High-throughput sequencing for microRNAs in uninjured and regenerating newt hearts
Ontology highlight
ABSTRACT:
ORGANISM(S): Notophthalmus viridescens
PROVIDER: GSE46527 | GEO | 2013/09/24
SECONDARY ACCESSION(S): PRJNA200731
REPOSITORIES: GEO
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Project description:We have developed a standardized and reproducible heart resection/regeneration model system in the red-spotted newt. In order to ascertain the involvement of microRNAs in this amazing process, we made and sequenced cDNA libraries for microRNAs in order to provide sequence data that we could use in further quantitative and qualitative studies. We constructed small RNA cDNA libraries for uninjured (Uninj), 7dpi and 21dpi heart samples, which were sequenced using Illumina-Solexa technology at SciLifeLabs (Stockholm, Sweden).
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Project description:The adult vertebrate red spotted newt is a champion of regeneration, demonstrating an amazing ability to regenerate damaged organs and tissues back to an uninjured state without the formation of scar or reduction in function. By developing a novel cardiac resection strategy, our group recently demonstrated that newt hearts could morphologically and functionally regenerate, without scarring, within a period of 2-3 months following injury. MicroRNAs (miRs) have been widely publicized as essential post-transcriptional gene regulators in a variety of biological processes, including regeneration. We have conducted a microarray screen for vertebrate miRs, with several candidate miRs showing significant differential expression at important time-points following injury to the newt heart. The newt microRNA expression between uninjured hearts and regenerating hearts, 7 and 21 days post-injury (dpi), was compared by microarray analysis. Three paired samples were analyzed: Uninjured, 7dpi and 21dpi newt hearts. Three arrays were hybridized comparing two-paired samples each time.
2013-09-24 | E-GEOD-44547 | biostudies-arrayexpress
Project description:The adult vertebrate red spotted newt is a champion of regeneration, demonstrating an amazing ability to regenerate damaged organs and tissues back to an uninjured state without the formation of scar or reduction in function. By developing a novel cardiac resection strategy, our group recently demonstrated that newt hearts could morphologically and functionally regenerate, without scarring, within a period of 2-3 months following injury. MicroRNAs (miRs) have been widely publicized as essential post-transcriptional gene regulators in a variety of biological processes, including regeneration. We have conducted a microarray screen for vertebrate miRs, with several candidate miRs showing significant differential expression at important time-points following injury to the newt heart. The newt microRNA expression between uninjured hearts and regenerating hearts, 7 and 21 days post-injury (dpi), was compared by microarray analysis.
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Project description:MicroRNA sequencing using Ion Torrent Proton platform of the undamaged heart of the red spotted newt Notophthalmus viridescens. MicroRNAS were identified using MIRPIPE
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Project description:Previous studies indicated that macrophages play a role during lens regeneration in newts, but their function has not been tested experimentally. Here we generated a transgenic newt reporter line in which macrophages can be visualized in vivo. Using this new tool, we analyzed the location of macrophages during lens regeneration. We uncovered early gene expression changes using bulk RNAseq in two newt species, Notophthalmus viridescens and Pleurodeles waltl. Next, we used clodronate liposomes to deplete macrophages, which inhibited lens regeneration in both newt species. Macrophage depletion induced the formation of scar-like tissue, an increased and sustained inflammatory response, an early decrease in iris pigment epithelial cell (iPEC) proliferation and a late increase in apoptosis. Some of these phenotypes persisted for at least 100 days and could be rescued by exogenous FGF2. Re-injury alleviated the effects of macrophage depletion and re-started the regeneration process. Together, our findings highlight the importance of macrophages in facilitating a pro-regenerative environment in the newt eye, helping to resolve fibrosis, modulating the overall inflammatory landscape and maintaining the proper balance of early proliferation and late apoptosis.
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Project description:Previous studies indicated that macrophages play a role during lens regeneration in newts, but their function has not been tested experimentally. Here we generated a transgenic newt reporter line in which macrophages can be visualized in vivo. Using this new tool, we analyzed the location of macrophages during lens regeneration. We uncovered early gene expression changes using bulk RNAseq in two newt species, Notophthalmus viridescens and Pleurodeles waltl. Next, we used clodronate liposomes to deplete macrophages, which inhibited lens regeneration in both newt species. Macrophage depletion induced the formation of scar-like tissue, an increased and sustained inflammatory response, an early decrease in iris pigment epithelial cell (iPEC) proliferation and a late increase in apoptosis. Some of these phenotypes persisted for at least 100 days and could be rescued by exogenous FGF2. Re-injury alleviated the effects of macrophage depletion and re-started the regeneration process. Together, our findings highlight the importance of macrophages in facilitating a pro-regenerative environment in the newt eye, helping to resolve fibrosis, modulating the overall inflammatory landscape and maintaining the proper balance of early proliferation and late apoptosis.
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Project description:Using a novel microfluidic chamber that allows the isolation of axons without contamination by nonaxonal material, we have for the first time purified mRNA from naive, matured CNS axons, and identified the presence of >300 mRNA transcripts. We demonstrate that the transcripts are axonal in nature, and that many of the transcripts present in uninjured CNS axons overlap with those previously identified in PNS injury-conditioned DRG axons. The axonal transcripts detected in matured cortical axons are enriched for protein translational machinery, transport, cytoskeletal components, and mitochondrial maintenance. We next investigated how the axonal mRNA pool changes after axotomy, revealing that numerous gene transcripts related to intracellular transport, mitochondria and the cytoskeleton show decreased localization 2 d after injury. In contrast, gene transcripts related to axonal targeting and synaptic function show increased localization in regenerating cortical axons, suggesting that there is an increased capacity for axonal outgrowth and targeting, and increased support for synapse formation and presynaptic function in regenerating CNS axons after injury. Our data demonstrate that CNS axons contain many mRNA species of diverse functions, and suggest that, like invertebrate and PNS axons, CNS axons synthesize proteins locally, maintaining a degree of autonomy from the cell body.
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Project description:Neuregulin1, a protein involved in signaling through the ErbB receptors, is required for the proper development of multiple organ systems. A complete understanding of the expression profile of Neuregulin1 is complicated by the presence of multiple isoform variants that result from extensive alternative splicing. Remarkably, these numerous protein products display a wide range of divergent functional roles, making the characterization of tissue-specific isoforms critical to understanding signaling. Recent evidence suggests an important role for Neuregulin1 signaling during olfactory epithelium development and regeneration. In order to understand the physiological consequences of this signaling, we sought to identify the isoform-specific and cell type-specific expression pattern of Neuregulin1 in the adult olfactory mucosa using a combination of RT-qPCR, FACS, and immunohistochemistry. To complement this information, we also analyzed the cell-type specific expression patterns of the ErbB receptors using immunohistochemistry. We found that multiple Neuregulin1 isoforms, containing predominantly the Type I and Type III N-termini, are expressed in the uninjured olfactory mucosa. Specifically, we found that Type III Neuregulin1 is highly expressed in mature olfactory sensory neurons and Type I Neuregulin1 is highly expressed in duct gland cells. Surprisingly, the divergent localization of these Neuregulin isoforms and their corresponding ErbB receptors does not support a role for active signaling during normal turnover and maintenance of the olfactory mucosa. Conversely, we found that injury to the olfactory epithelium specifically upregulates the Neuregulin1 Type I isoform bringing the expression pattern adjacent to cells expressing both ErbB2 and ErbB3 which is compatible with active signaling, supporting a functional role for Neuregulin1 specifically during regeneration.
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