Browsing by Author "Gregory, Simon G"

Fuchs endothelial corneal dystrophy (FECD) is a complex, late-onset disorder that is a frequent indication for corneal transplantation and affects women more frequently than men. Although linkage and association studies in patients of European and Asian ancestry have started to explain the genetic basis of this disorder, the mechanism by which FECD develops is still unclear. Three projects were undertaken to help elucidate the genetic basis of FECD. The first project examined a large, multigenerational family that exhibited strong familial clustering of FECD and identified evidence of linkage to chromosome 18. This locus that has also been implicated through work on large and small FECD families as well as unrelated patients. The second project examined African-Americans with FECD and is the first work to examine this population of patients with respect to the FECD phenotype. Novel variants in three FECD candidate genes, COL8A2, SLC4A11, and ZEB1 were identified at approximately the same rate as observed in patients of other ancestries, reinforcing the notion that these genes only contribute to a small fraction of FECD genetic susceptibility. Finally, the influence of environmental factors on FECD susceptibility was examined through the use of a risk factor questionnaire given to cases and controls at the time of study enrollment. Several factors, including gender, age, and cataracts, were found to significantly affect FECD risk. Gender and the number of cataract surgeries were found to significantly interact with a genetic variant, rs613872 in the TCF4 locus on chromosome 18 that has been consistently and reproducibly associated with FECD, to influence FECD susceptibility. Together, these findings indicate that the genetic basis of FECD is complex, and recent advances in the field show promise in accelerating the pace of discovery that will hopefully develop better FECD treatments in the near future.

Neural tube defects (NTDs) are a common class of human birth defects with a complex, multifactorial etiology. Although many contributing factors have been identified, an estimated 60% of human population risk remains unexplained. A portion of that risk is likely attributable to gene-gene and gene-environment interactions which have yet to be fully elucidated. In one project, we used whole-exome sequencing to identify candidate genetic factors in a multiplex anencephaly family, revealing an aggregation of rare and common variants in planar cell polarity genes among the affecteds. In the second project, we profiled the methylomes of a pair of monozygotic twins discordant for anencephaly and identified several differentially methylated sites which could contribute to NTD risk, particularly the mir-886 locus. Finally, we performed whole-exome and whole-methylome sequencing of mouse strains with differential susceptibility to fumonisin-induced NTDs, in combination with a human SNP association study. We identified epigenetic changes and variant associations which implicate Wnt and Hippo signaling genes as modifiers of the metabolic impacts of fumonisin exposure. These findings underscore the complexity of NTD pathogenesis and highlight the need to elucidate gene-gene and gene-environment interactions contributing to NTD etiology.

Chiari Type I Malformation (CMI) is a developmental disorder characterized by displacement of the cerebellar tonsils below the base of the skull, resulting in significant neurologic morbidity. While there are multiple proposed mechanisms for tonsillar herniation, "classical" CMI is thought to occur due to a compromised posterior cranial fossa (PF). As CMI patients display a high degree of clinical variability, it is hypothesized that this heterogeneous disorder has a complex etiology influenced by multiple genetic and environmental factors. Despite the fact that multiple lines of evidence support a genetic contribution to disease, no genes have been identified to date. Thus, the primary goal of this dissertation is to begin to dissect the genetic etiology of this important disorder and gain a better understanding of what factors contribute to the observed disease heterogeneity.

In order to address these goals, two studies and three distinct analytic approaches were carried out. In the first study, 367 individuals from 66 nonsyndromic, CMI multiplex families provided the basis for a whole genome linkage screen to identify genomic regions likely to harbor CMI susceptibility genes. Results from the linkage screen using the complete collection of families yielded limited evidence for linkage, likely due to genetic heterogeneity. Thus, two separate analytic approaches were applied to the data to reduce phenotypic and hopefully genetic heterogeneity, thereby increasing power to identify disease genes. In the first approach, families were stratified based on the presence or absence of connective tissue disorder (CTD) related conditions as hereditary CTDs are commonly associated with CMI and the presumed mechanism for tonsillar herniation differs between CMI patients with CTDs and "classical" CMI patients. Stratified analyses resulted in increased evidence for linkage to multiple genomic regions. Of particular interest were two regions located on chromosomes 8 and 12, both of which harbor growth differentiation factors, GDF6 and GDF3, which have been implicated in Klippel-Feil syndrome (KFS). In the second approach, a comprehensive evaluation of the genetic contribution to the PF was performed, followed by ordered subset analysis (OSA) using heritable, disease-relevant PF traits to identify increased evidence for linkage within subsets of families that were similar with respect to cranial base morphological traits. Much of the PF was found to be heritable and results from OSA identified multiple genomic regions showing increased evidence for linkage, including regions on chromosomes 1 and 22 which implicated several strong biological candidates for disease.

