Mechanisms underlying vertebrate limb regeneration: lessons from the salamander

A mathematical framework for understanding the spontaneous emergence of complexity applicable to growing multicellular systems

In embryonic development and organogenesis, cells sharing identical genetic codes acquire diverse gene expression states in a highly reproducible spatial distribution, crucial for multicellular formation and quantifiable through positional information. To understand the spontaneous growth of complexity, we constructed a one-dimensional division-decision model, simulating the growth of cells with identical genetic networks from a single cell. Our findings highlight the pivotal role of cell division in providing positional cues, escorting the system toward states rich in information. Moreover, we pinpointed lateral inhibition as a critical mechanism translating spatial contacts into gene expression. Our model demonstrates that the spatial arrangement resulting from cell division, combined with cell lineages, imparts positional information, specifying multiple cell states with increased complexity-illustrated through examples in C.elegans. This study constitutes a foundational step in comprehending developmental intricacies, paving the way for future quantitative formulations to construct synthetic multicellular patterns.

Suppressors of cGAS-STING are downregulated during fin-limb regeneration and aging in aquatic vertebrates

During the early stages of limb and fin regeneration in aquatic vertebrates (i.e., fishes and amphibians), blastema undergo transcriptional rewiring of innate immune signaling pathways to promote immune cell recruitment. In mammals, a fundamental component of innate immune signaling is the cytosolic DNA sensing pathway, cGAS-STING. However, to what extent the cGAS-STING pathway influences regeneration in aquatic anamniotes is unknown. In jawed vertebrates, negative regulation of cGAS-STING activity is accomplished by suppressors of cytosolic DNA such as Trex1, Pml, and PML-like exon 9 (Plex9) exonucleases. Here, we examine the expression of these suppressors of cGAS-STING, as well as inflammatory genes and cGAS activity during caudal fin and limb regeneration using the spotted gar (Lepisosteus oculatus) and axolotl (Ambystoma mexicanum) model species, and during age-related senescence in zebrafish (Danio rerio). In the regenerative blastema of wounded gar and axolotl, we observe increased inflammatory gene expression, including interferon genes and interleukins 6 and 8. We also observed a decrease in axolotl Trex1 and gar pml expression during the early phases of wound healing which correlates with a dramatic increase in cGAS activity. In contrast, the plex9.1 gene does not change in expression during wound healing in gar. However, we observed decreased expression of plex9.1 in the senescing cardiac tissue of aged zebrafish, where 2'3'-cGAMP levels are elevated. Finally, we demonstrate a similar pattern of Trex1, pml, and plex9.1 gene regulation across species in response to exogenous 2'3'-cGAMP. Thus, during the early stages of limb-fin regeneration, Pml, Trex1, and Plex9.1 exonucleases are downregulated, presumably to allow an evolutionarily ancient cGAS-STING activity to promote inflammation and the recruitment of immune cells.

Effect of larval thermal conditions on limb regeneration in a ladybird beetle, Cheilomenes sexmaculata

In view of global environmental change, ecological factors especially temperature, affect development of the poikilotherms like insects. Since ladybirds are at risk of injury under mass-rearing conditions, their ability to regenerate injured limbs is highly crucial for their survival. Therefore, the effect of limb regeneration in relation to temperature forms the basis of the present study. The immature stages of insects, being more vulnerable to the surrounding temperature, were considered to study the effect of the prior thermal experience of larvae on regeneration. We exposed the early larval stages of the ladybird beetle, Cheilomenes sexmaculata, to different temperature conditions pre- and postamputation. Exposure of immature stages to extreme temperatures did not affect the ability to regenerate and regeneration occurred at given temperature conditions. However, the regenerated legs were smaller in size across given temperatures as compared to unamputated legs. Body weights in amputated treatments showed no difference and remained unchanged across temperatures when compared to unamputated treatments. Postamputation developmental duration, equivalent to recovery time postlimb amputation, was found to be affected by larval thermal conditions. Recovery was faster in larval treatments exposed to higher temperatures. Thus, larval thermal conditions though did not affect the ability to regenerate lost limbs directly, it does modulate the time taken to regenerate.

Morphology and ontogeny of carpus and tarsus in stereospondylomorph temnospondyls

