Biology App Answers

[Fortun Bawa]

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

The potential for basic research to uncover the inner workings of regenerative processes and produce meaningful medical therapies has inspired scientists, clinicians, and patients for hundreds of years. Decades of studies using a handful of highly regenerative model organisms have significantly advanced our knowledge of key cell types and molecular pathways involved in regeneration. However, many questions remain about how regenerative processes unfold in regeneration-competent species, how they are curtailed in non-regenerative organisms, and how they might be induced (or restored) in humans. Recent technological advances in genomics, molecular biology, computer science, bioengineering, and stem cell research hold promise to collectively provide new experimental evidence for how different organisms accomplish the process of regeneration. In theory, this new evidence should inform the design of new clinical approaches for regenerative medicine. A deeper understanding of how tissues and organs regenerate will also undoubtedly impact many adjacent scientific fields. To best apply and adapt these new technologies in ways that break long-standing barriers and answer critical questions about regeneration, we must combine the deep knowledge of developmental and evolutionary biologists with the hard-earned expertise of scientists in mechanistic and technical fields. To this end, this perspective is based on conversations from a workshop we organized at the Banbury Center, during which a diverse cross-section of the regeneration research community and experts in various technologies discussed enduring questions in regenerative biology. Here, we share the questions this group identified as significant and unanswered, i.e., known unknowns. We also describe the obstacles limiting our progress in answering these questions and how expanding the number and diversity of organisms used in regeneration research is essential for deepening our understanding of regenerative capacity. Finally, we propose that investigating these problems collaboratively across a diverse network of researchers has the potential to advance our field and produce unexpected insights into important questions in related areas of biology and medicine.

Despite the varied expertise among workshop participants and wide-ranging discussions about how regeneration occurs among diverse species, we found broad agreement on identifying several enduring, fundamental questions where scientists should direct their efforts. Importantly, our task was to identify common problems that are not overly reductionist or specific to a particular organism. In essence, we focused on the forest to identify major driving questions while at the same time considering why some trees remain undescribed, hidden, or unknown. We found common ground on the notion that regeneration remains vastly understudied, in part because the most commonly used model organisms do not have robust regenerative capacities. Unsurprisingly, there was no strong impetus for creating new technologies to specifically study regeneration; the enduring technological hurdle in our field is the application of specific transgenic tools to highly regenerative research models. Thus, the perspective put forth here represents a synthesis of focused discussions that aim to stimulate an exchange of ideas and future collaborations between experts in many fields, including regeneration.

The ideas presented in this paper emerged from discussions at a Cold Spring Harbor Laboratory Banbury Center workshop organized by the authors (for information about The Banbury Center, see ). The workshop (Enduring Questions in Regenerative Biology) convened biologists and technologists to consider how basic research can advance our understanding of what endows some species and tissues with regenerative capacity, discuss if new tools and technologies are needed to sustain progress in this endeavor, and to consider how these findings could create the next generation of regenerative therapeutics. The workshop participants worked together to identify enduring questions in regenerative biology and why they persist before exploring collaborative approaches to answer them. The three authors were joined at the Banbury Center workshop by Carrie Adler, Maria Barna, Jeff Biernaskie, Sarah Calve, Joshua Currie, Celina Juliano, Je Hyuk Lee, Malcolm Maden, Francesca Mariani, Phillip Newmark, Bret Pearson, Tania Rozario, Tatiana Sandoval Guzmn, Jennifer Simkin, Mansi Srivastava, Kryn Stankunas, and Bo Wang. We note that in addition to discussions at the Banbury Center, participants contributed to reviewing and editing this paper.

After defining component processes common to regeneration, we considered how these events might vary across an ever-broadening set of organisms. For instance, complex tissue regeneration may be evolutionarily constrained such that the entire regenerative response, including all component processes, is canalized with low variation between species for any specific process or set of interrelated processes (Fig. 1a, b). This could be true even if regenerative ability has evolved multiple times in different lineages. Conversely, regeneration could have arisen via convergent evolution (i.e., homoplasy) and variability among component processes may be large across the entire process set or for most of the processes (Fig. 1c). Alternatively, variation across species could be relatively large for some processes yet low for others, i.e., high conservation of specific processes (Fig. 1d). Defining the processes outlined in Table 1 as component parts of regeneration provides a framework to study each one across organisms and facilitates the generation of testable hypotheses to ask what is lacking (or modified) in non-regenerative organisms. For example, one testable hypothesis is that events one through five outlined in Table 1 constitute a general wound response that occurs in all animals, regardless of subsequent steps, with regeneration requiring a distinct mechanism that transitions tissues into regenerative healing (steps six through nine, Table 1). Another hypothesis is that specific events occur during the early wounding response to trigger regenerative healing.

In line with the second hypothesis, one enduring question is whether a particular injury signal predicts the final healing outcome. For example, is there a unique trigger for wound healing versus regeneration5? Many investigators have advanced the hypothesis that particular immune cells and their products are specifically required for regeneration, independent of their role in regulating and resolving inflammation6. For instance, studies in several adult regeneration models suggest blocking immune cell infiltration (e.g., monocytes and macrophages) or depleting specific immune cell subtypes (e.g., macrophages) prevents normal wound healing and the transition to regenerative healing7,8,9,10,11. In contrast, removing similar immune cell types when trying to stimulate regeneration can enhance the response (microglia)12. However, it remains an open question if immune phenotypes exist that regulate and promote regeneration-specific processes. The hypothesis that regeneration-promoting immune cell states exist could be tested by comparing immune system responses across different types of injuries in the same species, i.e., where one injury induces regeneration and the other does not (e.g., lizard tails vs. limbs). This hypothesis could also be tested by comparing the immune response in different aged animals or closely related species in which identical tissues heal via regeneration and fibrotic repair, respectively. Comparing the regenerative response in divergent regenerative species may also offer insight into whether components of the immune response are permissive or instructive relative to regeneration.

Component processes and the transitions between them are also critical to define because they establish a framework for generating specific datasets (i.e., cell type and time-point specific) that can capture cell state changes to compare across species. Specifically, changes in chromatin state or genomic architecture, which impact gene regulatory networks (GRNs) and their outputs, may be broadly conserved at these cellular and temporal transitions13. Importantly, cell state changes accompanying reactivation of developmental genes can provide signposts for exploring chromatin states associated with activation or repression of gene expression and thus provide insight into both activation and constraint of regenerative ability14. These types of comparisons also lay the groundwork for evaluating cell-type evolution models as they relate to the presence or absence of regenerative capacity15,16. Lastly, breaking regeneration into component processes provides a framework for comparing cellular transitions as they occur during regeneration and embryonic development (Boxes 3 and 4).

But what happens when our neatly divided paradigms collide? For example, invertebrates such as planarians and Hydra exhibit high tissue turnover and almost unlimited regenerative capacity (i.e., whole-body regeneration). Although their response to injury features hallmarks of epimorphic regeneration, including the accumulation of proliferating cells at the wound site, they also maintain pluripotent somatic cells that constantly replenish the entire animal, such that all their tissues (including those that are not typically replenished in vertebrates, like the central nervous system) are in a perpetual state of renewal. Nevertheless, such animals provide an opportunity for studying the intersection of regeneration, homeostatic tissue renewal, and repair as they apply to all organisms. These examples underscore how a term like regeneration can be used in reference to functionally different processes, even though the differences may seem nuanced to those outside the field. This is especially evident when defining the basic component processes that comprise regeneration (Table 1) and determining the degree to which examples of regeneration in diverse species (or life stages) represent convergent or homologous events.

c80f0f1006