This thesis presents genetic studies aiming at enlarging our knowledge regarding the genetic factors underlying two immune-mediated diseases, hypothyroidism and autoimmune Addison’s disease (AAD), in dogs and humans, respectively. Genetic and environmental factors are indicated to contribute to canine hypothyroidism, which can be considered a model for human Hashimoto’s thyroiditis (HT). In Paper I we performed the first genome-wide association (GWA) study of this disease in three high-risk dog breeds (Gordon Setter, Hovawart and Rhodesian Ridgeback). Using an integrated GWA and meta-analysis strategy, we identified a novel hypothyroidism risk haplotype located on chromosome 12 being shared by the three breeds. The identified haplotype, harboring three genes previously not associated with hypothyroidism, is independent of the dog leukocyte antigen region and significantly enriched across the affected dogs. In Paper II we performed a GWA study in another high-risk breed (Giant Schnauzer) and detected an associated locus located on chromosome 11 and conferring protection to hypothyroidism. After whole genome resequencing of a subset of samples with key haplotypes, we fine mapped the region of association that was subsequently screened for the presence of structural variants. We detected a putative copy number variant overlapping with the upstream region of the IFNA7 gene, which is located in a region of high genomic complexity. Remarkably, perturbed activities of type I Interferons have been extensively associated with HT and general autoimmunity. In Paper III we performed the first large-scale genetic study of human AAD, a rare autoimmune disorder characterized by dysfunction and ultimately destruction of the adrenal cortex. We resequenced 1853 immune-related genes comprising of their coding sequences, untranslated regions, as well as conserved intronic and intergenic regions in extensively characterized AAD patients and control samples, all collected in Sweden. We identified BACH2 gene as a novel risk locus associated with AAD, and we showed its independent association with isolated AAD. In addition, we confirmed the previously established AAD association with the human leukocyte antigen complex. The results of these studies will hopefully help increasing the understanding of such diseases in dogs and humans, eventually promoting their well-being.

Telomerase reverse transcriptase (TERT) is the catalytic subunit of telomerase and the limiting factor for the enzyme activity. The expression of TERT and telomerase activity is increased in atherosclerotic plaques. However, the role of TERT dysregulation during atherosclerosis formation remains unknown. The work herein first identified a multi-tiered regulation of TERT expression in smooth muscle cells (SMC) through histone deacetylase (HDAC) inhibition. HDAC inhibition induces TERT transcription and promoter activation. At the protein level in contrast, HDAC inhibition decreases TERT protein abundance through enhanced degradation, which decreases telomerase activity and induces senescence. Furthermore, during vascular remodeling in vivo, TERT protein expression in the neointima is prevented by HDAC inhibition. These data illustrate a differential regulation of TERT transcription and protein stability by HDAC inhibition. TERT is highly expressed in replicating SMC of atherosclerotic and neointimal lesions. Using a model of guidewire-induced arterial injury, neointima formation was reduced in TERT-deficient mice. Studies in SMC isolated from TERT-deficient and TERT overexpressing mice with normal telomere length established that TERT is necessary and sufficient for cell proliferation. TERT deficiency did not induce a senescent phenotype but resulted in G1 arrest albeit hyperphosphorylation of the retinoblastoma protein. This proliferative arrest was associated with stable silencing of the E2F1-dependent S-phase gene expression program which could not be reversed by ectopic overexpression of E2F1. Chromatin immunoprecipitation and accessibility assays revealed that TERT was recruited to E2F1 target sites to increase chromatin accessibility for E2F1 by facilitating the acquisition of permissive histone modifications. These data indicate a mitogenic effect of TERT on SMC growth and neointima formation through epigenetic regulation of proliferative gene expression. Furthermore, TERT expression is induced in activated macrophages during experimental and human atherosclerosis formation. To investigate the role for TERT in lesional macrophages and the subsequent effect on atherosclerosis formation, TERT-deficient mice were crossbred with LDL-receptor-deficient (LDLr-/-) mice to generate first generation G1TERT-/-LDLr-/- offsprings, which were then further intercrossed to obtain third generation G3TERT-/-LDLr-/- mice. G1TERT-/-LDLr-/- mice revealed no telomere shortening while severe telomere attrition was evident in G3TERT-/-LDLr-/- mice. When fed an atherogenic diet, G1TERT-/-LDLr-/- and G3TERT-/-LDLr-/- mice were both protected from atherosclerosis formation compared to their wild-type controls, indicating that genetic TERT-deletion prevents atherosclerosis, and formation of the disease is not affected by telomere attrition. Similarly, atherosclerosis development was decreased in chimeric LDLr-/- mice with TERT deletion in hematopoietic stem cells after bone marrow transplantation. TERT deficiency reduced macrophage accumulation in atherosclerotic lesions and altered chemokine expression, including CXC1/2/3, CCL3, CCL5, CCL21, CCR7, IL-6, and IL-1α. In isolated macrophages, gene ontology (GO) enrichment analysis of silenced inflammatory genes indicated that TERT positively regulates signal transducer and activator of transcription (STAT) cascade, which was confirmed by the decreased tyrosine phosphorylation of STAT3 protein resulting from TERT deletion. These findings indicate genetic TERT deficiency decreases atherosclerosis formation by silencing inflammatory chemokine transcription through inactivation of the STAT3 signaling pathway in activated macrophages. In conclusion, the dysregulation of TERT expression within atherosclerotic plaques plays a causative role for vascular remodeling, including injury-induced neointima formation and hypercholesterolemia-induced atherosclerosis, through inducing SMC proliferation and a pro-inflammatory phenotype in infiltrating macrophages. These findings unveil a mechanism of TERT exacerbating the pathological vascular remodeling, which may provide a novel therapeutic target to combating vascular diseases.