Skeletal development is well known in temnospondyls, the most diverse group of Paleozoic and Mesozoic amphibians. However, the elements of carpus and tarsus (i.e., the mesopodium) were always the last bones to ossify relative to the other limb bones and with regard to the rest of the skeleton, and are preserved only in rare cases. Thus, in contrast to the other parts of the limb skeleton, little is known about the ontogeny and sequence of ossification of the temnospondyl carpus and tarsus. We intended to close this gap by studying the ontogenies of a number of Permo/Carboniferous stereospondylomorphs, the only temnospondyls with preserved growth series in which the successive ossification of carpals and tarsals can be traced. Studying the degree of mesopodial ossification within the same species show that it is not necessarily correlated with body size. This indicates that individual age rather than size determined the degree of mesopodial ossification in stereospondylomorphs and that the largest individuals are not necessarily the oldest ones. In the stereospondylomorph tarsus, the distal tarsals show preaxial development in accordance with most early tetrapods and salamanders. However, the more proximal mesopodials exhibit postaxial dominance, i.e., the preaxial column (tibiale, centrale 1) consistently started to ossify after the central column (centralia 2-4, intermedium) and the postaxial column (fibulare). Likewise, we observed preaxial development of the distal carpals in the stereospondylomorph carpus, as in most early tetrapods for which a statement can be made. However, in contrast to the tarsus, the more proximal carpals were formed by preaxial development, i.e., the preaxial column (radiale, centrale 1) ossified after the central column (centralia 2-4, intermedium) and before the postaxial column (ulnare). This pattern is unique among known early tetrapods and occurs only in certain extant salamanders. Furthermore, ossification proceeded from distal to proximal in the central column of the stereospondylomorph carpus, whereas the ossification advanced from proximal to distal in the central column of the tarsus. Despite these differences, a general ossification pattern that started from proximolateral (intermedium or centrale 4) to mediodistal (distal tarsal and carpal 1) roughly in a diagonal line is common to all stereospondylomorph mesopodials investigated. This pattern might basically reflect the alignment of stress within the mesopodium during locomotion. Our observations might point to a greater variability in the development of the mesopodium in stereospondylomorphs and probably other early tetrapods than in most extant tetrapods, possibly mirroring a similar variation as seen in the early phases of skeletogenesis in salamander carpus and tarsus.

Clade-specific genes and the evolutionary origin of novelty; new tools in the toolkit

Clade-specific (a.k.a. lineage-specific) genes are very common and found at all taxonomic levels and in all clades examined. They can arise by duplication of previously existing genes, which can involve partial truncations or combinations with other protein domains or regulatory sequences. They can also evolve de novo from non-coding sequences, leading to potentially truly novel protein domains. Finally, since clade-specific genes are generally defined by lack of sequence homology with other proteins, they can also arise by sequence evolution that is rapid enough that previous sequence homology can no longer be detected. In such cases, where the rapid evolution is followed by constraint, we consider them to be ontologically non-novel but likely novel at a functional level. In general, clade-specific genes have received less attention from biologists but there are increasing numbers of fascinating examples of their roles in important traits. Here we review some selected recent examples, and argue that attention to clade-specific genes is an important corrective to the focus on the conserved developmental regulatory toolkit that has been the habit of evo-devo as a field. Finally, we discuss questions that arise about the evolution of clade-specific genes, and how these might be addressed by future studies. We highlight the hypothesis that clade-specific genes are more likely to be involved in synapomorphies that arose in the stem group where they appeared, compared to other genes.

Advances in protein glycosylation and its role in tissue repair and regeneration

After tissue damage, a series of molecular and cellular events are initiated to promote tissue repair and regeneration to restore its original structure and function. These events include inter-cell communication, cell proliferation, cell migration, extracellular matrix differentiation, and other critical biological processes. Glycosylation is the crucial conservative and universal post-translational modification in all eukaryotic cells [1], with influential roles in intercellular recognition, regulation, signaling, immune response, cellular transformation, and disease development. Studies have shown that abnormally glycosylation of proteins is a well-recognized feature of cancer cells, and specific glycan structures are considered markers of tumor development. There are many studies on gene expression and regulation during tissue repair and regeneration. Still, there needs to be more knowledge of complex carbohydrates' effects on tissue repair and regeneration, such as glycosylation. Here, we present a review of studies investigating protein glycosylation in the tissue repair and regeneration process.

Deciphering regeneration through non-model animals: A century of experiments on cephalopod mollusks and an outlook at the future

The advent of marine stations in the last quarter of the 19th Century has given biologists the possibility of observing and experimenting upon myriad marine organisms. Among them, cephalopod mollusks have attracted great attention from the onset, thanks to their remarkable adaptability to captivity and a great number of biologically unique features including a sophisticate behavioral repertoire, remarkable body patterning capacities under direct neural control and the complexity of nervous system rivalling vertebrates. Surprisingly, the capacity to regenerate tissues and complex structures, such as appendages, albeit been known for centuries, has been understudied over the decades. Here, we will first review the limited in number, but fundamental studies on the subject published between 1920 and 1970 and discuss what they added to our knowledge of regeneration as a biological phenomenon. We will also speculate on how these relate to their epistemic and disciplinary context, setting the base for the study of regeneration in the taxon. We will then frame the peripherality of cephalopods in regeneration studies in relation with their experimental accessibility, and in comparison, with established models, either simpler (such as planarians), or more promising in terms of translation (urodeles). Last, we will explore the potential and growing relevance of cephalopods as prospective models of regeneration today, in the light of the novel opportunities provided by technological and methodological advances, to reconsider old problems and explore new ones. The recent development of cutting-edge technologies made available for cephalopods, like genome editing, is allowing for a number of important findings and opening the way toward new promising avenues. The contribution offered by cephalopods will increase our knowledge on regenerative mechanisms through cross-species comparison and will lead to a better understanding of the complex cellular and molecular machinery involved, shedding a light on the common pathways but also on the novel strategies different taxa evolved to promote regeneration of tissues and organs. Through the dialogue between biological/experimental and historical/contextual perspectives, this article will stimulate a discussion around the changing relations between availability of animal models and their specificity, technical and methodological developments and scientific trends in contemporary biology and medicine.

