Distinct gene expression dynamics in developing and regenerating crustacean limbs

Two transcriptional cascades orchestrate cockroach leg regeneration

The mystery of appendage regeneration has fascinated humans for centuries, while the underlying regulatory mechanisms remain unclear. In this study, we establish a transcriptional landscape of regenerating leg in the American cockroach, Periplaneta americana, an ideal model in appendage regeneration studies showing remarkable regeneration capacity. Through a large-scale in vivo screening, we identify multiple signaling pathways and transcription factors controlling leg regeneration. Specifically, zfh-2 and bowl contribute to blastema cell proliferation and morphogenesis in two transcriptional cascades: bone morphogenetic protein (BMP)/JAK-STAT-zfh-2-B-H2 and Notch-drm/bowl-bab1. Notably, we find zfh-2 is working as a direct target of BMP signaling to promote cell proliferation in the blastema. These mechanisms might be conserved in the appendage regeneration of vertebrates from an evolutionary perspective. Overall, our findings reveal that two crucial transcriptional cascades orchestrate distinct cockroach leg regeneration processes, significantly advancing the comprehension of molecular mechanism in appendage regeneration.

The ctenophore Mnemiopsis leidyi deploys a rapid injury response dating back to the last common animal ancestor

Regenerative potential is widespread but unevenly distributed across animals. However, our understanding of the molecular mechanisms underlying regenerative processes is limited to a handful of model organisms, restricting robust comparative analyses. Here, we conduct a time course of RNA-seq during whole body regeneration in Mnemiopsis leidyi (Ctenophora) to uncover gene expression changes that correspond with key events during the regenerative timeline of this species. We identified several genes highly enriched in this dataset beginning as early as 10 minutes after surgical bisection including transcription factors in the early timepoints, peptidases in the middle timepoints, and cytoskeletal genes in the later timepoints. We validated the expression of early response transcription factors by whole mount in situ hybridization, showing that these genes exhibited high expression in tissues surrounding the wound site. These genes exhibit a pattern of transient upregulation as seen in a variety of other organisms, suggesting that they may be initiators of an ancient gene regulatory network linking wound healing to the initiation of a regenerative response.

Marine Invertebrates One Cell at A Time: Insights from Single-Cell Analysis

Over the past decade, single-cell RNA-sequencing (scRNA-seq) has made it possible to study the cellular diversity of a broad range of organisms. Technological advances in single-cell isolation and sequencing have expanded rapidly, allowing the transcriptomic profile of individual cells to be captured. As a result, there has been an explosion of cell type atlases created for many different marine invertebrate species from across the tree of life. Our focus in this review is to synthesize current literature on marine invertebrate scRNA-seq. Specifically, we provide perspectives on key insights from scRNA-seq studies, including descriptive studies of cell type composition, how cells respond in dynamic processes such as development and regeneration, and the evolution of new cell types. Despite these tremendous advances, there also lie several challenges ahead. We discuss the important considerations that are essential when making comparisons between experiments, or between datasets from different species. Finally, we address the future of single-cell analyses in marine invertebrates, including combining scRNA-seq data with other 'omics methods to get a fuller understanding of cellular complexities. The full diversity of cell types across marine invertebrates remains unknown and understanding this diversity and evolution will provide rich areas for future study.

Transcriptomic landscape of posterior regeneration in the annelid Platynereis dumerilii

BACKGROUND

Restorative regeneration, the capacity to reform a lost body part following amputation or injury, is an important and still poorly understood process in animals. Annelids, or segmented worms, show amazing regenerative capabilities, and as such are a crucial group to investigate. Elucidating the molecular mechanisms that underpin regeneration in this major group remains a key goal. Among annelids, the nereididae Platynereis dumerilii (re)emerged recently as a front-line regeneration model. Following amputation of its posterior part, Platynereis worms can regenerate both differentiated tissues of their terminal part as well as a growth zone that contains putative stem cells. While this regeneration process follows specific and reproducible stages that have been well characterized, the transcriptomic landscape of these stages remains to be uncovered.

RESULTS

We generated a high-quality de novo Reference transcriptome for the annelid Platynereis dumerilii. We produced and analyzed three RNA-sequencing datasets, encompassing five stages of posterior regeneration, along with blastema stages and non-amputated tissues as controls. We included two of these regeneration RNA-seq datasets, as well as embryonic and tissue-specific datasets from the literature to produce a Reference transcriptome. We used this Reference transcriptome to perform in depth analyzes of RNA-seq data during the course of regeneration to reveal the important dynamics of the gene expression, process with thousands of genes differentially expressed between stages, as well as unique and specific gene expression at each regeneration stage. The study of these genes highlighted the importance of the nervous system at both early and late stages of regeneration, as well as the enrichment of RNA-binding proteins (RBPs) during almost the entire regeneration process.

CONCLUSIONS

In this study, we provided a high-quality de novo Reference transcriptome for the annelid Platynereis that is useful for investigating various developmental processes, including regeneration. Our extensive stage-specific transcriptional analysis during the course of posterior regeneration sheds light upon major molecular mechanisms and pathways, and will foster many specific studies in the future.

Development, regeneration and aging: a bizarre love triangle

The Jacques Monod Conference on 'Growth and regeneration during development and aging' was organized by Claude Desplan and Allison Bardin in May 2023. The conference took place in Roscoff, France, where participants shared recent conceptual advances under the general motto that developmental processes do not end with embryogenesis. The meeting covered various aspects of how development relates to fitness, regeneration and aging across a refreshing diversity of evolutionarily distant organisms.

