Multi-omic analysis of hearing difficulty risk loci and gene regulatory networks in the mammalian cochlea

Abstract

The sensory cells of the mammalian cochlea do not have the capacity to regenerate. Studies have identified some genes and pathways that are critical for hair cell formation; however, the conditions necessary to regenerate fully functional hair cells remain unknown, as the genetic and genomic architecture of hearing loss and hair cell regeneration is only partially defined due to different experimental conditions and models used in each study. This dissertation improves our understanding of these conditions by taking a systems biology approach, combining diverse multi-omic data into genome-scale models for predicting target genes in the mammalian cochlea and in vitro systems. Using a meta-analysis of summary statistics from hearing-related traits, I identified 31 genome-wide significant risk loci for self-reported hearing difficulty. I then investigated the regulatory and cell specific expression for these loci and found that risk-associated genes were most strongly enriched for expression in cochlear epithelial cells, as well as for genes related to sensory perception and known Mendelian deafness genes, supporting their relevance to auditory function. My epigenomic and statistical fine-mapping most strongly supported 50 putative risk genes. To derive target genes from a model of hair cell regeneration, I characterized cochlear organoids derived from murine progenitor cells through bioinformatic analysis of single-cell RNA sequencing and bulk RNA sequencing data. For comparison, I integrated data from six previous studies of cochlear and utricular cell types in vivo and report an improved list of marker genes for each inner ear cell type. I found that cells in organoids mimic nearly all subtypes of supporting cells and hair cells in the cochlea and that the resulting hair cells reach a mature identity. I reconstructed a gene regulatory model from these data to gain insight into the transcription factors driving the trans-differentiation of progenitors to hair cells. My model identified known regulators of hair cell development and predicts novel regulatory factors. I validated these networks across transcriptional datasets, demonstrating dynamic changes in the expression of these transcription factors. Overall, I report new risk genes for hearing difficulty and new transcription factors that play a role in hair cell regeneration.