proteome were performed.
2018-12-17 | PXD012091 | iProX
Project description:Amphibians such as the salamanders and the African clawed frog Xenopus are great models for regeneration studies because they can fully regenerate their lost organs. While axolotl can regenerate damaged organs throughout its lifetime, Xenopus has a limited regeneration capacity after metamorphosis. The ecotropic viral integrative factor 5 (Evi5), a cell-cycle-regulated protein that prevents cells from entering mitosis prematurely, is of great interest for it is highly upregulated in the limb blastema of axolotls, but its expression level remains unchanged in the fibroblastema of postmetamorphic frogs. Yet, its role in regeneration competent context in Xenopus has not been fully analyzed. Here we show that Evi5 is also upregulated in Xenopus tadpoles after limb and tail amputation, as it is in axolotls. Down-regulation of Evi5 with morpholino antisense oligos (Mo) impairs wound healing and blastema formation in limbs and tails in both axolotls and Xenopus tadpoles, suggesting a conserved function for Evi5 in regeneration. Using skin punch as a healing model we show that Evi5 is also involved in cell migration during wound healing. RNA-sequencing analysis shows that in addition to reduced signaling of Lepr, Pdgfa, Gdf5, evi5 Mo also downregulate lysine demethylases kdm6b and kdm7a, which are also required for limb regeneration. Thus, our results demonstrate that Evi5 plays a critical role in the regeneration of multiple systems in amphibians.
2022-11-24 | GSE218034 | GEO
Project description:In axolotls, stem cells are systemically prompted to re-enter the cell cycle upon amputation. We sought to identify whether the proliferating cells of the systemically-activated limbs are epigenetically different from those of homeostatic limbs. identify which cells drive systemic-activation response in the limbs distant to the amputation.
2023-05-13 | GSE232080 | GEO
Project description:Salamander limb regeneration is dependent upon tissue interactions that are local to the amputation site. Communication among limb epidermis, peripheral nerves, and mesenchyme coordinate cell migration, cell proliferation, and tissue patterning to generate a blastema, a mass of progenitor cells that forms missing limb structures. An outstanding question is how molecular cross-talk between these tissues gives rise to the regeneration blastema. To identify genes associated with epidermis-nerve-mesenchymal interactions during limb regeneration, we examined histological and transcriptional changes during the first week following injury in the wound epidermis and subjacent cells between three injury types; 1) a flank wound on the side of the animal that will not regenerate a limb, 2) a denervated limb that will not regenerate a limb, and 3) an innervated limb that will regenerate a limb. Early, histological and transcriptional changes were highly similar between the three injury types, presumably because a common wound-healing program is employed across anatomical locations. However, we identified transcripts that were enriched in the limb compared to the flank and are associated with vertebrate limb development. Many of these genes were activated before blastema outgrowth and in situ hybridization showed that some of these genes were expressed in specific tissue types including the epidermis, peripheral nerve, and mesenchyme. We also identified a relatively small group of transcripts that were more highly expressed in innervated limbs versus denervated limbs. These transcripts encode for proteins that are associated with myelination of peripheral nerves, epidermal maintenance, and cell proliferation, suggesting that denervation affects myelinating Schwann cells, epidermal cell function, and proliferation of mesenchymal cells. Overall, our study identifies limb-specific and nerve-dependent genes that are upstream of regenerative growth, and thus promising candidates for the regulation of blastema formation. We used microarray analysis to determine the gene expression changes that take place during limb regeneration, flank wound healing, and an denervated amputated limb. Epidermal tissue and cells adhered to the epidermis were collected as samples. Two harvested samples was pooled for each animal. Four biological replicates were collected from uninjured epidermis (D0) and at 1, 3, and 7 days post injury.
2012-09-17 | E-GEOD-37198 | biostudies-arrayexpress
Project description:In axolotls, stem cells are systemically prompted to re-enter the cell cycle upon amputation. We sought to identify which cells drive systemic-activation response in the limbs distant to the amputation.
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Project description:The salamander has the remarkable ability to regenerate its limb after amputation. Cells at the site of amputation form a blastema and then proliferate and differentiate to regrow the limb. To better understand this process, we have performed deep RNA sequencing of the blastema over a time course. We find genes expressed in three phases with a prominent burst in oncogene expression during the first day, blastemal/limb bud genes peaking at 7 to 14 days, and markers for terminal differentiation upregulated later. We compare these expression patterns to those in a mouse digit amputation model to identify genes specific to the regenerative response. We find that limb patterning genes, SALL genes, and genes involved in the proteasome, adult stem cell, embryonic stem cell, retinoid metabolism, and WNT and NOTCH signaling are regeneration-specific. We establish the “Axolomics” Database, which provides a tool for depositing, retrieving, and searching axolotl-related “omic” information. The experiment includes two time course data sets. One is from mouse digit amputation, another is from Axolotl digit amputation
2013-09-01 | E-GEOD-34394 | biostudies-arrayexpress
Project description:Treatment with midkine inhibitor iMDK inhibits limb regeneration. To elucidate the transcriptional mechanisms of iMDK treatment, we sequenced regenerating limbs treated with either DMSO or iMDK (bulk) in biological triplicate at 11 days post-amputation (dpa).