In the second study, 44 pediatric, surgical CMI patients were ascertained in order to establish disease subtypes using whole genome expression profiles generated from patient blood and dura mater samples and radiological data consisting of PF morphometrics. Sparse k-means clustering as well as a modified version were used to cluster patients using the biological and radiological data both separately and collectively. The most significant patient classes were identified from the pure biological clustering analyses. Further characterization of these classes implicated strong biological candidates involved in endochondral ossification from the dura analysis and a blood gene expression profile exhibiting a global down-regulation in protein synthesis and related pathways that may be associated with comorbid conditions.

Collectively, these studies established several strong biological disease candidates, as well as emphasized the need to better understand and account for disease heterogeneity, re-evaluate the current diagnostic criteria for CMI, and continue to investigate the use of endophenotypes, such as cranial base morphometrics, when conducting genetic studies.

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Human beings are inherently social. As we grow, the interactions we have with those around us become the foundation of the relationships with our families, friends, educators, and caretakers. Aberrant social behavioral traits can put a strain on these relationships and negatively impact an individual's quality of life. When severe, these disruptions represent core etiological features of many neurodevelopmental and behavioral disorders, including addiction, schizophrenia, and autism spectrum disorder (ASD).

Advances in the fields of psychology, psychiatry, neuroscience, and the behavioral sciences have developed a wide range of techniques to disentangle the biological and behavioral components of complex social traits, often with the goal of developing targeted interventions to improve outcomes for affected individuals. Still, there remains a massive unmet need for pharmaceutical interventions that ameliorate these aberrant social phenotypes, and current interventions are costly and labor intensive. A particularly promising candidate to address this unmet need is \Oxy, an endogenously expressed neuropeptide, with demonstrated pro-social effects in both humans and animal models, and low incidence of adverse effects. However, clinical trials of \oxy in ASD have had mixed results, likely due to a range of issues from inadequately powered study designs, difficulty in quantifying changes in social behavior over time, heterogeneous study populations, and an inadequate understanding of the underlying mechanisms of \oxy signaling in the brain.

The work described in this dissertation aims to address some of these gaps in knowledge. First, the results of a collaboration with a phase-2 clinical trial of \inoxy are discussed, in which I contributed to identifying a number of biological markers that were associated with \enoxy production in human participants. I discuss how this may be an important component of predicting an individuals response to \exoxy.

I will then discuss our findings in the \cd{} mouse model of ASD-like behaviors. These mice exhibit a unique socially divergent phenotype in which some mice will display very little social motivation within litters while the others behave normally. Importantly, these antisocial mice are responsive to treatment with \exoxy, but the mechanisms behind their unique social phenotype and responsiveness to \oxy remain unknown. I quantified broad patterns of differential gene expression and DNA methylation in the brains of \cd{} mice and their closely related but highly social \cs{} counterparts. This work identified a pattern of differential gene expression in the hippocampus of \cs{} mice that may offer insights into the nature of their naturally occurring social divergence.

Collectively, the findings of these two projects provide valuable information to the field of \oxy and ASD research. The results of the human trial can be used to guide new studies into the endogenous regulation of \oxy, providing potential targets for future interventions to responsive candidates. The results of the mouse experiments identified a myriad of underlying biological pathways that distinguish \cd{} from \cs{} mice, which can serve as the foundation for new targeted hypotheses and to test expanded pharmaceutical interventions to enhance the effects of \exoxy.