Making a new limb out of old cells: exploring endogenous cell reprogramming and its role during limb regeneration

Cellular reprogramming is characterized by the induced dedifferentiation of mature cells into a more plastic and potent state. This process can occur through artificial reprogramming manipulations in the laboratory such as nuclear reprogramming and induced pluripotent stem cell (iPSC) generation, and endogenously in vivo during amphibian limb regeneration. In amphibians such as the Mexican axolotl, a regeneration permissive environment is formed by nerve-dependent signaling in the wounded limb tissue. When exposed to these signals, limb connective tissue cells dedifferentiate into a limb progenitor-like state. This state allows the cells to acquire new pattern information, a property called positional plasticity. Here, we review our current understanding of endogenous reprogramming and why it is important for successful regeneration. We will also explore how naturally induced dedifferentiation and plasticity were leveraged to study how the missing pattern is established in the regenerating limb tissue.

Material properties in regenerating axolotl limbs using inverse finite element analysis

BACKGROUND

The extracellular mechanical environment plays an important role in the skeletal development process. Characterization of the material properties of regenerating tissues that recapitulate development, provides insights into the mechanical environment experienced by the cells and the maturation of the matrix. In this study, we estimated the viscoelastic material properties of regenerating forelimbs in the axolotl (Ambystoma mexicanum) at three different regeneration stages: 27 days post-amputation (mid-late bud) and 41 days post-amputation (palette stage), and fully-grown time points. A stress-relaxation indentation test followed by two-term Prony series viscoelastic inverse finite element analysis was used to obtain material parameters. Glycosaminoglycan (GAG) content was estimated using a 1,9- dimethyl methylene blue assay.

RESULTS

The instantaneous and equilibrium shear moduli significantly increased with regeneration while the short-term stress relaxation time significantly decreased with limb regeneration. The long-term stress relaxation time in the fully-grown time point was significantly lower than 27 and 41 DPA groups. The GAG content was not significantly different between 27 and 41 DPA but the GAG content of cartilage in the fully-grown group was significantly greater than in 27 and 41 DPA.

CONCLUSIONS

The mechanical environment of the proliferating cells changes drastically during limb regeneration. Understanding how the tissue's mechanical properties change during limb regeneration is critical for linking molecular-level matrix production of the cells to tissue-level behavior and mechanical signals.

GROSS AND ULTRASONOGRAPHIC ANATOMY OF THE COELOMIC ORGANS OF HEALTHY AXOLOTLS (AMBYSTOMA MEXICANUM)

The objectives of this study were to describe the gross anatomy and ultrasonographic appearance of coelomic organs in subadult and adult axolotls (Ambystoma mexicanum), to describe an ultrasound technique, and to test correlations of ultrasonographic measurement with body length, width, and weight. Necropsies of coelomic organs were conducted on 10 axolotls (females = 5; males = 5) and ultrasound on 11 (males = 5; females = 6). Animals were kept in water and maintained conscious during ultrasound. The heart, caudal vena cava, liver, gallbladder, spleen, esophagus, stomach, colon, kidneys, ovaries, and fat bodies were identified in all study subjects, although testicles were identified in only 6/7 subjects. The pancreas and adrenal glands could not be identified in any animals, either during necropsy or ultrasonography. Coelomic and pericardial effusion was present in all animals. Ultrasonographic measurements of the liver, spleen, myocardial thickness, and right and left kidney length were highly repeatable (correlation value [CV] < 5%) and the esophagus, spleen, caudal vena cava, fat bodies, gallbladder, colon thickness, right kidney height and width, and right testicle diameter were statistically repeatable (CV < 10%).

Age- and dose-dependent susceptibility of axolotls (Ambystoma mexicanum) by bath exposure to Ambystoma tigrinum virus (ATV)

Ranaviruses are large, dsDNA viruses that have significant ecological and economic impact on cold-blooded vertebrates. However, our understanding of the viral proteins and subsequent host immune response(s) that impact susceptibility to infection and disease is not clear. The ranavirus Ambystoma tigrinum virus (ATV), originally isolated from the Sonoran tiger salamander (Ambystoma mavortium stebbinsi), is highly pathogenic at low doses of ATV at all tiger salamander life stages and this model has been used to explore the host-pathogen interactions of ATV infection. However, inconsistencies in the availability of laboratory reared larval tiger salamanders required us to look at the well characterized axolotl (A. mexicanum) as a model for ATV infection. Data obtained from five infection experiments over different developmental timepoints suggest that axolotls are susceptible to ATV in an age- and dose-dependent manner. These data support the use of the ATV-axolotl model to further explore the host-pathogen interactions of ranavirus infections.

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

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

Matrisomal components involved in regenerative wound healing in axolotl and Acomys: implications for biomaterial development

Achieving regeneration in humans has been a long-standing goal of many researchers. Whereas amphibians like the axolotl (Ambystoma mexicanum) are capable of regenerating whole organs and even limbs, most mammals heal their wounds via fibrotic scarring. Recently, the African spiny mouse (Acomys sp.) has been shown to be injury resistant and capable of regenerating several tissue types. A major focal point of research with Acomys has been the identification of drivers of regeneration. In this search, the matrisome components related to the extracellular matrix (ECM) are often overlooked. In this review, we compare Acomys and axolotl skin wound healing and blastema-mediated regeneration by examining their wound healing responses and comparing the expression pattern of matrisome genes, including glycosaminoglycan (GAG) related genes. The goal of this review is to identify matrisome genes that are upregulated during regeneration and could be potential candidates for inclusion in pro-regenerative biomaterials. Research papers describing transcriptomic or proteomic coverage of either skin regeneration or blastema formation in Acomys and axolotl were selected. Matrisome and GAG related genes were extracted from each dataset and the resulting lists of genes were compared. In our analysis, we found several genes that were consistently upregulated, suggesting possible involvement in regenerative processes. Most of the components have been implicated in regulation of cell behavior, extracellular matrix remodeling and wound healing. Incorporation of such pro-regenerative factors into biomaterials may help to shift pro-fibrotic processes to regenerative responses in treated wounds.

