Genomics and epigenomics of axolotl regeneration.

The axolotl (Ambystoma mexicanum) has been a widely studied organism due to its capacity to regenerate most of its cells, tissues and whole-body parts. Since its genome was sequenced, several molecular tools have been developed to study the mechanisms behind this outstanding and extraordinary ability. The complexity of its genome due to its sheer size and the disproportionate expansion of a large number of repetitive elements, may be a key factor at play during tissue remodeling and regeneration mechanisms. Transcriptomic analysis has provided information to identify candidate genes networks and pathways that might define successful or failed tissue regeneration. Nevertheless, the epigenetic machinery that may participate in this phenomenon has largely not been studied. In this review, we outline a broad overview of both genetic and epigenetic molecular processes related to regeneration in axolotl, from the macroscopic to the molecular level. We also explore the epigenetic mechanisms behind regenerative pathways, and its potential importance in future regeneration research. Altogether, understanding the genomics and global regulation in axolotl will be key for elucidating the special biology of this organism and the fantastic phenomenon that is regeneration.

Exploring the role of microRNAs in axolotl regeneration.

The axolotl, Ambystoma mexicanum, is used extensively for research in developmental biology, particularly for its ability to regenerate and restore lost organs, including in the nervous system, to full functionality. Regeneration in mammals typically depends on the healing process and scar formation with limited replacement of lost tissue. Other organisms, such as spiny mice (Acomys cahirinus), salamanders, and zebrafish, are able to regenerate some damaged body components. Blastema is a tissue that is formed after tissue injury in such organisms and is composed of progenitor cells or dedifferentiated cells that differentiate into various cell types during regeneration. Thus, identifying the molecules responsible for initiation of blastema formation is an important aspect for understanding regeneration. Introns, a major source of noncoding RNAs (ncRNAs), have characteristic sizes in the axolotl, particularly in genes associated with development. These ncRNAs, particularly microRNAs (miRNAs), exhibit dynamic regulation during regeneration. These miRNAs play an essential role in timing and control of gene expression to order and organize processes necessary for blastema creation. Master keys or molecules that underlie the remarkable regenerative abilities of the axolotl remain to be fully explored and exploited. Further and ongoing research on regeneration promises new knowledge that may allow improved repair and renewal of human tissues.

Limb regeneration in salamanders: the plethodontid tale.

Salamanders are the only vertebrates that can regenerate limbs as adults. This makes them ideal models to investigate the cellular and molecular mechanisms of tissue regeneration. Ambystoma mexicanum and Nothopthalmus viridescens have long served as primary salamander models of limb regeneration, and the recent sequencing of the axolotl genome now provides a blueprint to mine regeneration insights from other salamander species. In particular, there is a need to study South American plethodontid salamanders that present different patterns of limb development and regeneration. A broader sampling of species using next-generation sequencing approaches is needed to reveal shared and unique mechanisms of regeneration, and more generally, the evolutionary history of salamander limb regeneration.

Conservation analysis of core cell cycle regulators and their transcriptional behavior during limb regeneration in Ambystoma mexicanum.

Ambystoma mexicanum (axolotl) has been one of the major experimental models for the study of regeneration during the past 100 years. Axolotl limb regeneration takes place through a multi-stage and complex developmental process called epimorphosis that involves diverse events of cell reprogramming. Such events start with dedifferentiation of somatic cells and the proliferation of quiescent stem cells to generate a population of proliferative cells called blastema. Once the blastema reaches a mature stage, cells undergo progressive differentiation into the diverse cell lineages that will form the new limb. Such pivotal cell reprogramming phenomena depend on the fine-tuned regulation of the cell cycle in each regeneration stage, where cell populations display specific proliferative capacities and differentiation status. The axolotl genome has been fully sequenced and released recently, and diverse RNA-seq approaches have also been generated, enabling the identification and conservatory analysis of core cell cycle regulators in this species. We report here our results from such analyses and present the transcriptional behavior of key regulatory factors during axolotl limb regeneration. We also found conserved protein interactions between axolotl Cyclin Dependent Kinases 2, 4 and 6 and Cyclins type D and E. Canonical CYC-CDK interactions that play major roles in modulating cell cycle progression in eukaryotes.

BMP signaling is essential for sustaining proximo-distal progression in regenerating axolotl limbs.

Amputation of a salamander limb triggers a regeneration process that is perfect. A limited number of genes have been studied in this context and even fewer have been analyzed functionally. In this work, we use the BMP signaling inhibitor LDN193189 on Ambystoma mexicanum to explore the role of BMPs in regeneration. We find that BMP signaling is required for proper expression of various patterning genes and that its inhibition causes major defects in the regenerated limbs. Fgf8 is downregulated when BMP signaling is blocked, but ectopic injection of either human or axolotl protein did not rescue the defects. By administering LDN193189 treatments at different time points during regeneration, we show clearly that limb regeneration progresses in a proximal to distal fashion. This demonstrates that BMPs play a major role in patterning of regenerated limbs and that regeneration is a progressive process like development.