Post-amputation reactive oxygen species production is necessary for axolotls limb regeneration

Introduction: Reactive oxygen species (ROS) represent molecules of great interest in the field of regenerative biology since several animal models require their production to promote and favor tissue, organ, and appendage regeneration. Recently, it has been shown that the production of ROS such as hydrogen peroxide (H₂O₂) is required for tail regeneration in Ambystoma mexicanum. However, to date, it is unknown whether ROS production is necessary for limb regeneration in this animal model. Methods: forelimbs of juvenile animals were amputated proximally and the dynamics of ROS production was determined using 2′7- dichlorofluorescein diacetate (DCFDA) during the regeneration process. Inhibition of ROS production was performed using the NADPH oxidase inhibitor apocynin. Subsequently, a rescue assay was performed using exogenous hydrogen peroxide (H₂O₂). The effect of these treatments on the size and skeletal structures of the regenerated limb was evaluated by staining with alcian blue and alizarin red, as well as the effect on blastema formation, cell proliferation, immune cell recruitment, and expression of genes related to proximal-distal identity. Results: our results show that inhibition of post-amputation limb ROS production in the A. mexicanum salamander model results in the regeneration of a miniature limb with a significant reduction in the size of skeletal elements such as the ulna, radius, and overall autopod. Additionally, other effects such as decrease in the number of carpals, defective joint morphology, and failure of integrity between the regenerated structure and the remaining tissue were identified. In addition, this treatment affected blastema formation and induced a reduction in the levels of cell proliferation in this structure, as well as a reduction in the number of CD45⁺ and CD11b + immune system cells. On the other hand, blocking ROS production affected the expression of proximo-distal identity genes such as Aldha1a1, Rarβ, Prod1, Meis1, Hoxa13, and other genes such as Agr2 and Yap1 in early/mid blastema. Of great interest, the failure in blastema formation, skeletal alterations, as well as the expression of the genes evaluated were rescued by the application of exogenous H₂O₂, suggesting that ROS/H₂O₂ production is necessary from the early stages for proper regeneration and patterning of the limb.

A Morphological and Histological Investigation of Imperfect Lungfish Fin Regeneration

Regeneration, the replacement of body parts in a living animal, has excited scientists for centuries and our knowledge of vertebrate appendage regeneration has increased significantly over the past decades. While the ability of amniotes to regenerate body parts is very limited, members of other vertebrate clades have been shown to have rather high regenerative capacities. Among tetrapods (four-limbed vertebrates), only salamanders show unparalleled capacities of epimorphic tissue regeneration including replacement of organ and body parts in an apparently perfect fashion. The closest living relatives of Tetrapoda, the lungfish, show regenerative abilities that are comparable to those of salamanders and recent studies suggest that these high regenerative capacities may indeed be ancestral for bony fish (osteichthyans) including tetrapods. While great progress has been made in recent years in understanding the cellular and molecular mechanisms deployed during appendage regeneration, comparatively few studies have investigated gross morphological and histological features of regenerated fins and limbs. Likewise, rather little is known about how fin regeneration compares morphologically to salamander limb regeneration. In this study, we investigated the morphology and histology of regenerated fins in all three modern lungfish families. Data from histological serial sections, 3D reconstructions, and x-ray microtomography scans were analyzed to assess morphological features, quality and pathologies in lungfish fin regenerates. We found several anomalies resulting from imperfect regeneration in regenerated fins in all investigated lungfish species, including fusion of skeletal elements, additional or fewer elements, and distal branching. The similarity of patterns in regeneration abnormalities compared to salamander limb regeneration lends further support to the hypothesis that high regenerative capacities are plesiomorphic for sarcopterygians.

Genetic basis for an evolutionary shift from ancestral preaxial to postaxial limb polarity in non-urodele vertebrates

In most tetrapod vertebrates, limb skeletal progenitors condense with postaxial dominance. Posterior elements (such as ulna and fibula) appear prior to their anterior counterparts (radius and tibia), followed by digit-appearance order with continuing postaxial polarity. The only exceptions are urodele amphibians (salamanders), whose limb elements develop with preaxial polarity and who are also notable for their unique ability to regenerate complete limbs as adults. The mechanistic basis for this preaxial dominance has remained an enigma and has even been proposed to relate to the acquisition of novel genes involved in regeneration. However, recent fossil evidence suggests that preaxial polarity represents an ancestral rather than derived state. Here, we report that 5'Hoxd (Hoxd11-d13) gene deletion in mouse is atavistic and uncovers an underlying preaxial polarity in mammalian limb formation. We demonstrate this shift from postaxial to preaxial dominance in mouse results from excess Gli3 repressor (Gli3R) activity due to the loss of 5'Hoxd-Gli3 antagonism and is associated with cell-cycle changes promoting precocious cell-cycle exit in the anterior limb bud. We further show that Gli3 knockdown in axolotl results in a shift to postaxial dominant limb skeleton formation, as well as expanded paddle-shaped limb-bud morphology and ensuing polydactyly. Evolutionary changes in Gli3R activity level, which also played a key role in the fin-to-limb transition, appear to be fundamental to the shift from preaxial to postaxial polarity in formation of the tetrapod limb skeleton.