Continuous anesthesia for 60 days in an isosmotic environment does not impair limb or cardiac regeneration in the axolotl

Longitudinal animal experiments in the field of regenerative biology often require repeated use of short-term anesthesia (minutes to a few hours). Regain of consciousness limits the level of acceptable invasiveness of procedures, and it makes it difficult to untangle behavioral changes caused by injury to physiological processes involved in the regenerative response. Therefore, a method to keep a regenerative research animal in a comatose state under continuous anesthesia during regenerative experiments often spanning months, would be ethically and experimentally desirable. Here we report on a method using propofol based anesthesia in an isosmotic environment that allows for continuous anesthesia of regenerating axolotls for 60 days with a 75% survival rate, thus spanning the majority of a full regenerative cycle following limb amputation or cryoinjury to the heart. No differences were detected in the axolotl's ability to regenerate amputated limbs and cardiac cryo-injury while anesthetized, however some regenerative failures in the limb were observed in both anesthetized and unanesthetized control groups, most likely caused by prolonged fasting. Sixty days of anesthesia may be approaching a level were kidney function is affected, but the 75% surviving anesthetized animals recovered well after anesthesia and showed a full behavioral recovery within 17 days.

Two is not necessarily better than one: A double lens in a pre-metamorphic adult axolotl (Ambystoma mexicanum)

An 8-year-old female pre-metamorphic axolotl (Ambystoma mexicanum) was examined for a suspected anterior lens luxation. Slit-lamp biomicroscopy revealed two lens-like structures in the anterior chamber of the right eye (OD), each with cataractous change. Ultrasound biomicroscopy and optical coherence tomography (OCT) were performed without sedation, and revealed small lenticular structures each with distinct nuclei and cortices. Although a distinct connection of the two lenticular structures could not be definitively ruled out, the structures appeared separate. Each of the lenticular structures was closely associated with its respective iris leaflet. This report demonstrates application of advanced imaging for diagnostic use in axolotl ophthalmology, showing that imaging of the lens can be performed without sedation, topical anesthetic, nor contact gel with high diagnostic quality. Although two distinct lenses were diagnosed with no historical evidence of trauma, the small sizes of each lenticular structure, with no detectable connection between them, are suggestive of a possible regenerative abnormality. This report opens discussion for the regenerative capabilities of the pre-metamorphic adult axolotl and possible implementations of their use in regenerative medicine research for the development of future therapies.

Navigation and Use of Custom Tracks within the Axolotl Genome Browser

The availability of the chromosome-scale axolotl genome sequences has made it possible to explore genome evolution, perform cross-species comparisons, and use additional sequencing data to analyze both genome-wide features and individual genes. Here, we will focus on the UCSC genome browser and demonstrate in a step-by-step manner how to use it to integrate different data to approach a broad question of the Fgf8 locus evolution and analyze the neighborhood of a gene that was reported missing in axolotl - Pax3.

A Reproducible Spinal Cord Crush Injury in the Regeneration-Permissive Axolotl

Following injury, axolotls are able to functionally regenerate their spinal cord, regaining both motor and sensory control. In contrast, humans respond to severe spinal cord injury by forming a glial scar, which prevents further damage but also inhibits any regenerative growth, resulting in loss of function caudal to the injury site. The axolotl has become a popular system to elucidate the underlying cellular and molecular events that contribute to successful CNS regeneration. However, the experimental injuries (tail amputation and transection) that are utilized in axolotls do not mimic the blunt trauma that is often sustained in humans. Here, we report a more clinically relevant model for spinal cord injuries in the axolotl using a weight-drop technique. This reproducible model allows precise control over the severity of the injury by regulating the drop height, weight, compression, and position of the injury.

Methods for Studying Appendicular Skeletal Biology in Axolotls

The axolotl is a great model for studying cartilage, bone and joint regeneration, fracture healing, and evolution. Stainings such as Alcian Blue/Alizarin Red have become workhorses in skeletal analyses, but additional methods complement the detection of different skeletal matrices. Here we describe protocols for studying skeletal biology in axolotls, particularly Alcian Blue/Alizarin Red staining, microcomputed tomography (μCT) scan and live staining of calcified tissue. In addition, we describe a method for decalcification of skeletal elements to ease sectioning.

Characterization of the developing axolotl nasal cavity supports multiple evolution of the vertebrate choana

All tetrapods (mammals, birds, reptiles, and amphibians) share the ability to breathe with their mouths closed due to the formation of choanae, which are openings that allow communication between the nasal and oral cavities. In most fishes, the nasal cavities serve a strictly olfactory function, possessing incurrent and excurrent nares that lie outside of the mouth and therefore, never communicate with the respiratory system. It is not until the evolution of tetrapods, in which the nasal cavities consistently open into the mouth, that they are used both for olfaction and for respiration. However, this developmental transition is poorly understood, with no consensus on the evolutionary origin of the choana in various groups despite decades of debate. Here, we use high-contrast 3D imaging in conjunction with histology and apoptotic cell analysis in non-mineralized embryonic tissues to study the formation of the choana in the axolotl (Ambystoma mexicanum), an aquatic salamander species. We show that the axolotl choana forms from an extension of the embryonic nasal sac, which pushes through intervening mesenchyme and connects with the palate epithelium of the oral cavity, eventually breaking through. This mechanism differs from caecilians, mammals and reptiles, where fusion across a bucconasal groove plays an active role in choana formation. Nevertheless, caecilians, mammals and axolotls converge on the development of a transient epithelial tissue that has to break down in order to develop a patent choana, adding another twist to the intriguing arguments on the evolutionary history of the choana.