Comparison of protein expression profile of limb regeneration between neotenic and metamorphic axolotl.

The axolotl (Ambystoma mexicanum) salamander, a urodele amphibian, has an exceptional regenerative capacity to fully restore an amputated limb throughout the life-long lasting neoteny. By contrast, when axolotls are experimentally induced to metamorphosis, attenuation of the limb's regenerative competence is noticeable. Here, we sought to discern the proteomic profiles of the early stages of blastema formation of neotenic and metamorphic axolotls after limb amputation by employing LC-MS/MS technology. We quantified a total of 714 proteins and qRT-PCR for selected genes was performed to validate the proteomics results and provide evidence for the putative link between immune system activity and regenerative potential. This study provides new insights for examination of common and distinct molecular mechanisms in regeneration-permissive neotenic and regeneration-deficient metamorphic stages at the proteome level.

Longitudinal 16S rRNA data derived from limb regenerative tissue samples of axolotl Ambystoma mexicanum.

The Mexican axolotl (Ambystoma mexicanum) is a critically endangered species and a fruitful amphibian model for regenerative biology. Despite growing body of research on the cellular and molecular biology of axolotl limb regeneration, microbiological aspects of this process remain poorly understood. Here, we describe bacterial 16S rRNA amplicon dataset derived from axolotl limb tissue samples in the course of limb regeneration. The raw data was obtained by sequencing V3-V4 region of 16S rRNA gene and comprised 14,569,756 paired-end raw reads generated from 21 samples. Initial data analysis using DADA2 pipeline resulted in amplicon sequence variant (ASV) table containing a total of ca. 5.9 million chimera-removed, high-quality reads and a median of 296,971 reads per sample. The data constitute a useful resource for the research on the microbiological aspects of axolotl limb regeneration and will also broadly facilitate comparative studies in the developmental and conservation biology of this critically endangered species.

2D and 3D Echocardiography in the Axolotl (Ambystoma Mexicanum).

Cardiac malfunction as a result of ischemic heart disease is a major challenge, and regenerative therapies to the heart are in high demand. A few model species such as zebrafish and salamanders that are capable of intrinsic heart regeneration hold promise for future regenerative therapies for human patients. To evaluate the outcome of cardioregenerative experiments it is imperative that heart function can be monitored. The axolotl salamander (A. mexicanum) represents a well-established model species in regenerative biology attaining sizes that allows for evaluation of cardiac function. The purpose of this protocol is to establish methods to reproducibly measure cardiac function in the axolotl using echocardiography. The application of different anesthetics (benzocaine, MS-222, and propofol) is demonstrated, and the acquisition of two-dimensional (2D) echocardiographic data in both anesthetized and unanesthetized axolotls is described. 2D echocardiography of the three-dimensional (3D) heart can suffer from imprecision and subjectivity of measurements, and to alleviate this phenomenon a solid method, namely intra/inter-operator/observer analysis, to measure and minimize this bias is demonstrated. Finally, a method to acquire 3D echocardiographic data of the beating axolotl heart at a very high spatiotemporal resolution and with pronounced blood-to-tissue contrast is described. Overall, this protocol should provide the necessary methods to evaluate cardiac function and model anatomy, and flow dynamics in the axolotl using ultrasound imaging with applications in both regenerative biology and general physiological experiments.

Bapx1 is required for jaw joint development in amphibians.

The acquisition of a movable jaw and a jaw joint are key events in gnathostome evolution. Jaws are derived from the neural crest derived pharyngeal skeleton and the transition from jawless to jawed vertebrates consists of major morphological changes, which must have a genetic foundation. Recent studies on the effects of bapx1 knockdown in fish and chicken indicate that bapx1 has acquired such a role in primary jaw joint development during vertebrate evolution, but evidence from amphibians is missing so far. In the present study, we use Ambystoma mexicanum, Bombina orientalis, and Xenopus laevis to investigate the effects of bapx1 knockdown on the development of these three different amphibians. Using morpholinos we downregulated the expression of bapx1 and obtain morphants with altered mandibular arch morphology. In the absence of bapx1 Meckels cartilage and the palatoquadrate jaw joint initially develop separately but during further development the joint cavity between both fills with chondrocytes. This results in the fusion of both cartilages and the loss of the jaw joint. Despite this the jaw itself remains usable for feeding and breathing. We show that bapx1 plays a role in jaw joint maintenance during development and that the morphants morphology possibly mirrors the morphology of the jawless ancestors of the gnathostomes.

Changes in the appendicular skeleton during metamorphosis in the axolotl salamander (Ambystoma mexicanum).