Repeated ecological and life cycle transitions make salamanders an ideal model for evolution and development

Observations on the ontogeny and diversity of salamanders provided some of the earliest evidence that shifts in developmental trajectories have made a substantial contribution to the evolution of animal forms. Since the dawn of evo-devo there have been major advances in understanding developmental mechanisms, phylogenetic relationships, evolutionary models, and an appreciation for the impact of ecology on patterns of development (eco-evo-devo). Molecular phylogenetic analyses have converged on strong support for the majority of branches in the Salamander Tree of Life, which includes 764 described species. Ancestral reconstructions reveal repeated transitions between life cycle modes and ecologies. The salamander fossil record is scant, but key Mesozoic species support the antiquity of life cycle transitions in some families. Colonization of diverse habitats has promoted phenotypic diversification and sometimes convergence when similar environments have been independently invaded. However, unrelated lineages may follow different developmental pathways to arrive at convergent phenotypes. This article summarizes ecological and endocrine-based causes of life cycle transitions in salamanders, as well as consequences to body size, genome size, and skeletal structure. Salamanders offer a rich source of comparisons for understanding how the evolution of developmental patterns has led to phenotypic diversification following shifts to new adaptive zones.

Salamanders: The molecular basis of tissue regeneration and its relevance to human disease

Salamanders are recognized for their ability to regenerate a broad range of tissues. They have also have been used for hundreds of years for classical developmental biology studies because of their large accessible embryos. The range of tissues these animals can regenerate is fascinating, from full limbs to parts of the brain or heart, a potential that is missing in humans. Many promising research efforts are working to decipher the molecular blueprints shared across the organisms that naturally have the capacity to regenerate different tissues and organs. Salamanders are an excellent example of a vertebrate that can functionally regenerate a wide range of tissue types. In this review, we outline some of the significant insights that have been made that are aiding in understanding the cellular and molecular mechanisms of tissue regeneration in salamanders and discuss why salamanders are a worthy model in which to study regenerative biology and how this may benefit research fields like regenerative medicine to develop therapies for humans in the future.

Cellular and molecular mechanisms that regulate mammalian digit tip regeneration

Digit tip regeneration is one of the few examples of true multi-tissue regeneration in an adult mammal. The key step in this process is the formation of the blastema, a transient proliferating cell mass that generates the different cell types of the digit to replicate the original structure. Failure to form the blastema results in a lack of regeneration and has been postulated to be the reason why mammalian limbs cannot regrow following amputation. Understanding how the blastema forms and functions will help us to determine what is required for mammalian regeneration to occur and will provide insights into potential therapies for mammalian tissue regeneration and repair. This review summarizes the cellular and molecular mechanisms that influence murine blastema formation and govern digit tip regeneration.

Immunity in salamander regeneration: Where are we standing and where are we headed?

Salamanders exhibit the most extensive regenerative repertoire among vertebrates, being able to accomplish scar-free healing and faithful regeneration of significant parts of the eye, heart, brain, spinal cord, jaws and gills, as well as entire appendages throughout life. The cellular and molecular mechanisms underlying salamander regeneration are currently under extensive examination, with the hope of identifying the key drivers in each context, understanding interspecies differences in regenerative capacity, and harnessing this knowledge in therapeutic settings. The immune system has recently emerged as a potentially critical player in regenerative responses. Components of both innate and adaptive immunity have been found at critical stages of regeneration in a range of salamander tissues. Moreover, functional studies have identified a requirement for macrophages during heart and limb regeneration. However, our knowledge of salamander immunity remains scarce, and a thorough definition of the precise roles played by its members is lacking. Here, we examine the evidence supporting roles for immunity in various salamander regeneration models. We pinpoint observations that need revisiting through modern genetic approaches, uncover knowledge gaps, and highlight insights from various model organisms that could guide future explorations toward an understanding of the functions of immunity in regeneration.

