Since its inception, REGENERATE-IT has structured 12 individual research projects across 9 European institutions, each focusing on distinct aspects of regeneration (e.g. limb regrowth, stem cell dynamics, and immune system interactions) and trained 12 doctoral candidates through hands-on workshops, secondments, annual consortium meetings and a bioinformatics summer school.
During the project, substantial progress was achieved across diverse research areas. One early milestone was the development of OneSABER, an improved RNA in situ hybridization method offering greater flexibility and lower costs, making gene expression studies more accessible.
A regeneration sufficiency assay was established to systematically characterize the regenerative potential of specific genes, providing insights into tissue permissibility, spatial and temporal aspects of regenerative responses, and identifying genes capable of inducing regeneration—knowledge applicable to mammalian systems.
By selecting and cloning regeneration-specific genes based on transcriptomic activity pre- and post-injury, researchers began mapping their spatial expression, with several showing localized activation at amputation sites. An ATACseq dataset covering the entire regeneration timeline was generated to identify enhancer elements that drive gene expression specifically during regeneration, helping minimize side effects.
In Parhyale, new tools were created to study microbial influences on wound healing and regeneration.
In planarians, glutathione-responsive nanocarriers enabled real-time imaging of redox dynamics, revealing spatial antioxidant regulation when combined with antibody staining and FISH. Enhanced immobilization techniques using linalool improved live imaging of these processes.
A reproducible 3D spheroid culture system for axolotl fibroblasts was developed, offering a robust platform to screen for factors that promote multipotency and limb regeneration. The discovery of novel species-specific microRNAs in regenerating limbs provided new insight into regenerative mechanisms.
In mammalian systems, spatial transcriptomics and single-cell RNA sequencing identified a unique macrophage subtype in regenerating spiny mouse tissue that may promote regeneration. Tools to study gene and protein expression in these cells were developed, and protocols were established for differentiating mouse, spiny mouse, and human macrophages into pro-regenerative types. Efforts are underway to derive pro-regenerative macrophages from human iPSCs.
Spiny mouse satellite cells showed enhanced differentiation potential over those from standard lab mice, highlighting new therapeutic strategies for muscle regeneration and muscular dystrophy. In studies on colonic epithelial regeneration, canonical Wnt signaling was shown to play a dynamic, essential role, with critical activation windows identified using reporter mice and ongoing single-cell RNA-seq to dissect pathway control.
For skin regeneration, a group of gene markers was identified to assess stem cell content in skin grafts, offering a molecular tool for evaluating graft quality. A reference transcriptomic model of human epidermal stem cells was created, while a CRISPRa-based platform now enables high-throughput screening of genes for reprogramming progenitors into durable epidermal stem cells.
A new theoretical model describes how mitochondrial electron transport chain conformation affects metabolism and regenerative ability in the zebrafish heart. Standardized methods were introduced to evaluate caudal fin regeneration in adult zebrafish, with preliminary evidence that specific tyrosine phosphatases downstream of ROS may influence the process, pending further validation.
