Salamander Insights Into Ageing and Rejuvenation

Biomarkers of aging: from molecules and surrogates to physiology and function

Many countries face an unprecedented challenge in aging demographics. This has led to an exponential growth in research on aging, which, coupled to a massive financial influx of funding in the private and public sectors, has resulted in seminal insights into the underpinnings of this biological process. However, critical validation in humans has been hampered by the limited translatability of results obtained in model organisms, additionally confined by the need for extremely time-consuming clinical studies in the ostensible absence of robust biomarkers that would allow monitoring in shorter time frames. In the future, molecular parameters might hold great promise in this regard. In contrast, biomarkers centered on function, resilience, and frailty are available at the present time, with proven predictive value for morbidity and mortality. In this review, the current knowledge of molecular and physiological aspects of human aging, potential antiaging strategies, and the basis, evidence, and potential application of physiological biomarkers in human aging are discussed.

Recent Advances in Anti-Aging Therapeutic Strategies Targeting DNA Damage Response and Senescence-Associated Secretory Phenotype-Linked Signaling Cascade

Aging is considered the contributory accumulation of abruptions occurring through cell signaling cascades, which ultimately cause changes in physical functions, cell fate, and damage across all organ systems. DNA damage response (DDR) also occurs through telomere shortening, tumor formation, mitochondrial dysfunction, and so forth. Cellular aging occurs through cell cycle arrest, which is the result of extended DDR cascade signaling networks via MDC1, 53BP1, H2AX, ATM, ARF, P53, P13-Akt, BRAF, Sirtuins, NAD + , and so forth. These persistent cell cycle arrests initiated by DDR and other associated stress-induced signals promote a permanent state of cell cycle arrest called senescence-associated secretory phenotype (SASP). However, cellular aging gets accelerated with faulty DNA repair systems, and the produced senescent cells further generate various promoting contributors to age-related dysfunctional diseases including SASP. Any changes to these factors contribute to age-related disease development. Therefore, this review explores anti-aging factors targeting DDR and SASP regulation and their detailed signaling networks. In addition, it allows researchers to identify anti-aging targets and anti-aging therapeutic strategies based on identified and nonidentified targets.

Investigating Neotenic and Metamorphic Axolotl Brain Complexity: A Stereological and Immunohistochemical Perspective

The ability of certain tetrapods, such as amphibians, to regenerate complex structures, such as organs or limbs, is well-established, though this capacity varies significantly across species, with humans exhibiting limited regenerative potential. Ependymoglia cells in the ventricular region of the brain are known to exhibit proliferative properties during homeostasis and damage and to perform stem cell functions. This study investigated changes occurring in neurons and glia in the central nervous system following metamorphosis in axolotls. Morphological alterations in brain tissue, newly formed neurons, and cellular organizations in different brain regions were assessed using stereological and immunohistochemical methods, as well as light and electron microscopy. Interestingly, we observe no statistically significant difference in total neuron numbers in the telencephalon region between neotenic and metamorphic axolotls. However, the proliferation index and the numbers of cells expressing NeuN were significantly higher in metamorphic axolotls. Furthermore, structural changes in neuronal nuclei and myelin sheath organization were determined at the light and electron microscopic levels post-metamorphosis. Ultrastructural analyses revealed a change in chromatin organization from euchromatic to heterochromatic in neurons after metamorphosis, and morphological changes were also demonstrated in myelinated nerve fibers in the telencephalon. Additionally, mucopolysaccharide-containing secretory sacs were also identified on the apical surfaces of a subgroup of ependymoglia cells located in the lateral ventricle wall. Overall, this study sheds useful light on the intricate changes occurring in the central nervous system during metamorphosis in axolotls and provides valuable insights into the mechanisms underlying these processes.

Emerging insights in senescence: pathways from preclinical models to therapeutic innovations

Senescence is a crucial hallmark of ageing and a significant contributor to the pathology of age-related disorders. As committee members of the young International Cell Senescence Association (yICSA), we aim to synthesise recent advancements in the identification, characterisation, and therapeutic targeting of senescence for clinical translation. We explore novel molecular techniques that have enhanced our understanding of senescent cell heterogeneity and their roles in tissue regeneration and pathology. Additionally, we delve into in vivo models of senescence, both non-mammalian and mammalian, to highlight tools available for advancing the contextual understanding of in vivo senescence. Furthermore, we discuss innovative diagnostic tools and senotherapeutic approaches, emphasising their potential for clinical application. Future directions of senescence research are explored, underscoring the need for precise, context-specific senescence classification and the integration of advanced technologies such as machine learning, long-read sequencing, and multifunctional senoprobes and senolytics. The dual role of senescence in promoting tissue homoeostasis and contributing to chronic diseases highlights the complexity of targeting these cells for improved clinical outcomes.