A histological study of normal and pathological limb regeneration in the Mexican axolotl Ambystoma mexicanum

Salamanders show unparalleled capacities of tissue regeneration amongst tetrapods (four-legged vertebrates), being able to repair and renew lost or damage body parts, such as tails, jaws, and limbs in a seemingly perfect fashion. Despite countless studies on axolotl (Ambystoma mexicanum) regeneration, only a few studies have thus far compared gross morphological and histological features of the original and regenerated limb skeleton. Therein, most studies have focused on nerves or muscles, while even fewer have provided detailed information about bones and cartilage. This study compares skeletal tissue structures of original and regenerated limbs with respect to tissue level histology. Histological serial sections of 55 axolotl larvae were generated, including 29 limbs that were severed by conspecifics, and 26 that were subject to targeted amputations. Amputations were executed in several larval stages (48, 52, and 53) and at different limb positions (humeral midshaft, above the mesopod). In addition, 3D reconstructions were prepared based on X-ray microtomography scans. The results demonstrate that regenerated forelimbs show a diversity of limb and digit abnormalities as a result of imperfect regeneration. Furthermore, abnormalities were more severe and more frequent in regenerated forelimbs caused by natural bites as compared with regenerated forelimbs after amputation. The results indicate that abnormalities occur frequently after regeneration in larval axolotls contradicting the notion of regeneration generally resulting in perfect limbs.

Acquisition of a Unique Mesenchymal Precursor-like Blastema State Underlies Successful Adult Mammalian Digit Tip Regeneration

Here, we investigate the origin and nature of blastema cells that regenerate the adult murine digit tip. We show that Pdgfra-expressing mesenchymal cells in uninjured digits establish the regenerative blastema and are essential for regeneration. Single-cell profiling shows that the mesenchymal blastema cells are distinct from both uninjured digit and embryonic limb or digit Pdgfra-positive cells. This unique blastema state is environmentally determined; dermal fibroblasts transplanted into the regenerative, but not non-regenerative, digit express blastema-state genes and contribute to bone regeneration. Moreover, lineage tracing with single-cell profiling indicates that endogenous osteoblasts or osteocytes acquire a blastema mesenchymal transcriptional state and contribute to both dermis and bone regeneration. Thus, mammalian digit tip regeneration occurs via a distinct adult mechanism where the regenerative environment promotes acquisition of a blastema state that enables cells from tissues such as bone to contribute to the regeneration of other mesenchymal tissues such as the dermis.

Proteomics Analysis of Extracellular Matrix Remodeling During Zebrafish Heart Regeneration

Adult zebrafish, in contrast to mammals, are able to regenerate their hearts in response to injury or experimental amputation. Our understanding of the cellular and molecular bases that underlie this process, although fragmentary, has increased significantly over the last years. However, the role of the extracellular matrix (ECM) during zebrafish heart regeneration has been comparatively rarely explored. Here, we set out to characterize the ECM protein composition in adult zebrafish hearts, and whether it changed during the regenerative response. For this purpose, we first established a decellularization protocol of adult zebrafish ventricles that significantly enriched the yield of ECM proteins. We then performed proteomic analyses of decellularized control hearts and at different times of regeneration. Our results show a dynamic change in ECM protein composition, most evident at the earliest (7 days postamputation) time point analyzed. Regeneration associated with sharp increases in specific ECM proteins, and with an overall decrease in collagens and cytoskeletal proteins. We finally tested by atomic force microscopy that the changes in ECM composition translated to decreased ECM stiffness. Our cumulative results identify changes in the protein composition and mechanical properties of the zebrafish heart ECM during regeneration.

Deep evolutionary origin of limb and fin regeneration

Salamanders and lungfishes are the only sarcopterygians (lobe-finned vertebrates) capable of paired appendage regeneration, regardless of the amputation level. Among actinopterygians (ray-finned fishes), regeneration after amputation at the fin endoskeleton has only been demonstrated in polypterid fishes (Cladistia). Whether this ability evolved independently in sarcopterygians and actinopterygians or has a common origin remains unknown. Here we combine fin regeneration assays and comparative RNA-sequencing (RNA-seq) analysis of Polypterus and axolotl blastemas to provide support for a common origin of paired appendage regeneration in Osteichthyes (bony vertebrates). We show that, in addition to polypterids, regeneration after fin endoskeleton amputation occurs in extant representatives of 2 other nonteleost actinopterygians: the American paddlefish (Chondrostei) and the spotted gar (Holostei). Furthermore, we assessed regeneration in 4 teleost species and show that, with the exception of the blue gourami (Anabantidae), 3 species were capable of regenerating fins after endoskeleton amputation: the white convict and the oscar (Cichlidae), and the goldfish (Cyprinidae). Our comparative RNA-seq analysis of regenerating blastemas of axolotl and Polypterus reveals the activation of common genetic pathways and expression profiles, consistent with a shared genetic program of appendage regeneration. Comparison of RNA-seq data from early Polypterus blastema to single-cell RNA-seq data from axolotl limb bud and limb regeneration stages shows that Polypterus and axolotl share a regeneration-specific genetic program. Collectively, our findings support a deep evolutionary origin of paired appendage regeneration in Osteichthyes and provide an evolutionary framework for studies on the genetic basis of appendage regeneration.