Local mechanical stimuli correlate with tissue growth in axolotl salamander joint morphogenesis

Movement-induced forces are critical to correct joint formation, but it is unclear how cells sense and respond to these mechanical cues. To study the role of mechanical stimuli in the shaping of the joint, we combined experiments on regenerating axolotl (Ambystoma mexicanum) forelimbs with a poroelastic model of bone rudiment growth. Animals either regrew forelimbs normally (control) or were injected with a transient receptor potential vanilloid 4 (TRPV4) agonist during joint morphogenesis. We quantified growth and shape in regrown humeri from whole-mount light sheet fluorescence images of the regenerated limbs. Results revealed significant differences in morphology and cell proliferation between groups, indicating that TRPV4 desensitization has an effect on joint shape. To link TRPV4 desensitization with impaired mechanosensitivity, we developed a finite element model of a regenerating humerus. Local tissue growth was the sum of a biological contribution proportional to chondrocyte density, which was constant, and a mechanical contribution proportional to fluid pressure. Computational predictions of growth agreed with experimental outcomes of joint shape, suggesting that interstitial pressure driven from cyclic mechanical stimuli promotes local tissue growth. Predictive computational models informed by experimental findings allow us to explore potential physical mechanisms involved in tissue growth to advance our understanding of the mechanobiology of joint morphogenesis.

A constitutively expressed fluorescent ubiquitination-based cell-cycle indicator (FUCCI) in axolotls for studying tissue regeneration

Regulation of cell cycle progression is essential for cell proliferation during regeneration following injury. After appendage amputation, the axolotl (Ambystoma mexicanum) regenerates missing structures through an accumulation of proliferating cells known as the blastema. To study cell division during blastema growth, we generated a transgenic line of axolotls that ubiquitously expresses a bicistronic version of the fluorescent ubiquitination-based cell-cycle indicator (FUCCI). We demonstrate near-ubiquitous FUCCI expression in developing and adult tissues, and validate these expression patterns with DNA synthesis and mitosis phase markers. We demonstrate the utility of FUCCI for live and whole-mount imaging, showing the predominantly local contribution of cells during limb and tail regeneration. We also show that spinal cord amputation results in increased proliferation at least 5 mm from the site of injury. Finally, we use multimodal staining to provide cell type information for cycling cells by combining fluorescence in situ hybridization, EdU click-chemistry and immunohistochemistry on a single FUCCI tissue section. This new line of animals will be useful for studying cell cycle dynamics using in situ endpoint assays and in vivo imaging in developing and regenerating animals.

The MAPK Signaling Pathway Presents Novel Molecular Targets for Therapeutic Intervention after Traumatic Spinal Cord Injury: A Comparative Cross-Species Transcriptional Analysis

Despite the debilitating consequences following traumatic spinal cord injury (SCI), there is a lack of safe and effective therapeutics in the clinic. The species-specific responses to SCI present major challenges and opportunities for the clinical translation of biomolecular and pharmacological interventions. Recent transcriptional analyses in preclinical SCI studies have provided a snapshot of the local SCI-induced molecular responses in different animal models. However, the variation in the pathogenesis of traumatic SCI across species is yet to be explored. This study aims to identify and characterize the common and inconsistent SCI-induced differentially expressed genes across species to identify potential therapeutic targets of translational relevance. A comprehensive search of open-source transcriptome datasets identified four cross-compatible microarray experiments in rats, mice, and salamanders. We observed consistent expressional changes in extracellular matrix components across the species. Conversely, salamanders showed downregulation of intracellular MAPK signaling compared to rodents. Additionally, sequence conservation and interactome analyses highlighted the well-preserved sequences of Fn1 and Jun with extensive protein-protein interaction networks. Lastly, in vivo immunohistochemical staining for fibronectin was used to validate the observed expressional pattern. These transcriptional changes in extracellular and MAPK pathways present potential therapeutic targets for traumatic SCI with promising translational relevance.

Finding Solutions for Fibrosis: Understanding the Innate Mechanisms Used by Super-Regenerator Vertebrates to Combat Scarring

Soft tissue fibrosis and cutaneous scarring represent massive clinical burdens to millions of patients per year and the therapeutic options available are currently quite limited. Despite what is known about the process of fibrosis in mammals, novel approaches for combating fibrosis and scarring are necessary. It is hypothesized that scarring has evolved as a solution to maximize healing speed to reduce fluid loss and infection. This hypothesis, however, is complicated by regenerative animals, which have arguably the most remarkable healing abilities and are capable of scar-free healing. This review explores the differences observed between adult mammalian healing that typically results in fibrosis versus healing in regenerative animals that heal scarlessly. Each stage of wound healing is surveyed in depth from the perspective of many regenerative and fibrotic healers so as to identify the most important molecular and physiological variances along the way to disparate injury repair outcomes. Understanding how these powerful model systems accomplish the feat of scar-free healing may provide critical therapeutic approaches to the treatment or prevention of fibrosis.

Himalaquinones A-G, Angucyclinone-Derived Metabolites Produced by the Himalayan Isolate Streptomyces sp. PU-MM59

Himalaquinones A-G, seven new anthraquinone-derived metabolites, were obtained from the Himalayan-based Streptomyces sp. PU-MM59. The chemical structures of the new compounds were identified based on cumulative analyses of HRESIMS and NMR spectra. Himalaquinones A-F were determined to be unique anthraquinones that contained unusual C-4a 3-methylbut-3-enoic acid aromatic substitutions, while himalaquinone G was identified as a new 5,6-dihydrodiol-bearing angucyclinone. Comparative bioactivity assessment (antimicrobial, cancer cell line cytotoxicity, impact on 4E-BP1 phosphorylation, and effect on axolotl embryo tail regeneration) revealed cytotoxic landomycin and saquayamycin analogues to inhibit 4E-BP1p and inhibit regeneration. In contrast, himalaquinone G, while also cytotoxic and a regeneration inhibitor, did not affect 4E-BP1p status at the doses tested. As such, this work implicates a unique mechanism for himalaquinone G and possibly other 5,6-dihydrodiol-bearing angucyclinones.

