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Single-cell level transcriptomic anaylsis of the homeostatic and regenerating axolotl limb

ABSTRACT: Single-cell level transcriptomic anaylsis of the homeostatic and regenerating axolotl limb

PROVIDER: PRJNA498286 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8147030.fastq.gz	Fastqsanger.gz
	SRR8147031.fastq.gz	Fastqsanger.gz
	SRR8147022.fastq.gz	Fastqsanger.gz
	SRR8147032.fastq.gz	Fastqsanger.gz
	SRR8147023.fastq.gz	Fastqsanger.gz

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Single-cell level transcriptomic anaylsis of the homeostatic and regenerating axolotl limb

Project description:Regeneration of complex multi-tissue structures, such as limbs, requires the coordinated effort of multiple cell types. In axolotl limb regeneration, the wound epidermis and blastema have been extensively studied via histology, grafting, and bulk-tissue RNA-sequencing. However, studying the contributions of these tissues is hindered due to limited information regarding the molecular identity of the cell types in regenerating limbs. By performing unbiased single-cell RNA-sequencing on over 25,000 cells from axolotl limbs, we identify a plethora of cellular diversity within epidermal, mesenchymal, and hematopoietic lineages in homeostatic and regenerating limbs. We identify regeneration-induced genes, develop putative trajectories for blastema cell differentiation, and propose the molecular identity and origin of fibroblast-derived blastema progenitor cells residing in homeostatic limbs. This work will enable application of molecular techniques to assess the contribution of these populations to limb regeneration. It will also facilitate work aimed at identifying transcripts and cells critical for limb regeneration.

2018-10-25 | GSE121737 | GEO

Gene Expression During the First 28 Days of Axolotl Limb Regeneration

Project description:Here we report the results of a robust microarray experiment that examined the first 28 days of axolotl forelimb regeneration. At each of 20 post-amputation time points, we estimated gene expression for 10 replicate RNA samples that were isolated from 1m of heterogeneous tissue collected from the distal limb tip. The distal 1.0mm of heterogeneous tissue from regenerating limb tip were removed and used for RNA extraction. 10 samples were collected for each of 20 time points.

2015-04-20 | E-GEOD-67118 | biostudies-arrayexpress

Expression data from regenerating axolotl forelimbs

Project description:Salamanders are capable of regenerating amputated limbs by generating a mass of lineage-restricted cells called a blastema. Blastemas only generate structures distal to their origin unless treated with retinoic acid (RA), which results in proximodistal (PD) limb duplications. Little is known about the transcriptional network that regulates PD duplication. In this study, we identified expression patterns that explain PD duplication including upregulation of proximal homeobox gene expression and silencing of distal-associated genes whereas limb truncation was associated with disrupted skeletal differentiation. Overall, mechanisms were identified that regulate RAR’s multifaceted roles in the salamander limb including regulation of skeletal patterning during epimorphic regeneration, skeletal tissue differentiation during regeneration, and homeostatic regeneration of intact limbs.

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Retinoic acid receptors and the control of positional information in the regenerating axolotl limb

Project description:We know little about the control of positional information (PI) during axolotl limb regeneration which ensures that the limb regenerates exactly what was amputated and the work reported here investigates this phenomenon. Retinoic acid administration changes the PI in a proximal direction so that a complete limb can be regenerated from a hand. Rather that identifying all the genes altered by RA treatment of the limb, we have eliminated many off-target effects by using retinoic acid receptor selective agonists. We firstly identify the receptor involved in this respecification process as RARα and secondly identify the genes involved by RNA sequencing of the RARα-treated blastemal mesenchyme. We find 1177 up-regulated genes and 1403 down-regulated genes which could be identified using the axolotl genome. These include several genes known to be involved in retinoic acid metabolism and in patterning. Since positional in-formation is thought to be a property of the cell surface of blastemal cells when we examine our dataset with an emphasis on this aspect, we find the top canonical pathway is integrin signaling. In the extracellular matrix compartment, we find an MMP and several collagens are up-regulated and several cell membrane genes and secretory factors are also up-regulated. This provides data for future testing of the function of these candidates in the control of PI during limb regeneration.

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Multi-species atlas resolves an axolotl limb development and regeneration paradox

Project description:Humans and other tetrapods are considered to require apical-ectodermal-ridge, AER, cells for limb development, and AER-like cells are suggested to be re-formed to initiate limb regeneration. Paradoxically, the presence of AER in the axolotl, the primary regeneration model organism, remains controversial. Here, by leveraging a single-cell transcriptomics-based multi-species atlas, composed of axolotl, human, mouse, chicken, and frog cells, we first established that axolotls contain cells with AER characteristics. Surprisingly, further analyses and spatial transcriptomics revealed that axolotl limbs do not fully re-form AER cells during regeneration. Moreover, the axolotl mesoderm displays part of the AER machinery, revealing a novel program for limb (re)growth. These results clarify the debate about the axolotl AER and the extent to which the limb developmental program is recapitulated during regeneration.

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Retinoic acid receptors and the control of positional information in the regenerating axolotl limb

Project description:Retinoic acid receptors and the control of positional information in the regenerating axolotl limb

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Project description:We examined uninjured and regenerating axolotl salamander retinas, including their transcriptional profile. We report that at 27 days after a retinectomy (early-mid regeneration), regenerating axolotl retinas exhibit downregulation of genes associated with neuronal networks but upregulation of genes associated with angiogenesis and the extracellular matrix. We also report differential expression of two Notch pathway effector genes, Hes1 and Hes5.

2022-04-10 | GSE200423 | GEO

Axolotl mandible regeneration occurs through mechanical gap closure and a shared regenerative program with the limb

Project description:The mandible plays an essential part in human life and, thus, defects in this structure can dramatically impair the quality of life in patients. Axolotls, unlike humans, are capable of regenerating their lower jaws; however, the underlying mechanisms and their similarity to those in limb regeneration are unknown. In this work, we used morphological, histological, and transcriptomic approaches to analyze the regeneration of lateral resection defects in the axolotl mandible. We found that this structure can regenerate all missing tissues in 90 days through gap minimization, blastema formation, and finally tissue growth, differentiation, and integration. Moreover, transcriptomic comparisons of regenerating mandibles and limbs showed that they share molecular phases of regeneration, that these similarities peak during blastema stages, and that mandible regeneration occurs at a slower pacing. Altogether, our study demonstrates the existence of a shared regenerative program used in two different regenerating body structures with different embryonic origins in the axolotl, and contributes to our understanding of the minimum requirements for a successful regeneration in vertebrates, bringing us closer to understand similar lesions in human mandibles.

2024-08-29 | GSE271056 | GEO

A tissue-mapped axolotl de novo transcriptome enables identification of limb regeneration factors

Project description:Discovery of genes driving axolotl limb regeneration has been challenging due to limited genomic resources. We assembled 42 RNA-Seq samples totaling approximately 1.3 billion 100 base paired-end reads using Trinity (Grabherr M.G. et al, Nature Biotechnology, 2011; Haas B.J. et al, Nature Protocols, 2013): https://github.com/trinityrnaseq/trinityrnaseq/wiki). We created a transcriptome with complete sequence information for most axolotl genes, identified transcriptional profiles that distinguish blastemas from differentiated limb tissues, and uncovered functional roles for cirbp and kazald1 in limb regeneration.

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Microarray Analysis of microRNA Expression during Axolotl Limb Regeneration

Project description:The salamander microRNA expression between mid-bud limb regenerating blastemas (17 days post amputation) and non-regenerating stump tissues was compared by microarray analysis.

2012-11-06 | GSE29727 | GEO

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