Genomic Gigantism is not Associated with Reduced Selection Efficiency in Neotropical Salamanders

Genome size variation in eukaryotes has myriad effects on organismal biology from the genomic to whole-organism level. Large genome size may be associated with lower selection efficiency because lower effective population sizes allow fixation of deleterious mutations via genetic drift, increasing genome size and decreasing selection efficiency. Because of a hypothesized negative relationship between genome size and recombination rate per base pair, increased genome size could also increase the effect of linked selection in the genome, decreasing the efficiency with which natural selection can fix or remove mutations. We used a transcriptomic dataset of 15 and a subset of six Neotropical salamander species ranging in genome size from 12 to 87 pg to study the relationship between genome size and efficiency of selection. We estimated dN/dS of salamanders with small and large genomes and tested for relaxation of selection in the larger genomes. Contrary to our expectations, we did not find a significant relationship between genome size and selection efficiency or strong evidence for higher dN/dS values in species with larger genomes for either species set. We also found little evidence for relaxation of selection in species with larger genomes. A positive correlation between genome size and range size (a proxy of population size) in this group disagrees with predictions of stronger drift in species with larger genomes. Our results highlight the complex interactions between the many forces shaping genomic variation in organisms with genomic gigantism.

Aging as a loss of morphostatic information: A developmental bioelectricity perspective

Maintaining order at the tissue level is crucial throughout the lifespan, as failure can lead to cancer and an accumulation of molecular and cellular disorders. Perhaps, the most consistent and pervasive result of these failures is aging, which is characterized by the progressive loss of function and decline in the ability to maintain anatomical homeostasis and reproduce. This leads to organ malfunction, diseases, and ultimately death. The traditional understanding of aging is that it is caused by the accumulation of molecular and cellular damage. In this article, we propose a complementary view of aging from the perspective of endogenous bioelectricity which has not yet been integrated into aging research. We propose a view of aging as a morphostasis defect, a loss of biophysical prepattern information, encoding anatomical setpoints used for dynamic tissue and organ homeostasis. We hypothesize that this is specifically driven by abrogation of the endogenous bioelectric signaling that normally harnesses individual cell behaviors toward the creation and upkeep of complex multicellular structures in vivo. Herein, we first describe bioelectricity as the physiological software of life, and then identify and discuss the links between bioelectricity and life extension strategies and age-related diseases. We develop a bridge between aging and regeneration via bioelectric signaling that suggests a research program for healthful longevity via morphoceuticals. Finally, we discuss the broader implications of the homologies between development, aging, cancer and regeneration and how morphoceuticals can be developed for aging.

Polyphenism predicts actuarial senescence and lifespan in tiger salamanders

Actuarial senescence (called 'senescence' hereafter) often shows broad variation at the intraspecific level. Phenotypic plasticity likely plays a central role in among-individual heterogeneity in senescence rate (i.e. the rate of increase in mortality with age), although our knowledge on this subject is still very fragmentary. Polyphenism-the unique sub-type of phenotypic plasticity where several discrete phenotypes are produced by the same genotype-may provide excellent study systems to investigate if and how plasticity affects the rate of senescence in nature. In this study, we investigated whether facultative paedomorphosis influences the rate of senescence in a salamander, Ambystoma mavortium nebulosum. Facultative paedomorphosis, a unique form of polyphenism found in dozens of urodele species worldwide, leads to the production of two discrete, environmentally induced phenotypes: metamorphic and paedomorphic individuals. We leveraged an extensive set of capture-recapture data (8948 individuals, 24 years of monitoring) that were analysed using multistate capture-recapture models and Bayesian age-dependent survival models. Multistate models revealed that paedomorphosis was the most common developmental pathway used by salamanders in our study system. Bayesian age-dependent survival models then showed that paedomorphs have accelerated senescence in both sexes and shorter adult lifespan (in females only) compared to metamorphs. In paedomorphs, senescence rate and adult lifespan also varied among ponds and individuals. Females with good body condition and high lifetime reproductive success had slower senescence and longer lifespan. Late-breeding females also lived longer but showed a senescence rate similar to that of early-breeding females. Moreover, males with good condition had longer lifespan than males with poor body condition, although they had similar senescence rates. In addition, late-breeding males lived longer but, unexpectedly, had higher senescence than early-breeding males. Overall, our work provides one of the few empirical cases suggesting that environmentally cued polyphenism could affect the senescence of a vertebrate in nature, thus providing insights on the ecological and evolutionary consequences of developmental plasticity on ageing.