Axolotl salamanders (Ambystoma mexicanum) remain aquatic in their natural state, during which biomechanical forces on their diarthrodial limb joints are likely reduced relative to salamanders living on land. However, even as sexually mature adults, these amphibians can be induced to metamorphose into a weight-bearing terrestrial stage by environmental stress or the exogenous administration of thyroxine hormone. In some respects, this aquatic to terrestrial transition of axolotl salamanders through metamorphosis may model developmental and changing biomechanical skeletal forces in mammals during the prenatal to postnatal transition at birth and in the early postnatal period. To assess differences in the appendicular skeleton as a function of metamorphosis, anatomical and gene expression parameters were compared in skeletal tissues between aquatic and terrestrial axolotls that were the same age and genetically full siblings. The length of long bones and area of cuboidal bones in the appendicular skeleton, as well as the cellularity of cartilaginous and interzone tissues of femorotibial joints were generally higher in aquatic axolotls compared with their metamorphosed terrestrial siblings. A comparison of steady-state mRNA transcripts encoding aggrecan core protein (ACAN), type II collagen (COL2A1), and growth and differentiation factor 5 (GDF5) in femorotibial cartilaginous and interzone tissues did not reveal any significant differences between aquatic and terrestrial axolotls.

An interview with Elly Tanaka.

Elly Tanaka is a senior scientist at the Research Institute of Molecular Pathology in Vienna, Austria. Her lab's research uses the axolotl - which possesses impressive regenerative capacity - to understand the molecular and cellular mechanisms underlying limb and spinal cord regeneration. We met Elly in her office in Vienna on the occasion of the recent SY-Stem symposium (see Meeting Review by Porrello and Kirkeby in this issue) to talk about what drew her to regeneration research and the axolotl, the challenges of working in this field, and how she and her colleagues at the Vienna BioCenter are trying to support the new generation of stem cell researchers.

Protein expression pattern and analysis of differentially expressed peptides during various stages of tail regeneration in Hemidactylus flaviviridis.

Epimorphic regeneration is a process allowing the animal to regain its lost structure which depends on the resident pluripotent stem cells as well as de-differentiation of existing cells to form multi-potent stem cells. Many studies have been done to understand the appendage regeneration mechanism. The animal model used since decades is an urodele amphibian the axolotl. However, this ability is also seen in some members of reptiles, mainly lizards which on autotomy of tail regain the same by forming a replica of its lost tail. Lizards being closer to mammals are of greater interest and cannot be neglected. Hence, a stage specific protein profiling was undertaken in order to find the peptides playing a major role in epimorphosis. 2-DGE being basic tool for creating a protein profile was used. With advent of newer modern technology, label-free analysis which uses MS/MS was also performed. The study reports the peptides involved in apoptosis, inflammation and ECM remodelling across the stages of lizard tail regeneration for the first time. Apart from these peptides, structural protein, enzymes involved in metabolism have also been highlighted in the current study to give a bigger picture of the processes and the specific peptides required for tail regeneration.

Transcriptional correlates of proximal-distal identify and regeneration timing in axolotl limbs.

Cells within salamander limbs retain memories that inform the correct replacement of amputated tissues at different positions along the length of the arm, with proximal and distal amputations completing regeneration at similar times. We investigated the possibility that positional memory is associated with variation in transcript abundances along the proximal-distal limb axis. Transcripts were deeply sampled from Ambystoma mexicanum limbs at the time they were administered fore arm vs upper arm amputations, and at 19 post-amputation time points. After amputation and prior to regenerative outgrowth, genes typically expressed by differentiated muscle cells declined more rapidly in upper arms while cell cycle transcripts were expressed more highly. These and other expression patterns suggest upper arms undergo more robust tissue remodeling and cell proliferation responses after amputation, and thus provide an explanation for why the overall time to complete regeneration is similar for proximal and distal amputations. Additionally, we identified candidate positional memory genes that were expressed differently between fore and upper arms that encode a surprising number of epithelial proteins and a variety of cell surface, cell adhesion, and extracellular matrix molecules. Also, genes were discovered that exhibited different, bivariate patterns of gene expression between fore and upper arms, implicating dynamic transcriptional regulation for the first time in limb regeneration. Finally, 43 genes expressed differently between fore and upper arm samples showed similar transcriptional patterns during retinoic acid-induced reprogramming of fore arm blastema cells into upper arm cells. Our study provides new insights about the basis of positional information in regenerating axolotl limbs.

Lineage tracing of genome-edited alleles reveals high fidelity axolotl limb regeneration.

