COMPUTATIONAL APPROACHES TO REPROGRAM NEURONAL CELL IDENTITIES IN Ciona intestinalis

Abstract

Understanding cell type identity and what determines cell fate, are fundamental to understanding the basic units of life, from which the complexities of organisms arise and evolve. A powerful application of this knowledge is in the field of reprogramming, in which we attempt to convert one cell type into another. Beyond understanding these foundational biological principles, we can further our success in regenerative medicine, in which damaged tissues and organs can be replaced by first reprogramming their constituent cell types. In this dissertation, I explore questions of cell type identity and reprogramming in neural cell types in Ciona intestinalis, the invertebrate closest evolutionarily to vertebrates. In Chapter 2, I begin by uncovering the effects of misexpressing the transcription factor POU IV, a homolog of Brn3 in vertebrates, on the specification of sensory cell types. I find that the epidermal cells are transformed into BTN/PSC “hybrids”, or cells that predominantly exhibit properties of both BTNs and PSCs, due to ectopic coexpression of Neurogenin and Foxg that is triggered by an unexpected POU IV feedback loop. In Chapter 3, I focus on how to reliably reprogram neural cell types. I develop a computational framework, Circe, that predicts Cocktails, or combinations of transcription factors that can induce a given cell type when misexpressed. Circe is based on the premise that Cocktail transcription factors will be those that specify a cell type, and identifies them by analyzing a lineage tree reconstructed from single-cell data derived from all developmental stages in Ciona. I also present experimental evidence for the reprogramming of pigment and dorsal nerve cord cells into Bipolar Tail Neurons (BTNs).Finally, in Chapter 3, I turn my attention to the effects of Nodal signaling on the specification of neurons and embryonic patterning in Ciona. I recapitulated past findings and suggested new roles for Nodal, namely, a Nodal-mediated tradeoff between Nervous System (b) and Epidermal (b) Lineages, a Nodal signal at the 110-cell stage that is responsible for the specification of both pigment and Prop+ cells, and a “Fate Map Correction” between the 110-cell and Initial Tailbud stages. Taken together, this dissertation presents novel computational analyses and methods that further our understanding of how cell types are specified, defined, and reprogrammed.