Molecular Signatures Integral to Natural Reprogramming in the Pigment Epithelium Cells after Retinal Detachment in Pleurodeles waltl

The reprogramming of retinal pigment epithelium (RPE) cells into retinal cells (transdifferentiation) lies in the bases of retinal regeneration in several Urodela. The identification of the key genes involved in this process helps with looking for approaches to the prevention and treatment of RPE-related degenerative diseases of the human retina. The purpose of our study was to examine the transcriptome changes at initial stages of RPE cell reprogramming in adult newt Pleurodeles waltl. RPE was isolated from the eye samples of day 0, 4, and 7 after experimental surgical detachment of the neural retina and was used for a de novo transcriptome assembly through the RNA-Seq method. A total of 1019 transcripts corresponding to the differently expressed genes have been revealed in silico: the 83 increased the expression at an early stage, and 168 increased the expression at a late stage of RPE reprogramming. We have identified up-regulation of classical early response genes, chaperones and co-chaperones, genes involved in the regulation of protein biosynthesis, suppressors of oncogenes, and EMT-related genes. We revealed the growth in the proportion of down-regulated ribosomal and translation-associated genes. Our findings contribute to revealing the molecular mechanism of RPE reprogramming in Urodela.

Evolutionary Insights into the Relationship of Frogs, Salamanders, and Caecilians and Their Adaptive Traits, with an Emphasis on Salamander Regeneration and Longevity

The extant amphibians have developed uncanny abilities to adapt to their environment. I compared the genes of amphibians to those of other vertebrates to investigate the genetic changes underlying their unique traits, especially salamanders' regeneration and longevity. Using the well-supported Batrachia tree, I found that salamander genomes have undergone accelerated adaptive evolution, especially for development-related genes. The group-based comparison showed that several genes are under positive selection, rapid evolution, and unexpected parallel evolution with traits shared by distantly related species, such as the tail-regenerative lizard and the longer-lived naked mole rat. The genes, such as EEF1E1, PAFAH1B1, and OGFR, may be involved in salamander regeneration, as they are involved in the apoptotic process, blastema formation, and cell proliferation, respectively. The genes PCNA and SIRT1 may be involved in extending lifespan, as they are involved in DNA repair and histone modification, respectively. Some genes, such as PCNA and OGFR, have dual roles in regeneration and aging, which suggests that these two processes are interconnected. My experiment validated the time course differential expression pattern of SERPINI1 and OGFR, two genes that have evolved in parallel in salamanders and lizards during the regeneration process of salamander limbs. In addition, I found several candidate genes responsible for frogs' frequent vocalization and caecilians' degenerative vision. This study provides much-needed insights into the processes of regeneration and aging, and the discovery of the critical genes paves the way for further functional analysis, which could open up new avenues for exploiting the genetic potential of humans and improving human well-being.

Kimura's Theory of Non-Adaptive Radiation and Peto's Paradox: A Missing Link?

Karyotype diversity reflects genome integrity and stability. A strong correlation between karyotype diversity and species richness, meaning the number of species in a phylogenetic clade, was first reported in mammals over forty years ago: in mammalian phylogenetic clades, the standard deviation of karyotype diversity (KD) closely corresponded to species richness (SR) at the order level. These initial studies, however, did not control for phylogenetic signal, raising the possibility that the correlation was due to phylogenetic relatedness among species in a clade. Accordingly, karyotype diversity trivially reflects species richness simply as a passive consequence of adaptive radiation. A more recent study in mammals controlled for phylogenetic signals and established the correlation as phylogenetically independent, suggesting that species richness cannot, in itself, explain the observed corresponding karyotype diversity. The correlation is, therefore, remarkable because the molecular mechanisms contributing to karyotype diversity are evolutionarily independent of the ecological mechanisms contributing to species richness. Recently, it was shown in salamanders that the two processes generating genome size diversity and species richness were indeed independent and operate in parallel, suggesting a potential non-adaptive, non-causal but biologically meaningful relationship. KD depends on mutational input generating genetic diversity and reflects genome stability, whereas species richness depends on ecological factors and reflects natural selection acting on phenotypic diversity. As mutation and selection operate independently and involve separate and unrelated evolutionary mechanisms-there is no reason a priori to expect such a strong, let alone any, correlation between KD and SR. That such a correlation exists is more consistent with Kimura's theory of non-adaptive radiation than with ecologically based adaptive theories of macro-evolution, which are not excluded in Kimura's non-adaptive theory. The following reviews recent evidence in support of Kimura's proposal, and other findings that contribute to a wider understanding of the molecular mechanisms underlying the process of non-adaptive radiation.