Axolotls' and Mice's Oral-Maxillofacial Trephining Wounds Heal Differently

The Ambystoma maxicanum (axolotl) regenerates strikingly from wounds and amputations. Comparing its healing ability to non-regenerative species such as the mouse should help narrow in on mechanisms to improve human wound healing. Here, the tongue and intermandibular soft tissues of both mice (C57BL/6NCrl) and axolotls were wounded with a 2–2.5 mm punch biopsy. The study aimed to compare the differences between these 2 species following surgical resection with regard to the macroscopic and histological characteristics. These include wound closure times, epithelial wound sealing and thickness as well as acute immune marker myeloperoxidase (MPO) response over 30 days. Post surgery, mice visually showed greater haemorrhage; their wounds immediately collapsed while it took 14 days for the axolotls mandibular void to close. The epithelium sealed the axolotls’ wound margins within 24 h with a maximal mean thickness of 0.42 ± 0.13-fold normalized to unwounded skin. In mice, the epithelium separately sealed the ventral and dorsal sides, respectively at 7 and 7–30 days with mean maximal epithelial thicknesses reaching 13 ± 5.6 and 3.0 ± 0.63-fold. Mean MPO-positive cell values peaked in axolotls at 14 ± 1.5-fold between hours 6–12; while in mice, it peaked at 8.7 ± 0.9-fold between hours 24–96. We conclude that axolotls form smaller blood clots, have a faster and thinner epithelial cell migrating front, and a shorter MPO-positive cell response in comparison to mice. These observations may help refine future oral and facial wound-healing research and treatment.

Spatiotemporal control of cell cycle acceleration during axolotl spinal cord regeneration

Axolotls are uniquely able to resolve spinal cord injuries, but little is known about the mechanisms underlying spinal cord regeneration. We previously found that tail amputation leads to reactivation of a developmental-like program in spinal cord ependymal cells (Rodrigo Albors et al., 2015), characterized by a high-proliferation zone emerging 4 days post-amputation (Rost et al., 2016). What underlies this spatiotemporal pattern of cell proliferation, however, remained unknown. Here, we use modeling, tightly linked to experimental data, to demonstrate that this regenerative response is consistent with a signal that recruits ependymal cells during ~85 hours after amputation within ~830 μm of the injury. We adapted Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) technology to axolotls (AxFUCCI) to visualize cell cycles in vivo. AxFUCCI axolotls confirmed the predicted appearance time and size of the injury-induced recruitment zone and revealed cell cycle synchrony between ependymal cells. Our modeling and imaging move us closer to understanding bona fide spinal cord regeneration.

ECM-mediated positional cues are able to induce pattern, but not new positional information, during axolotl limb regeneration

The Mexican Axolotl is able to regenerate missing limb structures in any position along the limb axis throughout its life and serves as an excellent model to understand the basic mechanisms of endogenous regeneration. How the new pattern of the regenerating axolotl limb is established has not been completely resolved. An accumulating body of evidence indicates that pattern formation occurs in a hierarchical fashion, which consists of two different types of positional communications. The first type (Type 1) of communication occurs between connective tissue cells, which retain memory of their original pattern information and use this memory to generate the pattern of the regenerate. The second type (Type 2) of communication occurs from connective tissue cells to other cell types in the regenerate, which don’t retain positional memory themselves and arrange themselves according to these positional cues. Previous studies suggest that molecules within the extracellular matrix (ECM) participate in pattern formation in developing and regenerating limbs. However, it is unclear whether these molecules play a role in Type 1 or Type 2 positional communications. Utilizing the Accessory Limb Model, a regenerative assay, and transcriptomic analyses in regenerates that have been reprogrammed by treatment with Retinoic Acid, our data indicates that the ECM likely facilities Type-2 positional communications during limb regeneration.

Surface contraction waves or cell proliferation waves in the presumptive neurectoderm during amphibian gastrulation: Mexican axolotl versus African clawed frog

This essay represents a critical analysis of the literary data on various types of waves occurring in the amphibian embryos during gastrulation. A surface contraction wave travels through the presumptive neurectoderm during Mexican axolotl gastrulation. This wave coincides temporally and spatially with involution of the inducing chordomesoderm and with the prospective neural plate. By contrast, there is no similar surface contraction wave during African clawed frog gastrulation. However, the clawed frog displays the waves of DNA synthesis and mitosis in the presumptive neurectoderm during gastrulation, whereas no such waves were discovered in axolotl gastrulae. These sets of experimental data are in accordance with the contemporary concept of considerable ontogenetic diversity of the class Amphibia.

Zinc protection of fertilized eggs is an ancient feature of sexual reproduction in animals

One of the earliest and most prevalent barriers to successful reproduction is polyspermy, or fertilization of an egg by multiple sperm. To prevent these supernumerary fertilizations, eggs have evolved multiple mechanisms. It has recently been proposed that zinc released by mammalian eggs at fertilization may block additional sperm from entering. Here, we demonstrate that eggs from amphibia and teleost fish also release zinc. Using Xenopus laevis as a model, we document that zinc reversibly blocks fertilization. Finally, we demonstrate that extracellular zinc similarly disrupts early embryonic development in eggs from diverse phyla, including Cnidaria, Echinodermata, and Chordata. Our study reveals that a fundamental strategy protecting human eggs from fertilization by multiple sperm may have evolved more than 650 million years ago.