Meeting report: Third Franco-Japanese developmental biology meeting "New Frontiers in developmental biology: Celebrating the diversity of life"

The French and Japanese Developmental Biology Societies, teaming up with Human Frontier Science Program, were eager to meet back in person in November 2022 in the lovely city of Strasbourg. Top scientists in the developmental biology field from France and Japan, but also from United States, United Kingdom, Switzerland or Germany shared their exciting science during the 4 days of this meeting. Core fields of developmental biology such as morphogenesis, patterning, cell identity, and cell state transition, notably at the single cell level, were well represented, and a diversity of experimental models, including plants, animals, and other exotic organisms, as well as some in vitro cellular models, were covered. This event also extended the scope of classic scientific gatherings for two reasons. First the involvement of artists during the preparation of the event and on site. Second, part of the meeting was open for the general public through a series of outreach events, including a music and video presentation through projection mapping at Rohan palace, as well as public lectures.

Regeneration or Scarring Derive from Specific Evolutionary Environmental Adaptations of the Life Cycles in Different Animals

The ability to heal or even regenerate large injuries in different animals derives from the evolution of their specific life cycles during geological times. The present, new hypothesis tries to explain the distribution of organ regeneration among animals. Only invertebrates and vertebrates that include larval and intense metamorphic transformations can broadly regenerate as adults. Basically, regeneration competent animals are aquatic while terrestrial species have largely or completely lost most of the regeneration ability. Although genomes of terrestrial species still contain numerous genes that in aquatic species allow a broad regeneration ("regenerative genes"), the evolution of terrestrial species has variably modified the genetic networks linking these genes to the others that evolved during land adaptation, resulting in the inhibition of regeneration. Loss of regeneration took place by the elimination of intermediate larval phases and metamorphic transformations in the life cycles of land invertebrates and vertebrates. Once the evolution along a specific lineage generated species that could no longer regenerate, this outcome could not change anymore. It is therefore likely that what we learn from regenerative species will explain their mechanisms of regeneration but cannot or only partly be applied to non-regenerative species. Attempts to introduce "regenerative genes" in non-regenerative species most likely would disorder the entire genetic networks of the latter, determining death, teratomas and cancer. This awareness indicates the difficulty to introduce regenerative genes and their activation pathways in species that evolved genetic networks suppressing organ regeneration. Organ regeneration in non-regenerating animals such as humans should move to bio-engineering interventions in addition to "localized regenerative gene therapies" in order to replace lost tissues or organs.

Embracing the diversity of model systems to deconstruct the basis of regeneration and tissue repair

The eighth EMBO conference in the series 'The Molecular and Cellular Basis of Regeneration and Tissue Repair' took place in Barcelona (Spain) in September 2022. A total of 173 researchers from across the globe shared their latest advances in deciphering the molecular and cellular basis of wound healing, tissue repair and regeneration, as well as their implications for future clinical applications. The conference showcased an ever-expanding diversity of model organisms used to identify mechanisms that promote regeneration. Over 25 species were discussed, ranging from invertebrates to humans. Here, we provide an overview of the exciting topics presented at the conference, highlighting novel discoveries in regeneration and perspectives for regenerative medicine.

Wound healing and regeneration in the reef building coral Acropora millepora

Branching scleractinian corals are niche-constructing organisms, providing continuously-growing, structural foundation for spectacularly biodiverse coral reef ecosystems. A large part of their success lies in the ability to quickly regenerate following mechanical damage. Even now, when the corals undergo great decline due to anthropogenic weather and storm extremes, it is surprising how little is known about molecular mechanisms governing regeneration in these iconic organisms. In this study, we used RNA-seq to identify genes involved in the regeneration of Acropora millepora, starting with the initial wound closure up to complete rebuilding of lost structures. Many of the differentially expressed genes we found in the wound healing steps are homologues of genes known to be involved in wound healing and regeneration of bilaterian and other cnidarian species, prominently including multiple components of FGF and Wnt signalling pathways. Comparison between genes involved in wound healing and continuous growth of the colony demonstrates both similarity and distinctiveness of the genetic programmes controlling these processes. A striking example is specific expression of c-Fos, a transcription factor with conserved role in early injury response, during the earliest stages of wound healing of A. millepora. By comparing results obtained in diverse experimental conditions including a closed-loop, recirculating aquarium and a flow-through system of marine station, we have demonstrated feasibility of using zooxanthellate scleractinian corals as experimental models in fundamental biology research, including studies of regeneration.

Crustacean leg regeneration restores complex microanatomy and cell diversity

Animals can regenerate complex organs, yet this process frequently results in imprecise replicas of the original structure. In the crustacean Parhyale, embryonic and regenerating legs differ in gene expression dynamics but produce apparently similar mature structures. We examine the fidelity of Parhyale leg regeneration using complementary approaches to investigate microanatomy, sensory function, cellular composition, and cell molecular profiles. We find that regeneration precisely replicates the complex microanatomy and spatial distribution of external sensory organs and restores their sensory function. Single-nuclei sequencing shows that regenerated and uninjured legs are indistinguishable in terms of cell-type composition and transcriptional profiles. This remarkable fidelity highlights the ability of organisms to achieve identical outcomes via distinct processes.