Vertebrate Appendage Regeneration Research Articles

Positional information modulates transient regeneration-activated cell states during vertebrate appendage regeneration

Injury is common in the life of organisms. Because the extent of damage cannot be predicted, injured organisms must determine how much tissue needs to be restored. Although it is known that amputation position affects the regeneration speed of appendages, mechanisms conveying positional information remain unclear. We investigated tissue dynamics in regenerating caudal fins of the African killifish (Nothobranchius furzeri) and found position-specific, differential spatial distribution modulation, persistence, and magnitude of proliferation. Single-cell RNA sequencing revealed a transient regeneration-activated cell state (TRACS) in the basal epidermis that is amplified to match a given amputation position and expresses components and modifiers of the extracellular matrix (ECM). Notably, CRISPR-Cas9-mediated deletion of the ECM modifier sequestosome 1 (sqstm1) increased the regenerative capacity of distal injuries, suggesting that regeneration growth rate can be uncoupled from amputation position. We propose that basal epidermis TRACS transduce positional information to the regenerating blastema by remodeling the ECM.

Muscles are barely required for the patterning and cell dynamics in axolotl limb regeneration.

Regeneration of a complex appendage structure such as limb requires upstream and downstream coordination of multiple types of cells. Given type of cell may sit at higher upstream position to control the activities of other cells. Muscles are one of the major cell masses in limbs. However, the subtle functional relationship between muscle and other cells in vertebrate complex tissue regeneration are still not well established. Here, we use Pax7 mutant axolotls, in which the limb muscle is developmentally lost, to investigate limb regeneration in the absence of skeletal muscle. We find that the pattern of regenerated limbs is relative normal in Pax7 mutants compared to the controls, but the joint is malformed in the Pax7 mutants. Lack of muscles do not affect the early regeneration responses, specifically the recruitment of macrophages to the wound, as well as the proliferation of fibroblasts, another major population in limbs. Furthermore, using single cell RNA-sequencing, we show that, other than muscle lineage that is mostly missing in Pax7 mutants, the composition and the status of other cell types in completely regenerated limbs of Pax7 mutants are similar to that in the controls. Our study reveals skeletal muscle is barely required for the guidance of other cells, as well the patterning in complex tissue regeneration in axolotls, and provides refined views of the roles of muscle cell in vertebrate appendage regeneration.

Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors.

Vertebrate appendage regeneration requires precisely coordinated remodeling of the transcriptional landscape to enable the growth and differentiation of new tissue, a process executed over multiple days and across dozens of cell types. The heterogeneity of tissues and temporally-sensitive fate decisions involved has made it difficult to articulate the gene regulatory programs enabling regeneration of individual cell types. To better understand how a regenerative program is fulfilled by neural progenitor cells (NPCs) of the spinal cord, we analyzed pax6-expressing NPCs isolated from regenerating Xenopus tropicalis tails. By intersecting chromatin accessibility data with single-cell transcriptomics, we find that NPCs place an early priority on neuronal differentiation. Late in regeneration, the priority returns to proliferation. Our analyses identify Pbx3 and Meis1 as critical regulators of tail regeneration and axon organization. Overall, we use transcriptional regulatory dynamics to present a new model for cell fate decisions and their regulators in NPCs during regeneration.

XGSA: A statistical method for cross-species gene set analysis.

Gene set analysis is a powerful tool for determining whether an experimentally derived set of genes is statistically significantly enriched for genes in other pre-defined gene sets, such as known pathways, gene ontology terms, or other experimentally derived gene sets. Current gene set analysis methods do not facilitate comparing gene sets across different organisms as they do not explicitly deal with homology mapping between species. There lacks a systematic investigation about the effect of complex gene homology on cross-species gene set analysis. In this study, we show that not accounting for the complex homology structure when comparing gene sets in two species can lead to false positive discoveries, especially when comparing gene sets that have complex gene homology relationships. To overcome this bias, we propose a straightforward statistical approach, called XGSA, that explicitly takes the cross-species homology mapping into consideration when doing gene set analysis. Simulation experiments confirm that XGSA can avoid false positive discoveries, while maintaining good statistical power compared to other ad hoc approaches for cross-species gene set analysis. We further demonstrate the effectiveness of XGSA with two real-life case studies that aim to discover conserved or species-specific molecular pathways involved in social challenge and vertebrate appendage regeneration. The R source code for XGSA is available under a GNU General Public License at http://github.com/VCCRI/XGSA CONTACT: jho@victorchang.edu.au.