Mechanisms of urodele limb regeneration

This review explores the historical and current state of our knowledge about urodele limb regeneration. Topics discussed are (1) blastema formation by the proteolytic histolysis of limb tissues to release resident stem cells and mononucleate cells that undergo dedifferentiation, cell cycle entry and accumulation under the apical epidermal cap. (2) The origin, phenotypic memory, and positional memory of blastema cells. (3) The role played by macrophages in the early events of regeneration. (4) The role of neural and AEC factors and interaction between blastema cells in mitosis and distalization. (5) Models of pattern formation based on the results of axial reversal experiments, experiments on the regeneration of half and double half limbs, and experiments using retinoic acid to alter positional identity of blastema cells. (6) Possible mechanisms of distalization during normal and intercalary regeneration. (7) Is pattern formation is a self-organizing property of the blastema or dictated by chemical signals from adjacent tissues? (8) What is the future for regenerating a human limb?

Tetrapod limb and sarcopterygian fin regeneration share a core genetic programme

Salamanders are the only living tetrapods capable of fully regenerating limbs. The discovery of salamander lineage-specific genes (LSGs) expressed during limb regeneration suggests that this capacity is a salamander novelty. Conversely, recent paleontological evidence supports a deeper evolutionary origin, before the occurrence of salamanders in the fossil record. Here we show that lungfishes, the sister group of tetrapods, regenerate their fins through morphological steps equivalent to those seen in salamanders. Lungfish de novo transcriptome assembly and differential gene expression analysis reveal notable parallels between lungfish and salamander appendage regeneration, including strong downregulation of muscle proteins and upregulation of oncogenes, developmental genes and lungfish LSGs. MARCKS-like protein (MLP), recently discovered as a regeneration-initiating molecule in salamander, is likewise upregulated during early stages of lungfish fin regeneration. Taken together, our results lend strong support for the hypothesis that tetrapods inherited a bona fide limb regeneration programme concomitant with the fin-to-limb transition.

Could we also be regenerative superheroes, like salamanders?

Development of methods to reawaken the semi-dormant regenerative potential that lies within adult human tissues would hold promise for the restoration of diseased or damaged organs and tissues. While most of the regeneration potential is suppressed in many vertebrates, including humans, during adult life, urodele amphibians (salamanders) retain their regenerative ability throughout adulthood. Studies in newts and axolotls, two salamander models, have provided significant knowledge about adult limb regeneration. In this review, we present a comparative analysis of salamander and mammalian regeneration and discuss how evolutionarily altered properties of the regenerative environment can be exploited to restore full regenerative potential in the human body.

Positional Information and Pattern Formation

The concept of positional information proposes that cells acquire positional values as in a coordinate system, which they interpret by developing in particular ways to give rise to spatial patterns. Some of the best evidence for positional information comes from regeneration experiments, and the patterning of the leg and antenna in Drosophila, and the vertebrate limb. Central problems are how positional information is set up, how it is recorded, and then how it is interpreted by the cells. A number of models have been proposed for the setting up of positional gradients, and most are based on diffusion of a morphogen and its interactions with extracellular molecules; however, diffusion may not be reliable mechanism. There are also mechanisms based on timing. There is no good evidence for the quantitative aspects of any of the proposed gradients and details how they are set up. The way in which a signaling gradient regulates differential gene expression in a concentration-dependent manner also raises several technical and quite difficult issues. A key feature of positional information being the basis for pattern formation is that there is no prepattern in the embryo.

Regeneration versus scarring in vertebrate appendages and heart

Injuries to complex human organs, such as the limbs and the heart, result in pathological conditions, for which we often lack adequate treatments. While modern regenerative approaches are based on the transplantation of stem cell-derived cells, natural regeneration in lower vertebrates, such as zebrafish and newts, relies predominantly on the intrinsic plasticity of mature tissues. This property involves local activation of the remaining material at the site of injury to promote cell division, cell migration and complete reproduction of the missing structure. It remains an unresolved question why adult mammals are not equally competent to reactivate morphogenetic programmes. Although organ regeneration depends strongly on the proliferative properties of cells in the injured tissue, it is apparent that various organismic factors, such as innervation, vascularization, hormones, metabolism and the immune system, can affect this process. Here, we focus on a correlation between the regenerative capacity and cellular specialization in the context of functional demands, as illustrated by appendages and heart in diverse vertebrates. Elucidation of the differences between homologous regenerative and non-regenerative tissues from various animal models is essential for understanding the applicability of lessons learned from the study of regenerative biology to clinical strategies for the treatment of injured human organs.

A dynamic architecture of life

In recent decades, a profound conceptual transformation has occurred comprising different areas of biological research, leading to a novel understanding of life processes as much more dynamic and changeable. Discoveries in plants and animals, as well as novel experimental approaches, have prompted the research community to reconsider established concepts and paradigms. This development was taken as an incentive to organise a workshop in May 2014 at the Academia Nazionale dei Lincei in Rome. There, experts on epigenetics, regeneration, neuroplasticity, and computational biology, using different animal and plant models, presented their insights on important aspects of a dynamic architecture of life, which comprises all organisational levels of the organism. Their work demonstrates that a dynamic nature of life persists during the entire existence of the organism and permits animals and plants not only to fine-tune their response to particular environmental demands during development, but underlies their continuous capacity to do so. Here, a synthesis of the different findings and their relevance for biological thinking is presented.