2020-01-15 | GSE132325 | GEO
Project description:Salamander limb regeneration is dependent upon tissue interactions that are local to the amputation site. Communication among limb epidermis, peripheral nerves, and mesenchyme coordinate cell migration, cell proliferation, and tissue patterning to generate a blastema, a mass of progenitor cells that forms missing limb structures. An outstanding question is how molecular cross-talk between these tissues gives rise to the regeneration blastema. To identify genes associated with epidermis-nerve-mesenchymal interactions during limb regeneration, we examined histological and transcriptional changes during the first week following injury in the wound epidermis and subjacent cells between three injury types; 1) a flank wound on the side of the animal that will not regenerate a limb, 2) a denervated limb that will not regenerate a limb, and 3) an innervated limb that will regenerate a limb. Early, histological and transcriptional changes were highly similar between the three injury types, presumably because a common wound-healing program is employed across anatomical locations. However, we identified transcripts that were enriched in the limb compared to the flank and are associated with vertebrate limb development. Many of these genes were activated before blastema outgrowth and in situ hybridization showed that some of these genes were expressed in specific tissue types including the epidermis, peripheral nerve, and mesenchyme. We also identified a relatively small group of transcripts that were more highly expressed in innervated limbs versus denervated limbs. These transcripts encode for proteins that are associated with myelination of peripheral nerves, epidermal maintenance, and cell proliferation, suggesting that denervation affects myelinating Schwann cells, epidermal cell function, and proliferation of mesenchymal cells. Overall, our study identifies limb-specific and nerve-dependent genes that are upstream of regenerative growth, and thus promising candidates for the regulation of blastema formation.
2012-09-17 | GSE37198 | GEO
Project description:The induction of limb repair depends on signals that initiate regeneration and the successful transmission of those signals in vivo. Here, we characterize the effects of an integrated device-based in vivo delivery of drug compounds in adult Xenopus laevis, which normally regenerate only a cartilaginous spike after limb amputation. A wearable bioreactor containing a silk protein-based hydrogel containing progesterone that was applied to the wound site immediately after hind-limb amputation for 24 hours induced regeneration of flattened paddle-like structures in adult frogs. Molecular assays (ELISA and NGS), Morphometric analysis (soft-tissue patterning), X-ray imaging (bone regrowth), immunofluorescence (cell proliferation, immune response, neuro/vascular tissues), and behavioral data (functional use of regenerates) were used to characterize the differences between the paddle-like structures and the hypomorphic spike observed in untreated animals. Initially, treated animals exhibited an extensive wound epithelium, and increased nerve supply compared to controls. Subsequently, flattened structures with robust bone remodeling were formed, resembling comparable tissues of adult limbs at the early and middle stages of regeneration. The limbs ceased regeneration at the position where the digits usually form. Functional tests revealed that the response to the paddle-like structures was similar to that of uncut limbs. Analysis of the blastema transcriptome identified a number of key genes related to the combined intervention, and also revealed regulated transcripts related to hormonal and neural pathways, representing novel targets for emerging regenerative therapies. Our experiments (1) establish a new model for testing of therapeutic cocktails in vertebrate limb regeneration; (2) identify pro-regenerative activities of progesterone, and (3) provide proof-of-principle of using integrated device-based delivery of small molecule drugs as a viable strategy to induce and maintain a regenerative response.
2019-01-09 | GSE118454 | GEO
Project description:The salamander has the remarkable ability to regenerate its limb after amputation. Cells at the site of amputation form a blastema and then proliferate and differentiate to regrow the limb. To better understand this process, we have performed deep RNA sequencing of the blastema over a time course. We find genes expressed in three phases with a prominent burst in oncogene expression during the first day, blastemal/limb bud genes peaking at 7 to 14 days, and markers for terminal differentiation upregulated later. We compare these expression patterns to those in a mouse digit amputation model to identify genes specific to the regenerative response. We find that limb patterning genes, SALL genes, and genes involved in the proteasome, adult stem cell, embryonic stem cell, retinoid metabolism, and WNT and NOTCH signaling are regeneration-specific. We establish the “Axolomics” Database, which provides a tool for depositing, retrieving, and searching axolotl-related “omic” information.
2013-09-01 | GSE34394 | GEO