Reprogramming to the nervous system: a computational and candidate gene approach
Authors: Alicea Bradly 
Published: July 2018

The creation of stem-like cells, neuronal cells, and skeletal muscle fibers from a generic somatic precursor phenotype has many potential applications. These uses range from cell therapy to disease modeling. The enabling methodology for these applications is known as direct cellular reprogramming. While the biological underpinnings of cellular reprogramming go back to the work of Gurdon and other developmental biologists, the direct approach is a rather recent development.Therefore, our understanding of the reprogramming process is largely based on isolated findings and interesting results. A true synthesis, particularly from a systems perspective, is lacking. In this document, I will attempt to build toward an intellectual synthesis of direct reprogramming by critically examining four types of phenotypic conversion that result in production of nervous system components: induced pluripotency (iPS), induced neuronal (iN), induced skeletal muscle (iSM), and induced cardiomyocyte (iCM). Since potential applications range from tools for basic science to disease modeling and bionic technologies, the need for a common context is essential. This intellectual synthesis will be defined through several research endeavors.The first investigation introduces a set of experiments in which multiple fibroblast cell lines are converted to two terminal phenotypes: iN and iSM. The efficiency and infectability of cells subjected to each reprogramming regimen are then compared both statistically and quantitatively. This set of experiments also resulted in the development of novel analytical methods for measuring reprogramming efficiency and infectability.The second investigation features a critical review and statistical analysis of iPS reprogramming, specifically when compared to indirect reprogramming (SCNT-ES) and related stem-like cells. The third investigation is a review and theoretical synthesis which stakes out new directions in our understanding of the direct reprogramming process, including recent computational modeling endeavors and results from the iPS, iN and induced cardiomyocyte (iCM) experiments.To further unify the outcomes of these studies, additional results related to Chapter 2 and directions for future research will be presented. The additional results will allow for further interpretation and insight into the role of diversity in direct reprogramming. These future directions include both experimental approaches (a technique called mechanism disruption) and computational approaches (preliminary results for an agent-based population-level approximation of direct reprogramming). The insights provided here will hopefully provide a framework for theoretical development and a guide for traditional biologists and systems biologists alike.Several components of this volume have been previously published. Chapter 2 is published as an article in Stem Cells and Development (Volume 22, Issue 19). Chapter 3 is published as a book chapter (Chapter 37) in the book “Principles in Cloning, Volume III” (Elsevier). Special thanks go to Dr. Steven Suhr and Dr. Jose Cibelli, who are co-authors for Chapter 2 and Chapter 3, respectively.