Lag penalized weighted correlation for time series clustering

BACKGROUND

The similarity or distance measure used for clustering can generate intuitive and interpretable clusters when it is tailored to the unique characteristics of the data. In time series datasets generated with high-throughput biological assays, measurements such as gene expression levels or protein phosphorylation intensities are collected sequentially over time, and the similarity score should capture this special temporal structure.

RESULTS

We propose a clustering similarity measure called Lag Penalized Weighted Correlation (LPWC) to group pairs of time series that exhibit closely-related behaviors over time, even if the timing is not perfectly synchronized. LPWC aligns time series profiles to identify common temporal patterns. It down-weights aligned profiles based on the length of the temporal lags that are introduced. We demonstrate the advantages of LPWC versus existing time series and general clustering algorithms. In a simulated dataset based on the biologically-motivated impulse model, LPWC is the only method to recover the true clusters for almost all simulated genes. LPWC also identifies clusters with distinct temporal patterns in our yeast osmotic stress response and axolotl limb regeneration case studies.

CONCLUSIONS

LPWC achieves both of its time series clustering goals. It groups time series with correlated changes over time, even if those patterns occur earlier or later in some of the time series. In addition, it refrains from introducing large shifts in time when searching for temporal patterns by applying a lag penalty. The LPWC R package is available at https://github.com/gitter-lab/LPWC and CRAN under a MIT license.

The axolotl model for cancer research: a mini-review

Gastric cancer is the sixth most common cancer worldwide with increased associated morbidity and mortality. Although a multimodality treatment approach is necessary, surgery is still considered as the standard of care. There is a longstanding intercontinental debate between Eastern and Western upper GI surgeons in regards to the proper type of lymphadenectomy that should accompany the resection of the primary tumor. While D2 gastrectomy was performed as the standard procedure in eastern countries, the increased morbidity and mortality attributed initially to the D2 lymphadenectomy by the Medical Research Council (MRC), the Dutch and the Italian randomized control trial without respective survival benefits had led Western surgeons towards a more limited lymphadenectomy. Only 15 years after the conclusion of its accrual, the Dutch trial reported a significant decrease in recurrence rate after D2 procedure and attributed the D2-associated morbidity and mortality to the spleno-pancreatectomy that was routinely performed in the D2 arm of the study. As the D2 lymphadenectomy can be safely and adequately performed while preserving the spleen and/or the pancreas, it has been suggested as the recommended procedure for patients with resectable gastric cancer.

Direct Gene Knock-out of Axolotl Spinal Cord Neural Stem Cells via Electroporation of CAS9 Protein-gRNA Complexes

The axolotl has the unique ability to fully regenerate its spinal cord. This is largely due to the ependymal cells remaining as neural stem cells (NSCs) throughout life, which proliferate to reform the ependymal tube and differentiate into lost neurons after spinal cord injury. Deciphering how these NSCs retain pluripotency post-development and proliferate upon spinal cord injury to reform the exact pre-injury structure can provide valuable insight into how mammalian spinal cords may regenerate as well as potential treatment options. Performing gene knock-outs in specific subsets of NSCs within a restricted time period will allow study of the molecular mechanisms behind these regenerative processes, without being confounded by development perturbing effects. Described here is a method to perform gene knock-out in axolotl spinal cord NSCs using the CRISPR-Cas9 system. By injecting the CAS9-gRNA complex into the spinal cord central canal followed by electroporation, target genes are knocked out in NSCs within specific regions of the spinal cord at a desired timepoint, allowing for molecular studies of spinal cord NSCs during regeneration.

Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration

Amputation of the axolotl forelimb results in the formation of a blastema, a transient tissue where progenitor cells accumulate prior to limb regeneration. However, the molecular understanding of blastema formation had previously been hampered by the inability to identify and isolate blastema precursor cells in the adult tissue. We have used a combination of Cre-loxP reporter lineage tracking and single-cell messenger RNA sequencing (scRNA-seq) to molecularly track mature connective tissue (CT) cell heterogeneity and its transition to a limb blastema state. We have uncovered a multiphasic molecular program where CT cell types found in the uninjured adult limb revert to a relatively homogenous progenitor state that recapitulates an embryonic limb bud-like phenotype including multipotency within the CT lineage. Together, our data illuminate molecular and cellular reprogramming during complex organ regeneration in a vertebrate.

Buoyancy disorders in pet axolotls Ambystoma mexicanum: three cases

As far as we are aware, there are no previous reports on the pathologic conditions of buoyancy disorders in Ambystoma mexicanum. Herein, we describe various clinical test results, clinical outcomes, and the pathological findings of an experimental pneumonectomy procedure in 3 A. mexicanum exhibiting abnormal buoyancy. The 3 pet A. mexicanum were adults, and their respective ages and body weights were 1, 5, and 6 yr and 48, 55, and 56 g. Two of these cases were confirmed via radiographic examination to have free air within the body cavity, and all 3 cases were found via ultrasonography to have an acoustic shadow within the body cavity and were diagnosed with pneumocoelom. Lung perforations were detected macroscopically in 2 of the cases, and all 3 cases had fibrosis in the caudal ends of the lungs. Removal of the lung lesions eliminated the abnormal buoyancy in all 3 cases. We concluded that air had leaked into the body cavity from the lungs, and we propose that lung lesions are an important cause of buoyancy disorders in A. mexicanum.