An orphan gene is necessary for preaxial digit formation during salamander limb development

Limb development in salamanders differs from other tetrapods in that the first digits to form are the two most anterior (preaxial dominance). This has been proposed as a salamander novelty and its mechanistic basis is unknown. Salamanders are the only adult tetrapods able to regenerate the limb, and the contribution of preaxial dominance to limb regeneration is unclear. Here we show that during early outgrowth of the limb bud, a small cohort of cells express the orphan gene Prod1 together with Bmp2, a critical player in digit condensation in amniotes. Disruption of Prod1 with a gene-editing nuclease abrogates these cells, and blocks formation of the radius and ulna, and outgrowth of the anterior digits. Preaxial dominance is a notable feature of limb regeneration in the larval newt, but this changes abruptly after metamorphosis so that the formation of anterior and posterior digits occurs together within the autopodium resembling an amniote-like pattern.

No Sexual Dimorphism Detected in Digit Ratios of the Fire Salamander (Salamandra salamandra)

It has been proposed that digit ratio may be used as a biomarker of early developmental effects. Specifically, the second-to-fourth digit ratio (2D:4D) has been linked to the effects of sex hormones and their receptor genes, but other digit ratios have also been investigated. Across taxa, patterns of sexual dimorphism in digit ratios are ambiguous and a scarcity of studies in basal tetrapods makes it difficult to understand how ratios have evolved. Here, we focus on examining sex differences in digit ratios (2D:3D, 2D:4D, and 3D:4D) in a common amphibian, the fire salamander (Salamandra salamandra). We used graphic software to measure soft tissue digit length and digit bone length from X-rays. We found a nonsignificant tendency in males to have a lower 2D:3D than females; however, no sexual differences were detected in the other ratios. We discuss our results in the context of other studies of digit ratios, and how sex determination systems, as well as other factors, might impact patterns of sexual dimorphism, particularly in reptiles and in amphibians. Our findings suggest that caution is needed when using digit ratios as a potential indicator of prenatal hormonal effects in amphibians and highlight the need for more comparative studies to elucidate the evolutionary and genetic mechanisms implicated in sexually dimorphic patterns across taxonomic groups.

Early evolution of limb regeneration in tetrapods: evidence from a 300-million-year-old amphibian

Salamanders are the only tetrapods capable of fully regenerating their limbs throughout their entire lives. Much data on the underlying molecular mechanisms of limb regeneration have been gathered in recent years allowing for new comparative studies between salamanders and other tetrapods that lack this unique regenerative potential. By contrast, the evolution of animal regeneration just recently shifted back into focus, despite being highly relevant for research designs aiming to unravel the factors allowing for limb regeneration. We show that the 300-million-year-old temnospondyl amphibian Micromelerpeton, a distant relative of modern amphibians, was already capable of regenerating its limbs. A number of exceptionally well-preserved specimens from fossil deposits show a unique pattern and combination of abnormalities in their limbs that is distinctive of irregular regenerative activity in modern salamanders and does not occur as variants of normal limb development. This demonstrates that the capacity to regenerate limbs is not a derived feature of modern salamanders, but may be an ancient feature of non-amniote tetrapods and possibly even shared by all bony fish. The finding provides a new framework for understanding the evolution of regenerative capacity of paired appendages in vertebrates in the search for conserved versus derived molecular mechanisms of limb regeneration.

Identification of the orphan gene Prod 1 in basal and other salamander families

BACKGROUND

The urodele amphibians (salamanders) are the only adult tetrapods able to regenerate the limb. It is unclear if this is an ancestral property that is retained in salamanders but lost in other tetrapods or if it evolved in salamanders. The three-finger protein Prod 1 is implicated in the mechanism of newt limb regeneration, and no orthologs have been found in other vertebrates, thus providing evidence for the second viewpoint. It has also been suggested that this protein could play a role in salamander-specific aspects of limb development. There are ten families of extant salamanders, and Prod 1 has only been identified in two of them to date. It is important to determine if it is present in other families and, particularly, the basal group of two families which diverged approximately 200 MYA.

FINDINGS

We have used polymerase chain reaction (PCR) to identify Prod 1 in a Chinese hynobiid species Batrachuperus longdongensis. We obtained an intestinal transcriptome of the plethodontid Aneides lugubris and, from this, identified a primer which allowed PCR of two Prod 1 genes from this species. All known Prod 1 sequences from nine species in four families have been aligned, and a phylogenetic tree has been derived.

CONCLUSIONS

Prod 1 is found in basal salamanders of the family Hynobiidae, and in at least three other families, so it may be present in all extant salamanders. It remains a plausible candidate to have been involved in the origins of limb regeneration, as well as the apomorphic aspects of limb development.

