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Dissertation
Cellular and molecular consequences of genetic variants in inherited retinal disease
University of Iowa
Doctor of Philosophy (PhD), University of Iowa
Spring 2026
DOI: 10.25820/etd.008412
Abstract
Detecting the genetic variation that underlies inherited disease has become cost-effect and clinically feasible in recent years. However, difficulties remain in the interpretation of genetic variants and identification of potential therapeutic nodes in dysregulated genetic networks. Without these capabilities, the ever-expanding resource of human genome sequence data will remain underutilized. Problems associated with variant interpretation are compounded in cases such as inherited retinal disease, in which genetic variants exert their pathogenic effects in a tissue that is not accessible for direct study.
In this dissertation, I aim to show how phenotypic studies of the molecules and cells that are affected by inherited retinal disease variants can expose previously obscure aspects of genetic disease pathogenesis. Chapter 1 provides a broad introduction to the various biological levels at which genetic variation can impact an organism and set the stage for the subsequent chapters in which I present original data at each of these levels. In Chapter 2, I discuss experimental approaches to variant discovery and interpretation from a diagnostic perspective. The main techniques discussed in this chapter (i.e., stem cell-based retinal modeling and transcriptome analysis) serve as the basis for the results presented in the following chapters.
I begin the discussion of specific variant effects in Chapter 3 with the most proximal molecular consequence of a genetic variant, changes to RNA sequence. I describe how transcriptomic analysis of in vitro-generated retinal cells allowed for the discovery of a pathogenic splice variant in a rod photoreceptor-specific gene (NR2E3) that had been previously described as causing a single amino acid substitution. Chapter 4, in turn, describes the consequences of loss of NR2E3 function at a cellular level, again using patient-derived retinal organoids as a surrogate for developing human tissue.
While variants such as those in NR2E3 can influence the cell types produced during development, cell type can also influence the pathogenic effects of a variant within a tissue. A disease-causing variant may act only in one tissue, cell type, or anatomical region. In Chapter 5, I show how even within a specific type of retinal cell (retinal pigment epithelium), differences in the regulation of gene expression exist based on region within the eye. I go on to discuss how these differences may aid in understanding how common genetic variants contribute to age related macular degeneration.
Finally, Chapters 6 and 7 focus on a peculiar genetic system found within human cells, the mitochondrial genome (mtDNA). Mitochondria are semi-autonomous organelles that possess a small, high copy-number genome that encodes only 13 protein-coding genes yet is essential to life. Variants on the mtDNA are known to cause severe, multisystem disease that often involves the retina. In Chapter 6, I develop a system to measure the proportion of mtDNAs carrying a pathogenic variant and show a large variability in mutational burden between tissue types and individual patients. In Chapter 7, I apply a single-cell approach to measuring the burden of mutant mtDNA genomes and observe how the genetic contents of different cells in a patient retina vary by cell type, again highlighting the interplay between variant presence and cell type in informing variant effect.
Chapter 8 includes my brief commentary and reflections on how these and similar approaches may work to enhance our future understanding of genetic variation in the context of disease. Together, these chapters provide new data on the pathogenesis of two inherited retinal diseases and serve as a framework for discovery in broader classes of inherited disease.
Details
- Title: Subtitle
- Cellular and molecular consequences of genetic variants in inherited retinal disease
- Creators
- Nathaniel K Mullin
- Contributors
- Robert Mullins (Advisor)Budd Tucker (Advisor)Michael Anderson (Committee Member)Elaine Binkley (Committee Member)Terry Braun (Committee Member)Todd Scheetz (Committee Member)
- Resource Type
- Dissertation
- Degree Awarded
- Doctor of Philosophy (PhD), University of Iowa
- Degree in
- Genetics
- Date degree season
- Spring 2026
- DOI
- 10.25820/etd.008412
- Publisher
- University of Iowa
- Number of pages
- xxiv, 190 pages
- Copyright
- Copyright 2026 Nathaniel K Mullin
- Language
- English
- Description illustrations
- illustrations, graphs, tables
- Description bibliographic
- Includes bibliographical references (pages 165-190).
- Public Abstract (ETD)
Variants in the genetic code underlie many human traits, including the predisposition to disease. However, the mechanisms by which a variant may disrupt normal tissue function are not always obvious. This problem is compounded when disease-causing variants are found within genes used only in inaccessible tissues such as the retina. Here, I will demonstrate approaches for modeling inherited retinal disease to uncover otherwise obscure details of both disease pathogenesis and normal development.
At the most basic level, a genetic variant imparts its influence through RNA. I will discuss an approach to variant discovery using RNA-sequencing of retinal organoids, which can be derived from stem cells generated from patient samples. I will show how RNA sequence information is required to correctly ascertain the mechanism of a genetic variant in the transcription factor gene NR2E3. I will also show using RNA and DNA sequencing how loss of NR2E3 function in developing retinal organoids causes a developmental fate shift within the photoreceptor lineage. This shift causes an absence of rod photoreceptors and emergence of a novel population of hybrid photoreceptors we term “divergent rods” based on their provenance.
Finally, I will discuss a peculiar genetic feature of eukaryotic cells: the mitochondrial genome. This small, circular genome encodes essential mitochondrial genes and harbors variants that cause vision loss and multi-system disease. I will demonstrate how the proportion of mutant to normal mitochondrial genomes varies between cell types and discuss how these findings relate to the retinal disease caused by mitochondrial DNA variants.
- Academic Unit
- Interdisciplinary Graduate Program in Genetics
- Record Identifier
- 9985177274802771
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