W, Chen H, Yu C, Yang L, Fu Y, Li J, Fu S, Sun Z, Fei L, Guo Q, Wang J, Xiao Y, Wang X, Zhang P, Ma L, Ge D, Xu S, Caballero-Pérez J, Cruz-Ramírez A, Zhou Y, Chen M, Fei JF, Han X, Guo G. Construction of the axolotl cell landscape using combinatorial hybridization sequencing at single-cell resolution

The Mexican axolotl (Ambystoma mexicanum) is a well-established tetrapod model for regeneration and developmental studies. Remarkably, neotenic axolotls may undergo metamorphosis, a process that triggers many dramatic changes in diverse organs, accompanied by gradually decline of their regeneration capacity and lifespan. However, the molecular regulation and cellular changes in neotenic and metamorphosed axolotls are still poorly investigated. Here, we develop a single-cell sequencing method based on combinatorial hybridization to generate a tissue-based transcriptomic landscape of the neotenic and metamorphosed axolotls. We perform gene expression profiling of over 1 million single cells across 19 tissues to construct the first adult axolotl cell landscape. Comparison of single-cell transcriptomes between the tissues of neotenic and metamorphosed axolotls reveal the heterogeneity of non-immune parenchymal cells in different tissues and established their regulatory network. Furthermore, we describe dynamic gene expression patterns during limb development in neotenic axolotls. This system-level single-cell analysis of molecular characteristics in neotenic and metamorphosed axolotls, serves as a resource to explore the molecular identity of the axolotl and facilitates better understanding of metamorphosis.

The Mexican axolotl is a well-established tetrapod model for regeneration and development. Here the authors report a scRNA-seq method to profile neotenic, metamorphic and limb development stages, highlighting unique perturbation patterns of cell type-related gene expression throughout metamorphosis.

Gestörte Geweberegeneration durch entzündliche Prozesse bei Alterung, Seneszenz und degenerativen Erkrankungen – Interaktionen mit dem COVID-19-induzierten Zytokin-Sturm des angeborenen Immunsystems

Entzündung ist Bestandteil einer jeglichen Geweberegeneration. Verletzung und Schädigung von Geweben - inklusive exogene virale und bakterielle Infektionen - induzieren eine frühe pro-inflammatorische Phase, die durch Aktivierung von residenten und aus dem peripheren Blut und Knochenmark rekrutierten Zellen des angeborenen Immunsystems weiter propagiert wird. Diese Phase dient auch dem Clearing der Umgebung von vorgeschädigten Zellen und cell debris. Um eine erfolgreiche Geweberegeneration zu erreichen ist es essentiell, die Auflösung der Entzündung durch zeitgerechte Einleitung einer anti-inflammatorischen Phase der Geweberegeneration zu ermöglichen. Dieser Phase kann dann die Gewebeneubildung folgen, am Beispiel der Frakturheilung als „Modeling“ bezeichnet. Das schnell gebildete neue Gewebe wird in der letzten Phase der Regeneration an die physikalischen Bedingungen im Gewebeverband angepasst, bei der Frakturheilung „Remodeling“ genannt. Kann die zeitgerechte Auflösung der Entzündung nicht erfolgen, verhindert die persistierende Entzündung das Eintreten in die Phase der Gewebeneubildung und damit die erfolgreiche Regeneration. Es erfolgt dann entweder als „Notlösung“ eine Narbenheilung oder im Falle weiter ausufernder Entzündung eine Zerstörung des Gewebes. Die mit dem Alter sich verschlechternde Regenerationskapazität vieler Gewebe inklusive Knochen, Muskel und Sehnen ist unter anderem eine Folge der subklinischen chronischen Entzündung von Geweben, die Alterung („Inflammaging“) propagiert. Die Entzündung im Mikromillieu involviert neben den gewebe-typischen Zellen und deren adulten Progenitoren auch die Zellen des gewebeeigenen (residenten) angeborenen Immunsystems, allen voran Makrophagen. Auch diese unterliegen Alters-assoziierten Veränderungen wie Zellalterung und eine gesteigerte Suszeptibilität für pro-inflammatorische Überreaktionen. Chronische Inflammation mündet letztlich in die zelluläre Seneszenz, die begleitet ist von einem Seneszenz-assoziierten sekretorischen Phänotyp (SASP) mit hoher Produktion von Interleukinen 1, 6, 8, und anderen Zytokinen. Solange solche Zellen nicht in den geregelten Zelltod gehen, unterhalten sie die chronische Entzündung und damit die Voraussetzungen für insuffiziente Geweberegeneration. Eine COVID-19 Infektion triggert und unterhält identische inflammatorische Mechanismen und induziert zusätzlich Seneszenz. Dies kann in der Summe zu einem Zytokin-Sturm führen, der in einem circulus vitiosus eine zerstörerische Hyperinflammation unterhält und der umso schwerwiegender ausfällt je höher die Vorlast an seneszenten Zellen ist, wie das in den COVID-Risikopopulationen der Fall ist. Deren Zusammensetzung überlappt sehr stark mit unseren Risikopopulationen für degenerative muskuloskelettale Erkrankungen wie Osteoporose und Sarkopenie.