BioEssays 1∕2014

BioEssaysVolume 36, Issue 1 Cover PictureFree Access BioEssays 1∕2014 First published: 10 December 2013 https://doi.org/10.1002/bies.201370001AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Abstract What fuels appendage regeneration? On pages 27-32 of this issue, Love et al. examine the role of carbohydrate metabolism during vertebrate appendage regeneration. The authors largely focus their examination on recent studies using the Xenopus model, whose tadpoles and froglets (shown on the cover, tissues visualized with immunostaining and transgenesis) have the impressive ability to regenerate some of their appendages. The authors argue that increasing carbohydrate entry into anabolic pathways is critical to the regeneration program and that Xenopus represents a good model system to study the interplay between cellular metabolism and appendage regeneration. Cover by Nick R. Love. Volume36, Issue1January 2014 RelatedInformation

Carbohydrate metabolism during vertebrate appendage regeneration: What is its role? How is it regulated?

We recently examined gene expression during Xenopus tadpole tail appendage regeneration and found that carbohydrate regulatory genes were dramatically altered during the regeneration process. In this essay, we speculate that these changes in gene expression play an essential role during regeneration by stimulating the anabolic pathways required for the reconstruction of a new appendage. We hypothesize that during regeneration, cells use leptin, slc2a3, proinsulin, g6pd, hif1α expression, receptor tyrosine kinase (RTK) signaling, and the production of reactive oxygen species (ROS) to promote glucose entry into glycolysis and the pentose phosphate pathway (PPP), thus stimulating macromolecular biosynthesis. We suggest that this metabolic shift is integral to the appendage regeneration program and that the Xenopus model is a powerful experimental system to further explore this phenomenon.

Transcriptional components of anteroposterior positional information during zebrafish fin regeneration.

Many fish and salamander species regenerate amputated fins or limbs, restoring the size and shape of the original appendage. Regeneration requires that spared cells retain or recall information encoding pattern, a phenomenon termed positional memory. Few factors have been implicated in positional memory during vertebrate appendage regeneration. Here, we investigated potential regulators of anteroposterior (AP) pattern during fin regeneration in adult zebrafish. Sequence-based profiling from tissues along the AP axis of uninjured pectoral fins identified many genes with region-specific expression, several of which encoded transcription factors with known AP-specific expression or function in developing embryonic pectoral appendages. Transgenic reporter strains revealed that regulatory sequences of the transcription factor gene alx4a activated expression in fibroblasts and osteoblasts within anterior fin rays, whereas hand2 regulatory sequences activated expression in these same cell types within posterior rays. Transgenic overexpression of hand2 in all pectoral fin rays did not affect formation of the proliferative regeneration blastema, yet modified the lengths and widths of regenerating bones. Hand2 influenced the character of regenerated rays in part by elevation of the vitamin D-inactivating enzyme encoded by cyp24a1, contributing to region-specific regulation of bone metabolism. Systemic administration of vitamin D during regeneration partially rescued bone defects resulting from hand2 overexpression. Thus, bone-forming cells in a regenerating appendage maintain expression throughout life of transcription factor genes that can influence AP pattern, and differ across the AP axis in their expression signatures of these and other genes. These findings have implications for mechanisms of positional memory in vertebrate tissues.

