Network modelling of the regulatory pathways involved in organ regeneration

• Autores: Ines Rivero Garcia
• Directores de la Tesis: Miguel Torres Sánchez (dir. tes.)
• Lectura: En la Universidad Politécnica de Madrid ( España ) en 2024
• Idioma: inglés
• Programa de doctorado: Programa de Doctorado en Ingeniería Biomédica por la Universidad Politécnica de Madrid
• Calificación: Sobresaliente Cum Laude
• Materias:
  • Ciencias de la vida
    • Biología molecular
• Enlaces
  • Tesis en acceso abierto en: Archivo Digital UPM
• Resumen

  • Motivation: Fibrotic diseases cause long-term organ damage and are a heavy burden on health systems worldwide. While adult mammals usually generate a fibrotic scar in response to injury, neonatal mammals and other vertebrate species can fully regenerate certain body structures through the dedifferentiation and proliferation of preexisting, terminally differentiated cells. Complex biological processes such as rewiring of cellular identity require a holistic approximation, as the study of isolated components is not enough to obtain a realistic overview of the underlying mechanism in action. Gene regulatory networks model regulatory relationships between transcription factors and their target genes and are the main underlying determinants of cell identity.

    Objectives: In this thesis we hypothesize that physiological regenerative mechanisms are controlled by latent gene regulatory networks at least partially conserved between lower vertebrates and mammals. We used state-of-the-art computational approaches on bulk and single-cell transcriptomic data to model and perturb the gene regulatory networks that control regeneration in heart and bone, in order to identify new candidate genes with therapeutic potential.

    Findings: This thesis presents three sets of findings related to the understanding of gene regulatory networks in regeneration. (1) We inferred the gene regulatory network controlling axolotl cardiomyocyte sub-population transitions upon cryoinjury. By systematic in silico perturbations of the network, we identified the repressive role of Hey2 for the initiation of the injury response in border zone cardiomyocytes. Independently, footprint-based analysis of a mouse scRNA-seq data set with annotated cardiomyocyte number of nuclei suggested Hey2 as a positive regulator of cardiomyocyte polyploidization, which blocks regeneration. (2) Comparison of the transcriptional footprints caused by overexpression of caErbb2, Myc and Yap5sa in neonatal mouse cardiomyocytes identified two pro-regenerative gene expression programs, associated with cardiomyocyte proliferation and dedifferentiation. Boolean models of a core gene regulatory network controlling the emergence of these transcriptional states suggested the robust nature of the maturating cardiomyocyte gene regulatory network and identified a handful of perturbations with a potential therapeutic application. (3) We compared the gene regulatory networks between regenerating and fibrotic injuries in axolotl and identified an insufficient rewiring in the fibrotic network. We predicted partial antagonism in the function of the TCF/LEF transcription factors Lef1 and Tcf7l2 that might contribute to understand why fibrotic bone injuries fail to regenerate.

    Conclusions: By leveraging different types of transcriptomic data and computational and experimental approaches, we were able to model the cardiomyocyte and fibroblast gene regulatory networks in regenerative and fibrotic conditions. Furthermore, we identified candidate genes for their validation as therapeutic pro-regenerative agents and provided mechanistic hypotheses to understand the differences between regenerative and fibrotic injury responses.