Collaborative Research: EDGE CMT: Shared genetic and cellular mechanisms of vertebrate limb and fin regeneration.

Limb regeneration is a complex biological process not fully understood at the genetic level. Salamanders are the only vertebrates with limbs that can completely regrow a lost limb. However, some fish, like the African lungfish and the grey bichir (Polypterus), can fully regrow their fins, even if they are cut off at their base.

This ability is not found in commonly studied fish such as zebrafish. The proposed research will use a multilayered, comparative approach, looking at salamanders, lungfish, and Polypterus to identify the key elements needed for limb and fin regeneration. The hypothesis being tested is that these species deploy a shared genetic program of regeneration.

First, this proposal addresses whether a specific molecular signaling (the mTOR signaling pathway) is a common feature of both limb and fin regeneration. Next, a comprehensive dataset of gene expression information will be obtained from the animal models to search for a shared set of genetic and cellular tools for regrowing limbs and fins. Finally, DNA elements that control gene expression during limb and fin regeneration will be identified and the hypothesis that loss of the ability to regenerate is linked to changes in how tissues control gene activity will be tested.

These studies using multiple species will help reveal general mechanisms that control the complex process of regeneration. This project will train researchers at multiple academic stages, from undergraduates to postdoctoral researchers. Outreach to middle school students will provide research opportunities to underrepresented populations and therefore contribute to broadening participation in STEM.

Limb regeneration is a prime example of a complex biological trait for which the genetic and genomic underpinnings are poorly understood. Although salamanders are the only limbed vertebrate that can regenerate the entire limb, fishes such as the African lungfish (Protopterus annectens) and Polypterus fully regrow fins even when the amputation occurs at the very base of the fin, across the proximal endoskeleton.

This ability to regrow entire fins is lacking in traditional fish models such as the zebrafish. This proposal uses a phylogenetically-informed, multi-scale approach, using the axolotl, the lungfish and the Polypterus, to identify the core components of a shared “toolkit” of limb and fin regeneration. The first aim of the project tests the hypothesis that a rapid activation of an mTOR-mediated translational program is a conserved feature of limb and fin regeneration and identifies transcripts differentially translated during the early event of wound closure that marks the onset of regeneration.

The second aim is focused on the integration of bulk, single nucleus and spatial transcriptomics datasets to determine if our animal models activate an evolutionarily shared genetic and cellular “toolkit” for appendage regeneration. In the third aim, epigenetic profiling will be deployed to reveal shared gene regulatory networks of limb and fin regeneration and test the hypothesis that loss of regenerative capacity is associated with widespread divergence of tissue regeneration enhancers.

The multi-species, systems-level studies proposed here will bring the field closer to uncovering the general mechanisms governing the complex trait of regeneration.

This proposal is co-funded by the Division of Integrative Organismal Systems (via the EDGE program and the Developmental Systems Cluster), The Division of Emerging Frontiers, and the Division of Environmental Biology.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.