Origins, patterns, and consequences of somatic mutations in engineered, normal, and diseased cells

Abstract

This dissertation studies the origins, patterns, and consequences of somatic mutations in human cells through a series of three studies across different biological settings. Chapter 1 introduces what somatic mutations are, how often they occur, how they may arise, and how they can be studied experimentally or computationally. Chapter 2 explores the origins of genome-wide somatic mutations in human cells treated with adenine base editing (ABE) using single-cell whole-genome sequencing, mutational signatures analysis, and statistical modeling. Through an integrative analysis, we find that ABE contributes to elevated numbers of somatic mutations in cells by creating insufficiencies in the activity of global-genomic nucleotide excision repair (GG-NER). We propose a model in which ABE draws GG-NER machinery away from genomic regions that then accumulate unrepaired damage, and the resulting mutations resemble those in individuals with germline deficiencies in GG-NER activity. Chapter 3 describes insights into the development of the human cerebral cortex by analyzing the patterns of clonal somatic mutations as uncovered with a variety of experimental and computational technologies. We create spatial “maps” of clonal somatic mutation presence with bulk tissue sequencing, construct population genetic models based on single-cell lineage tracing to infer the times-of-origin of these mutations, and identify the cell types carrying these mutations using single-cell transcriptomics. We find that the progeny cells of cortical lineages become regionally restricted late in development, contributing to significant inter-region mingling of even rare neuronal populations observed across neurotypical individuals. We also provide in vivo evidence in humans for the late divergence of excitatory and inhibitory neurons, two functionally and developmentally distinct classes of neurons in the cortex, from a common cortical progenitor. Chapter 4 details one consequence of somatic structural variants in cancer: the generation of novel, unannotated peptides from the noncoding genome. This chapter provides a pan-cancer survey of transcription and translation of noncoding structural variation, as well as unannotated standalone transcripts and tumor-specific peptides induced by structural variation in cancer as detected by several complementary genomic and proteomic technologies. Chapter 5 concludes the dissertation with a forecast of how emerging technologies will refine the insights produced in this work.