Salamanders are unparalleled among tetrapods in their ability to regenerate many structures, including entire limbs, and the study of this ability may provide insights into human regenerative therapies. The complex structure of the limb poses challenges to the investigation of the cellular and molecular basis of its regeneration. Using CRISPR/Cas, we genetically labelled unique cell lineages within the developing axolotl embryo and tracked the frequency of each lineage within amputated and fully regenerated limbs. This allowed us, for the first time, to assess the contributions of multiple low frequency cell lineages to the regenerating limb at once. Our comparisons reveal that regenerated limbs are high fidelity replicas of the originals even after repeated amputations.

Ion channel signaling influences cellular proliferation and phagocyte activity during axolotl tail regeneration.

Little is known about the potential for ion channels to regulate cellular behaviors during tissue regeneration. Here, we utilized an amphibian tail regeneration assay coupled with a chemical genetic screen to identify ion channel antagonists that altered critical cellular processes during regeneration. Inhibition of multiple ion channels either partially (anoctamin1/Tmem16a, anoctamin2/Tmem16b, KV2.1, KV2.2, L-type CaV channels and H/K ATPases) or completely (GlyR, GABAAR, KV1.5 and SERCA pumps) inhibited tail regeneration. Partial inhibition of tail regeneration by blocking the calcium activated chloride channels, anoctamin1&2, was associated with a reduction of cellular proliferation in tail muscle and mesenchymal regions. Inhibition of anoctamin 1/2 also altered the post-amputation transcriptional response of p44/42 MAPK signaling pathway genes, including decreased expression of erk1/erk2. We also found that complete inhibition via voltage gated K+ channel blockade was associated with diminished phagocyte recruitment to the amputation site. The identification of H+ pumps as required for axolotl tail regeneration supports findings in Xenopus and Planaria models, and more generally, the conservation of ion channels as regulators of tissue regeneration. This study provides a preliminary framework for an in-depth investigation of the mechanistic role of ion channels and their potential involvement in regulating cellular proliferation and other processes essential to wound healing, appendage regeneration, and tissue repair.

Myocardial plasticity: cardiac development, regeneration and disease.

The adult mammalian heart is unable to recover from myocardial cell loss due to cardiac ischemia and infarction because terminally differentiated cardiomyocytes proliferate at a low rate. However, cardiomyocytes in other vertebrate animal models such as zebrafish, axolotls, newts and mammalian mouse neonates are capable of de-differentiating in order to promote cardiomyocyte proliferation and subsequent cardiac regeneration after injury. Although de-differentiation may occur in adult mammalian cardiomyocytes, it is typically associated with diseased hearts and pathologic remodeling rather than repair and regeneration. Here, we review recent studies of cardiac development, regeneration and disease that highlight how changes in myocardial identity (plasticity) is regulated and impacts adaptive and maladaptive cardiac responses.

Comparative Analysis of Cartilage Marker Gene Expression Patterns during Axolotl and Xenopus Limb Regeneration.

Axolotls (Ambystoma mexicanum) can completely regenerate lost limbs, whereas Xenopus laevis frogs cannot. During limb regeneration, a blastema is first formed at the amputation plane. It is thought that this regeneration blastema forms a limb by mechanisms similar to those of a developing embryonic limb bud. Furthermore, Xenopus laevis frogs can form a blastema after amputation; however, the blastema results in a terminal cone-shaped cartilaginous structure called a "spike." The causes of this patterning defect in Xenopus frog limb regeneration were explored. We hypothesized that differences in chondrogenesis may underlie the patterning defect. Thus, we focused on chondrogenesis. Chondrogenesis marker genes, type I and type II collagen, were compared in regenerative and nonregenerative environments. There were marked differences between axolotls and Xenopus in the expression pattern of these chondrogenesis-associated genes. The relative deficit in the chondrogenic capacity of Xenopus blastema cells may account for the absence of total limb regenerative capacity.

Thyroxine-induced metamorphosis in the axolotl (Ambystoma mexicanum).

The axolotl (Ambystoma mexicanum) has remained an important model for regeneration and developmental biology for over a century. Although axolotls in captive-bred colonies usually exist in an aquatic form, they retain the ability to undergo metamorphosis following exposure to thyroid hormone. Here we present a robust method for inducing metamorphosis in adult axolotls that results in high survivability and produces terrestrial animals that can be maintained in long-term captivity.

Limb regeneration.

Limb regeneration is observed in certain members of the animal phyla. Some animals keep this ability during their entire life while others lose it at some time during development. How do animals regenerate limbs? Is it possible to find unifying, conserved mechanisms of limb regeneration or have different species evolved distinct means of replacing a lost limb? How is limb regeneration similar or different to limb development? Studies on many organisms, including echinoderms, arthropods, and chordates have provided significant knowledge about limb regeneration. In this focus article, we concentrate on tetrapod limb regeneration as studied in three model amphibians: newts, axolotls, and frogs. We review recent progress on tissue interactions during limb regeneration, and place those findings into an evolutionary context.