A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors

Mammals have extremely limited regenerative capabilities; however, axolotls are profoundly regenerative and can replace entire limbs. The mechanisms underlying limb regeneration remain poorly understood, partly because the enormous and incompletely sequenced genomes of axolotls have hindered the study of genes facilitating regeneration. We assembled and annotated a de novo transcriptome using RNA-sequencing profiles for a broad spectrum of tissues that is estimated to have near-complete sequence information for 88% of axolotl genes. We devised expression analyses that identified the axolotl orthologs of cirbp and kazald1 as highly expressed and enriched in blastemas. Using morpholino anti-sense oligonucleotides, we find evidence that cirbp plays a cytoprotective role during limb regeneration whereas manipulation of kazald1 expression disrupts regeneration. Our transcriptome and annotation resources greatly complement previous transcriptomic studies and will be a valuable resource for future research in regenerative biology.

A new and improved algorithm for the quantification of chromatin condensation from microscopic data shows decreased chromatin condensation in regenerating axolotl limb cells

The nuclear landscape plays an important role in the regulation of tissue and positional specific genes in embryonic and developing cells. Changes in this landscape can be dynamic, and are associated with the differentiation of cells during embryogenesis, and the de-differentiation of cells during induced pluripotent stem cell (iPSC) formation and in many cancers. However, tools to quantitatively characterize these changes are limited, especially in the in vivo context, where numerous tissue types are present and cells are arranged in multiple layers. Previous tools have been optimized for the monolayer nature of cultured cells. Therefore, we present a new algorithm to quantify the condensation of chromatin in two in vivo systems. We first developed this algorithm to quantify changes in chromatin compaction and validated it in differentiating spermatids in zebrafish testes. Our algorithm successfully detected the typical increase in chromatin compaction as these cells differentiate. We then employed the algorithm to quantify the changes that occur in amphibian limb cells as they participate in a regenerative response. We observed that the chromatin in the limb cells de-compacts as they contribute to the regenerating organ. We present this new tool as an open sourced software that can be readily accessed and optimized to quantify chromatin compaction in complex multi-layered samples.

Methylene Blue Assay for Estimation of Regenerative Re-Epithelialization In Vivo

The rapidity with which epithelial cells cover a wound surface helps determine whether scarring or scar-less healing results. As methylene blue is a vital dye that is absorbed by damaged tissue but not undamaged epidermis, it can be used to assess wound closure. We sought to develop a quantitative methylene blue exclusion assay to estimate the timeframe for re-epithelialization in regenerating appendages in zebrafish and axolotls, two classic model systems of regeneration. Following application of methylene blue to the amputation plane and extensive washing, the regenerating tail was imaged in vivo until staining was no longer visible. The percent area of the amputation plane positive for methylene blue, representing the area of the amputation plane not yet re-epithelialized, was measured for each time point. The loss of methylene blue occurred rapidly, within ~2.5 h in larval and juvenile axolotls and <1 h in adult zebrafish, consistent with high rates of re-epithelialization in these models of regeneration. The assay allows simple, rapid estimation of the time course for regenerative re-epithelialization without affecting subsequent regenerative ability. This technique will permit comparison of re-epithelialization across different strains and stages, as well as under the influence of various pharmacological inhibitors that affect regeneration.

The organelle of differentiation in embryos: the cell state splitter

The cell state splitter is a membraneless organelle at the apical end of each epithelial cell in a developing embryo. It consists of a microfilament ring and an intermediate filament ring subtending a microtubule mat. The microtubules and microfilament ring are in mechanical opposition as in a tensegrity structure. The cell state splitter is bistable, perturbations causing it to contract or expand radially. The intermediate filament ring provides metastability against small perturbations. Once this snap-through organelle is triggered, it initiates signal transduction to the nucleus, which changes gene expression in one of two readied manners, causing its cell to undergo a step of determination and subsequent differentiation. The cell state splitter also triggers the cell state splitters of adjacent cells to respond, resulting in a differentiation wave. Embryogenesis may be represented then as a bifurcating differentiation tree, each edge representing one cell type. In combination with the differentiation waves they propagate, cell state splitters explain the spatiotemporal course of differentiation in the developing embryo. This review is excerpted from and elaborates on "Embryogenesis Explained" (World Scientific Publishing, Singapore, 2016).

Regulation of Axolotl (Ambystoma mexicanum) Limb Blastema Cell Proliferation by Nerves and BMP2 in Organotypic Slice Culture

We have modified and optimized the technique of organotypic slice culture in order to study the mechanisms regulating growth and pattern formation in regenerating axolotl limb blastemas. Blastema cells maintain many of the behaviors that are characteristic of blastemas in vivo when cultured as slices in vitro, including rates of proliferation that are comparable to what has been reported in vivo. Because the blastema slices can be cultured in basal medium without fetal bovine serum, it was possible to test the response of blastema cells to signaling molecules present in serum, as well as those produced by nerves. We also were able to investigate the response of blastema cells to experimentally regulated changes in BMP signaling. Blastema cells responded to all of these signals by increasing the rate of proliferation and the level of expression of the blastema marker gene, Prrx-1. The organotypic slice culture model provides the opportunity to identify and characterize the spatial and temporal co-regulation of pathways in order to induce and enhance a regenerative response.

High-efficiency electroporation of the spinal cord in larval axolotl

Axolotls are well known for their remarkable ability to regenerate complex body parts and structures throughout life, including the entire limb and tail. Particularly fascinating is their ability to regenerate a fully functional spinal cord after losing the tail. Electroporation of DNA plasmids or morpholinos is a valuable tool to gain mechanistic insight into the cellular and molecular basis of regeneration. It provides among other advantages a simple and fast method to test gene function in a temporally and spatially controlled manner. Some classic drawbacks of the method, such as low transfection efficiency and damage to the tissue, had hindered our understanding of the contribution of different signaling pathways to regeneration. Here, we describe a comprehensive protocol for electroporation of the axolotl spinal cord that overcomes this limitations using a combination of high-voltage and short-length pulses followed by lower-voltage and longer-length pulses. Our approach yields highly efficient transfection of spinal cord cells with minimal tissue damage, which now allows the molecular dissection of spinal cord regeneration.

