LEVERAGING TRANSCRIPTOMIC APPROACHES TO IDENTIFY DIFFERENCES IN GENETIC PROGRAMMING DRIVING TWO DISTINCT WOUND HEALING MECHANISMS, REGENERATION AND FIBROSIS, IN \u3ci\u3eACOMYS\u3c/i\u3e AND \u3ci\u3eMUS\u3c/i\u3e

Why can some animals and others cannot? This fundamental question has fueled scientists studying regeneration for hundreds of years since early observations in crayfish, salamanders and many other organisms. While most contemporary work in regeneration is done in a handful of species including salamanders, zebrafish and flatforms, these organisms lack a closely-related, non-regenerating sister species from which unique genetic differences can be identified. Additionally, while much has been learned from these organisms, they do not share fundamental biological traits with mammals (endothermy, metabolism and immune system) which limits the ability to translate this research for clinical medicine. To this end, our lab has developed a new mammalian model of regeneration: the African spiny mouse (Acomys spp.). Spiny mice are murids belonging to the subfamily Deomyinae, and are evolutionarily separated from lab mice (Mus musculus) by about 20 million years. More importantly, Acomys are able to regenerate large portions of skin as well as complex musculoskeletal tissue in the ear pinna while Mus create scar tissue, allowing us to use these two organisms in a comparative framework to identify differences between regeneration and fibrosis. Focusing specifically on the ear pinna, we use a 4mm biopsy punch injury through the ear pinna to evaluate wound healing in each species. In this dissertation, I first utilize this comparative model to analyze an RNA-seq dataset from 5 different time points: D0, D5, D10, D15 and D20 post-injury. Using two different pipelines, this dataset is analyzed both with and without the use of a spiny mouse genome to highlight the limitations of an analysis using a de novo assembled transcriptome as a reference. Then focusing on the use of the genome, the dataset is analyzed more rigorously with the addition of an evolutionary perspective, ultimately leading to the discovery of a novel insertion within the Col1a1 gene in spiny mouse that may contribute to some of the phenotypic differences observed within the subfamily Acomys. Next, I make use of a laser-capture microdissection (LCM) RNA-seq dataset to further interrogate gene expression in different tissue compartments (epidermis, mesenchyme and mesenchyme sub-compartments) during regeneration, allowing us to look at signaling patterns from one tissue compartment to another. The dissertation then moves away from computational analysis of regeneration towards a descriptive, histological analysis of ear pinna development in rodents, connecting development and regeneration through investigation of cell lineage. Interestingly, muscle appears to have a distinct cell lineage while the rest of the pinna mesenchyme is derived from the neural crest. This data also suggests that Bmp-signaling may play a role in differentiation of an early progenitor cell towards either an adipocyte or chondrocyte lineage. Finally, the dissertation concludes by discussing how the data presented advances our understanding of regeneration and propose future experiments to expand on these findings