Pseudotyped retroviruses for infecting axolotl in vivo and in vitro

Axolotls are poised to become the premiere model system for studying vertebrate appendage regeneration. However, very few molecular tools exist for studying crucial cell lineage relationships over regeneration or for robust and sustained misexpression of genetic elements to test their function. Furthermore, targeting specific cell types will be necessary to understand how regeneration of the diverse tissues within the limb is accomplished. We report that pseudotyped, replication-incompetent retroviruses can be used in axolotls to permanently express markers or genetic elements for functional study. These viruses, when modified by changing their coat protein, can infect axolotl cells only when they have been experimentally manipulated to express the receptor for that coat protein, thus allowing for the possibility of targeting specific cell types. Using viral vectors, we have found that progenitor populations for many different cell types within the blastema are present at all stages of limb regeneration, although their relative proportions change with time.

Retinoic acid signaling controls the formation, proliferation and survival of the blastema during adult zebrafish fin regeneration

Adult teleosts rebuild amputated fins through a proliferation-dependent process called epimorphic regeneration, in which a blastema of cycling progenitor cells replaces the lost fin tissue. The genetic networks that control formation of blastema cells from formerly quiescent stump tissue and subsequent blastema function are still poorly understood. Here, we investigated the cellular and molecular consequences of genetically interfering with retinoic acid (RA) signaling for the formation of the zebrafish blastema. We show that RA signaling is upregulated within the first few hours after fin amputation in the stump mesenchyme, where it controls Fgf, Wnt/β-catenin and Igf signaling. Genetic inhibition of the RA pathway at this stage blocks blastema formation by inhibiting cell cycle entry of stump cells and impairs the formation of the basal epidermal layer, a signaling center in the wound epidermis. In the established blastema, RA signaling remains active to ensure the survival of the highly proliferative blastemal population by controlling expression of the anti-apoptotic factor bcl2. In addition, RA signaling maintains blastema proliferation through the activation of growth-stimulatory signals mediated by Fgf and Wnt/β-catenin signaling, as well as by reducing signaling through the growth-inhibitory non-canonical Wnt pathway. The endogenous roles of RA in adult vertebrate appendage regeneration are uncovered here for the first time. They provide a mechanistic framework to understand previous observations in salamanders that link endogenous sources of RA to the regeneration process itself and support the hypothesis that the RA signaling pathway is an essential component of vertebrate tissue regeneration.

Genome-wide analysis of gene expression during Xenopus tropicalis tadpole tail regeneration

BackgroundThe molecular mechanisms governing vertebrate appendage regeneration remain poorly understood. Uncovering these mechanisms may lead to novel therapies aimed at alleviating human disfigurement and visible loss of function following injury. Here, we explore tadpole tail regeneration in Xenopus tropicalis, a diploid frog with a sequenced genome.ResultsWe found that, like the traditionally used Xenopus laevis, the Xenopus tropicalis tadpole has the capacity to regenerate its tail following amputation, including its spinal cord, muscle, and major blood vessels. We examined gene expression using the Xenopus tropicalis Affymetrix genome array during three phases of regeneration, uncovering more than 1,000 genes that are significantly modulated during tail regeneration. Target validation, using RT-qPCR followed by gene ontology (GO) analysis, revealed a dynamic regulation of genes involved in the inflammatory response, intracellular metabolism, and energy regulation. Meta-analyses of the array data and validation by RT-qPCR and in situ hybridization uncovered a subset of genes upregulated during the early and intermediate phases of regeneration that are involved in the generation of NADP/H, suggesting that these pathways may be important for proper tail regeneration.ConclusionsThe Xenopus tropicalis tadpole is a powerful model to elucidate the genetic mechanisms of vertebrate appendage regeneration. We have produced a novel and substantial microarray data set examining gene expression during vertebrate appendage regeneration.