[On the classification of the cleavage patterns in amphibian embryos]

This paper presents a brief survey and preliminary classification of embryonic cleavage patterns in the class Amphibia. We use published data on 41 anuran and 22 urodele species concerning the character of the third cleavage furrow (latitudinal or longitudinal) and the stage of transition from synchronous to asynchronous blastomere divisions in the animal hemisphere (4-8-celled stage, 8-16-celled stage or later). Based on this, four patterns of amphibian embryonic cleavage are recognized, and an attempt to elucidate the evolutionary relationships among these patterns is undertaken. The so-called "standard" cleavage pattern (the extensive series of synchronous blastomere divisions including latitudinal furrows of the third cleavage) with the typical model species Ambystoma mexicanum and Xenopus laevis seems to be derived and probably originated independently in the orders Anura and Caudata. The ancestral amphibian cleavage pattern seems to be represented by species with longitudinal furrows of the third cleavage and the loss ofsynchrony as early as the 8-celled stage (such as in primitive urodele species from the family Cryptobranchidae).

Positional information is reprogrammed in blastema cells of the regenerating limb of the axolotl (Ambystoma mexicanum)

The regenerating region of an amputated salamander limb, known as the blastema, has the amazing capacity to replace exactly the missing structures. By grafting cells from different stages and regions of blastemas induced to form on donor animals expressing Green Fluorescent Protein (GFP), to non-GFP host animals, we have determined that the cells from early stage blastemas, as well as cells at the tip of late stage blastemas are developmentally labile such that their positional identity is reprogrammed by interactions with more proximal cells with stable positional information. In contrast, cells from the adjacent, more proximal stump tissues as well as the basal region of late bud blastemas are positionally stable, and thus form ectopic limb structures when grafted. Finally, we have found that a nerve is required to maintain the blastema cells in a positionally labile state, thus indicating a role for reprogramming cues in the blastema microenvironment.

Comparative transcriptional profiling of the axolotl limb identifies a tripartite regeneration-specific gene program

Understanding how the limb blastema is established after the initial wound healing response is an important aspect of regeneration research. Here we performed parallel expression profile time courses of healing lateral wounds versus amputated limbs in axolotl. This comparison between wound healing and regeneration allowed us to identify amputation-specific genes. By clustering the expression profiles of these samples, we could detect three distinguishable phases of gene expression - early wound healing followed by a transition-phase leading to establishment of the limb development program, which correspond to the three phases of limb regeneration that had been defined by morphological criteria. By focusing on the transition-phase, we identified 93 strictly amputation-associated genes many of which are implicated in oxidative-stress response, chromatin modification, epithelial development or limb development. We further classified the genes based on whether they were or were not significantly expressed in the developing limb bud. The specific localization of 53 selected candidates within the blastema was investigated by in situ hybridization. In summary, we identified a set of genes that are expressed specifically during regeneration and are therefore, likely candidates for the regulation of blastema formation.

Skin regeneration in adult axolotls: a blueprint for scar-free healing in vertebrates

While considerable progress has been made towards understanding the complex processes and pathways that regulate human wound healing, regenerative medicine has been unable to develop therapies that coax the natural wound environment to heal scar-free. The inability to induce perfect skin regeneration stems partly from our limited understanding of how scar-free healing occurs in a natural setting. Here we have investigated the wound repair process in adult axolotls and demonstrate that they are capable of perfectly repairing full thickness excisional wounds made on the flank. In the context of mammalian wound repair, our findings reveal a substantial reduction in hemostasis, reduced neutrophil infiltration and a relatively long delay in production of new extracellular matrix (ECM) during scar-free healing. Additionally, we test the hypothesis that metamorphosis leads to scarring and instead show that terrestrial axolotls also heal scar-free, albeit at a slower rate. Analysis of newly forming dermal ECM suggests that low levels of fibronectin and high levels of tenascin-C promote regeneration in lieu of scarring. Lastly, a genetic analysis during wound healing comparing epidermis between aquatic and terrestrial axolotls suggests that matrix metalloproteinases may regulate the fibrotic response. Our findings outline a blueprint to understand the cellular and molecular mechanisms coordinating scar-free healing that will be useful towards elucidating new regenerative therapies targeting fibrosis and wound repair.

Reconstitution of the central nervous system during salamander tail regeneration from the implanted neurospheres

Urodele amphibians such as axolotl are well known for their regenerative potential of the damaged central nervous system structures. Upon tail amputation, neural stem cells behind the amputation plane undergo self-renewing divisions and contribute to the functional spinal cord in the newly formed regenerate. The neural stem cells, harboring this potential, can be isolated from the animal and cultured under the suspension conditions. After 2-3 weeks in vitro they will proliferate and form the floating aggregates of the spherical shape, so-called neurospheres. Reimplanted back into the animal, the neurospheres can efficiently integrate in the spinal cord lesion and contribute to the following spinal cord regeneration events. Here we demonstrate the unique method of the axolotl tail spinal cord regeneration from the implanted neurosphere.