Sexual selection drives the evolution of limb regeneration in Harmonia axyridis (Coleoptera: Coccinellidae)

When Harmonia axyridis larvae were subjected to amputation of a foreleg in the fourth instar, 83% survived and, of these, 75% regenerated the leg during pupation. Regenerators pupated at heavier weights than controls (unoperated) or non-regenerators, and spent longer in pupation. Regenerated males were preferred by females in choice tests and produced more viable progeny than control males. Unregenerated males were less preferred by females, copulated for shorter periods than control males, and reduced female fecundity. Amputation diminished beneficial paternal effects, whether males regenerated or not, resulting in progeny with slower development and smaller adult body mass relative to control paternity. Progeny of unregenerated males had lower survival and body mass, whether male or female, confirming that regeneration was an honest signal of mate quality. When offspring had a foreleg amputated, a regenerated paternity yielded higher survival than control paternity, but similar rates of regeneration, whereas an unregenerated paternity yielded lower rates of survival and leg regeneration than control paternity. Regenerating beetles were twice as likely to be melanic as non-regenerating or control beetles, suggesting pleiotropic effects of melanism on processes involved in regeneration. This is the first report of complete limb regeneration by a holometabolous insect in the pupal stage, and the first example of sexual selection for regenerative capacity.

Acellular matrix in urethral reconstruction

The treatment of severe urethral stenosis has always been a challenge even for skilled urologists. Classic urethroplasty, skin flaps and buccal mucosa grafting may not be used for long and complex strictures. In the quest for an ideal urethral substitute, acellular scaffolds have demonstrated the ability to induce tissue regeneration layer by layer. After several experimental studies, the use of acellular matrices for urethral reconstruction has become a clinical reality over the last decade. In this review we analyze advantages and limitations of both biological and polymeric scaffolds that have been reported in experimental and human studies. Important aspects such as graft extension, surgical technique and cell-seeding versus cell-free grafts will be discussed.

Variation in salamanders: an essay on genomes, development, and evolution

Regeneration is studied in a few model species of salamanders, but the ten families of salamanders show considerable variation, and this has implications for our understanding of salamander biology. The most recent classification of the families identifies the cryptobranchoidea as the basal group which diverged in the early Jurassic. Variation in the sizes of genomes is particularly obvious, and reflects a major contribution from transposable elements which is already present in the basal group.Limb development has been a focus for evodevo studies, in part because of the variable property of pre-axial dominance which distinguishes salamanders from other tetrapods. This is thought to reflect the selective pressures that operate on a free-living aquatic larva, and might also be relevant for the evolution of limb regeneration. Recent fossil evidence suggests that both pre-axial dominance and limb regeneration were present 300 million years ago in larval temnospondyl amphibians that lived in mountain lakes. A satisfying account of regeneration in salamanders may need to address all these different aspects in the future.

Expression of pluripotency factors in echinoderm regeneration

Cell dedifferentiation is an integral component of post-traumatic regeneration in echinoderms. As dedifferentiated cells become multipotent, we asked if this spontaneous broadening of developmental potential is associated with the action of the same pluripotency factors (known as Yamanaka factors) that were used to induce pluripotency in specialized mammalian cells. In this study, we investigate the expression of orthologs of the four Yamanaka factors in regeneration of two different organs, the radial nerve cord and the digestive tube, in the sea cucumber Holothuria glaberrima. All four pluripotency factors are expressed in uninjured animals, although their expression domains do not always overlap. In regeneration, the expression levels of the four genes were not regulated in a coordinated way, but instead showed different dynamics for individual genes and also were different between the radial nerve and the gut. SoxB1, the ortholog of the mammalian Sox2, was drastically downregulated in the regenerating intestine, suggesting that this factor is not required for dedifferentiation/regeneration in this organ. On the other hand, during the early post-injury stage, Myc, the sea cucumber ortholog of c-Myc, was significantly upregulated in both the intestine and the radial nerve cord and is therefore hypothesized to play a central role in dedifferentiation/regeneration of various tissue types.

Nanotechnology in the Regeneration of Complex Tissues

Modern medicine faces a growing crisis as demand for organ transplantations continues to far outstrip supply. By stimulating the body’s own repair mechanisms, regenerative medicine aims to reduce demand for organs, while the closely related field of tissue engineering promises to deliver “off-the-self” organs grown from patients’ own stem cells to improve supply. To deliver on these promises, we must have reliable means of generating complex tissues. Thus far, the majority of successful tissue engineering approaches have relied on macroporous scaffolds to provide cells with both mechanical support and differentiative cues. In order to engineer complex tissues, greater attention must be paid to nanoscale cues present in a cell’s microenvironment. As the extracellular matrix is capable of driving complexity during development, it must be understood and reproduced in order to recapitulate complexity in engineered tissues. This review will summarize current progress in engineering complex tissue through the integration of nanocomposites and biomimetic scaffolds.

The biochemical determinants of tissue regeneration

The field of regenerative medicine offers tantalizing hope for the repair and replacement of damaged organs and tissues, with the ultimate goal of restoring normal tissue function. This field represents an enormous range of biological, chemical and biophysical technologies that harness the restorative properties of living materials, especially human cells, to produce new molecular and cellular medicines, diagnostics, devices and healthcare research tools. The goal of this Biochemical Society Annual Symposium was to explore the key biochemical determinants of tissue regeneration, and we highlight the contribution of biochemistry to this emerging field of regenerative medicine.