NaV-mediated sodium transport is required for vertebrate appendage regeneration

NaV-mediated sodium transport is required for vertebrate appendage regeneration

NaV-Mediated Sodium Currents Are Necessary For Vertebrate Appendage Regeneration

Mammals have a limited ability to regenerate tissues. In contrast, amphibians such as frogs can restore lost developmental structures, including the lens and tail. A detailed understanding of natural regeneration is important for developing therapies for organ repair. Recently, ion transport has been implicated as a regulator of regeneration. While voltage-gated sodium channels play a well-known and important role in propagating action potentials in excitable cells, we have identified a novel role in regeneration for the ion transport function mediated by the voltage-gated sodium channel, NaV1.2. After Xenopus tadpole tail amputation, a regeneration bud (containing progenitors required for regenerative growth) is formed within 1 day at the injury site, and a new tail is re-grown by 7 days. NaV1.2 is expressed early in the bud, and its function is required for regeneration. Inhibition of its activity causes regenerative failure by greatly reducing expression of downstream genes that drive tail outgrowth and patterning, leading to decreased proliferation and altered axonal patterning in the regeneration bud. Significantly, NaV1.2 is not expressed under non-regenerative conditions, suggesting that its activity is a determinant of regenerative ability. Most importantly, pharmacological induction of a brief, transient sodium current into the regeneration bud after tail amputation is sufficient to restore full regeneration of the tail during the refractory period (an endogenous developmental period when regeneration is blocked). Our study demonstrates that sodium transport is a critical mechanism for controlling regeneration, and suggests that short-term modulations of ion transport could represent an exciting new approach to tissue repair in mammals.

Thyroid Hormone Control of Tail Regeneration: Differential in Loco and Systemic Effects and Seasonal Variation

Thyroid hormones have been implicated in the control of vertebrate appendage regeneration. In lizards, thyroid hormones have been reported to induce ependymal outgrowth and also exercise control over adaptive systemic metabolic activities. However, there have been no attempts to correlate the seasonal differences in regenerative performance with thyroid activity. The present study has evaluated the effect of induced thyroid hormone excess or deficiency (by T4 administration or methimazole treatment, respectively) on tail regeneration in H. flaviviridis on a seasonal basis in summer, monsoon and winter months. The experiments revealed a retardative influence of hypothyroidism in tail regeneration in both summer and winter months; however blastema formation occurred in the normal time course in the summer months. Hyperthyroidism induced by daily T4 administration, either systemically or in loco , hastened the formation of blastema and provided an early growth spurt but, ultimately, retarded regenerative growth in the summer months. However, T4 administration daily for the first 15 days and every other day thereafter favored a better regenerative growth. In contrast, during the monsoon months, both daily administration and administration every alternate day, either systemically or in loco , delayed blastema formation as well as retarded linear growth. Neither hypothyroidism nor hyperthyroidism exerted any influence on the sluggish performance characteristic of winter months. It is concluded that thyroid activity and thyroid hormone responsiveness vary on a seasonal basis with maximum activity at higher temperatures and minimal at lower temperatures. It can also be concluded that there is differential sensitivity to thyroid hormone during summer and monsoon seasons.

Temporal requirement for bone morphogenetic proteins in regeneration of the tail and limb of Xenopus tadpoles

Bone morphogenetic protein (BMP) signalling is necessary for both the development of the tail bud and for tail regeneration in Xenopus laevis tadpoles. Using a stable transgenic line in which expression of the soluble BMP inhibitor noggin is under the control of the temperature inducible hsp70 promoter, we have investigated the timing of the requirement for BMP signalling during tail regeneration. If noggin expression is induced followed by partial amputation of the tail, then wound closure and the formation of the neural ampulla occur normally but outgrowth of the regeneration bud is inhibited. Furthermore, we show that BMP signalling is also necessary for limb bud regeneration, which occurs in Xenopus tadpoles prior to differentiation. When noggin expression is induced, limb bud regeneration fails at an early stage and a stump is formed. The situation appears similar to the tail, with formation of the limb bud blastema occurring but renewed outgrowth inhibited. The transcriptional repressor Msx1, a direct target of BMP signalling with known roles in vertebrate appendage regeneration, fails to be re-expressed in both tail and limb in the presence of noggin. DNA labelling studies show that proliferation in the notochord and spinal cord of the tail, and of the blastema in the limb bud, is significantly inhibited by noggin induction, suggesting that in the context of these regenerating appendages BMP is mainly required, directly or indirectly, as a mitogenic factor.

The influence of the nerve in regeneration of the amphibian extremity.

The influence of the nerve in regeneration of the amphibian extremity.