The yeast two hybrid system in a screen for proteins interacting with axolotl (Ambystoma mexicanum) Msx1 during early limb regeneration

Urodele amphibians are exceptional in their ability to regenerate complex body structures such as limbs. Limb regeneration depends on a process called dedifferentiation. Under an inductive wound epidermis terminally differentiated cells transform to pluripotent progenitor cells that coordinately proliferate and eventually redifferentiate to form the new appendage. Recent studies have developed molecular models integrating a set of genes that might have important functions in the control of regenerative cellular plasticity. Among them is Msx1, which induced dedifferentiation in mammalian myotubes in vitro. Herein, we screened for interaction partners of axolotl Msx1 using a yeast two hybrid system. A two hybrid cDNA library of 5-day-old wound epidermis and underlying tissue containing more than 2×10⁶ cDNAs was constructed and used in the screen. 34 resulting cDNA clones were isolated and sequenced. We then compared sequences of the isolated clones to annotated EST contigs of the Salamander EST database (BLASTn) to identify presumptive orthologs. We subsequently searched all no-hit clone sequences against non redundant NCBI sequence databases using BLASTx. It is the first time, that the yeast two hybrid system was adapted to the axolotl animal model and successfully used in a screen for proteins interacting with Msx1 in the context of amphibian limb regeneration.

Highly restricted diversity of TCR delta chains of the amphibian Mexican axolotl (Ambystoma mexicanum) in peripheral tissues

Gammadelta T cells localize at mammalian epithelial surfaces to exert both protective and regulatory roles in response to infections. We have previously characterized the Mexican axolotl (Ambystoma mexicanum) T cell receptor delta (TRD) chain. In this study, TRD repertoires in spleen, liver, intestine and skin from larvae, pre-adult and adult axolotls were examined and compared to the thymic TRD repertoire. A TRDV transcript without N/D diversity, TRDV1S1-TRDJ1, dominates the TRD repertoires until sexual maturation. In adult tissues, this canonical transcript is replaced by another dominant TRDV1S1-TRDJ1 transcript. In the thymus, these two transcripts are detected early in development. Our results suggest that gammadelta T cells that express the canonical TRDV1S1-TRDJ1 transcript emerge from the thymus and colonize the peripheral tissues, where they are selectively expanded by recurrent ligands. This particular situation is probably related to the neotenic state and the slow development of the axolotl. In thymectomized axolotls, TRD repertoires appear different from those of normal axolotls, suggesting that extrathymic gammadelta T cell differentiation could occur. Gene expression analysis showed the importance of the gut in T cell development.

Preparation of cultured myofibers from larval salamander limbs for cellular plasticity studies

Identification of the mechanisms underlying cellular plasticity in salamander cells is important because these may give pointers to the restricted regenerative ability of mammals. The myofibers from salamanders are remarkable for their ability to undergo cellularization and cell-cycle re-entry during regeneration. Here, we describe a detailed method for the isolation and culture of larval salamander myofibers in numbers suitable for cellular plasticity studies. The basic protocol for isolation and purification of cells can be completed in 4 h.

Inhibition of Sonic hedgehog signaling leads to posterior digit loss in Ambystoma mexicanum: parallels to natural digit reduction in urodeles

Molecular mechanisms patterning the tetrapod limb, including anterior-posterior axis determination involving Sonic hedgehog (Shh), have received much attention, particularly in amniotes. Anterior-posterior patterning in urodele amphibians differs radically from that of amniotes in that it shows a pronounced anterior-to-posterior sequence of digit development. In contrast, amniotes develop their digits almost simultaneously with a slight posterior-to-anterior polarity. Here we use cyclopamine, an inhibitor of the Hedgehog signaling pathway, to investigate the role of Shh in anterior-posterior patterning in the urodele limb. Inhibition of Shh signal transduction affects digit number long before their morphological appearance. In accordance with the apparently derived order of digit development in urodeles, exposure reproducibly removes digits in a posterior-to-anterior sequence, the inverse of their developmental sequence. This pattern of digit loss mimics the order of digit loss in natural variation. We suggest that variation in Shh expression and/or signal transmission may explain natural variation in digit number in urodeles.

Measurement of in vivo stress resultants in neurulation-stage amphibian embryos

In order to obtain the first quantitative measurements of the in vivo stresses in early-stage amphibian embryos, we developed a novel instrument that uses a pair of parallel wires that are glued to the surface of an embryo normal to the direction in which the stress is to be determined. When a slit is made parallel to the wires and between them, tension in the surrounding tissue causes the slit to open. Under computer control, one of the wires is moved so as to restore the original wire spacing, and the steady-state closure force is determined from the degree of wire flexure. A cell-level finite element model is used to convert the wire bending force to an in-plane stress since the wire force is not proportional to the slit length. The device was used to measure stress resultants (force carried per unit of slit length) on the dorsal, ventral and lateral aspects of neurulation-stage axolotl (Ambystoma mexicanum) embryos. The resultants were anisotropic and varied with location and developmental stage, with values ranging from -0.17 mN/m to 1.92 mN/m. In general, the resultants could be decomposed into patterns associated with internal pressure in the embryo, bending of the embryo along its mid-sagittal plane and neural tube closure. The patterns of stress revealed by the experiments support a number of current theories about the mechanics of neurulation.

Do lamellipodia have the mechanical capacity to drive convergent extension?

Convergent extension (CE), a kinematic motif associated with several important morphogenetic movements in embryos, entails narrowing of a tissue in one in-plane direction and elongation in the other. Although the cell elongation and intercalation which accompany this process have been investigated and relevant genes and biochemical pathways have been studied in multiple organisms, a fundamental question that has not yet been answered is "Do the lamellipodia thought to drive these motions actually have the mechanical capacity to do so?" Here, we address this and a number of related issues using a state-of-the-art computational model which can replicate cell motions, changes in cell shape and tissue deformations. The model is based on the cell-level finite element approach of Chen and Brodland, but has additional features which allow it to model lamellipodium formation and contraction. In studying CE, computational models provide an important complement to molecular approaches because they reveal the "mechanical pathways" through which gene products must ultimately act in order to produce physical movements. The model shows that lamellipodia can drive CE, that they do so through cell intercalations and that the elongated cells characteristic of CE arise only when adjacent tissues resist convergence, a result which we confirm experimentally.