The retinoic acid induced 1 (RAI1) gene maps within the Smith-Magenis syndrome (SMS) region on chromosome 17p11.2. Interstitial deletion of 17p11.2 including RAI1 or mutation of RAI1 results in SMS, while duplication of 17p11.2, including RAI1, results in the dup(17)(p11.2) syndrome. Smith-Magenis syndrome is a complex disorder characterized by a constellation of ~30 features that includes mental retardation, sleep disturbance, craniofacial defects, neurological and behavioral anomalies, and variable systemic features. Dup(17)(p11.2) syndrome is characterized by mental retardation, craniofacial defects, developmental delay, failure to thrive, and hyperactivity. We hypothesized that RAI1 is a dosage-sensitive gene with specific roles in SMS and dup(17)(p11.2) syndrome. To understand the clinical consequences of haploinsufficiency of RAI1 in humans, 60 SMS patients were evaluated by fluorescent in situ hybridization and/or sequencing of RAI1 to identify 17p11.2 deletions or intragenic mutations. Phenotypic comparison between patients with deletions and those with RAI1 mutations show that 21 of 30 SMS features are the result of haploinsufficiency of RAI1. Other features such as cardiac and renal anomalies, speech and motor delay, chronic respiratory and ear infections, hypotonia, short stature, and ear and eye anomalies are associated with 17p11.2 deletions rather than RAI1 mutations (P <0.05). Mouse models were evaluated using both qualitative and quantitative methodologies for phenotypic consequences due to altered Rai1 dosage. To this extent, BAC transgenic mice overexpressing Rai1 1.5-fold (hemizygous) or 2-fold (homozygous) and Rai1-targeted heterozygous (Rai1+/-) mice with 0.5-fold dosage were utilized. Compared to wild type littermates, Rai1 overexpressing mice have growth retardation, increased locomotor activity, gait abnormalities, and abnormal anxiety-related behavior, while Rai1+/- mice are obese and hypoactive. Analyses of homozygous BAC transgenic mice revealed a dosage-dependent exacerbation of the phenotype. Both the Rai1-overexpressors and Rai1-haploinsufficient mice showed neurological deficits. To identify target genes altered due to haploinsufficiency of RAI1, RNA-interference-based knockdown (~50%) of RAI1 was achieved in HEK293T cell lines. Genome-wide gene expression profiling showed that ~60 genes were upregulated and ~200 genes were downregulated due to RAI1 haploinsufficiency. Real-time qPCR not only confirmed the gene expression profile in HEK293 cells but also in lymphoblastoid cell lines obtained from SMS patients with 17p11.2 deletion. Further, our analysis has identified several RAI1 downstream genes, implicated in circadian activity, growth regulation, lipid biosynthesis, and neuronal regulation, which are potential candidate genes for non-deletion/non-RAI1-mutation cases of SMS and SMS-like phenotypes. These results show that Rai1 dosage has major consequences on molecular processes involved in growth, development, circadian rhythm, and neurological and behavioral functions, thus providing evidence for several dosage-thresholds for phenotypic manifestations causing dup(17p11.2) syndrome or Smith-Magenis syndrome in humans.

The ras genes, including Harvey ras (H-ras) and Kirsten ras (K-ras), were among the first oncogenes discovered, and are the most commonly mutated oncogenes in human cancer. The H-ras and K-ras proteins are 85% identical and share considerable functional overlap. However, there is increasing evidence for functional differences between the two proteins that may impart different properties to tumors arising from mutations in these two genes. To study the functional differences between H-ras and K-ras in an in vivo setting, we used two different transgenic mouse tumor models, MMTV-H-ras and MMTV-K-ras mice. The MMTV-H-ras mice were originally developed in Dr. Leder's lab and have been well characterized with regard to tumor properties. We created a similar line of transgenic mice expressing mutant K-ras (G12V) under the control of the MMTV promoter. Female mice of both lines develop primarily mammary tumors. We compared differences between the H-ras and K-ras lines with regard to age of tumor onset, rate of tumor growth, and rates of tumor proliferation and apoptosis. The tumors were also characterized by microarray analysis to look for genes that are differentially expressed in the two tumor types. Finally, the response of tumors to two common chemotherapeutic agents, doxorubicin and taxol, was also measured. We found that tumors in the MMTV-H-ras and MMTV-K-ras mice were similar with respect to several tumor properties, including age of onset, histopathology, and proliferation and apoptotic indices. While tumors from mice of these two genotypes clustered separately in an unsupervised analysis of gene expression profiles, the differentially expressed genes did not fall within any well-defined signaling pathways. However, drug studies indicated differences in response to doxorubicin between the two isoforms, with H-ras tumors responding better than K-ras tumors. In conclusion, our studies point to specific differences between H-ras and K-ras that may represent novel signaling pathways not currently known to be regulated by Ras. In spite of the few differences in properties of tumors arising from H-ras and K-ras mutation, there might be differences in response to chemotherapeutic agents that could have clinical significance.

p53 is an important tumor suppressor gene which is mutated in ~50% of all human cancers. Some of the p53 mutants appear to have acquired novel functions beyond merely losing wild-type functions. To investigate these gain-of-function effects in vivo, we interbred MMTV-v-Ha-ras transgenic mice to either p53-/- knock-out mice or p53R172H/+ knock-in mice to generate mice of three different genotypes: MMTV-ras, MMTV-ras/p53-/-, and MMTV-ras/p53R172H/R172H. Male mice of each of these genotypes were characterized with regard to age of salivary tumor onset and the tumors were characterized with regard to mean growth rates, proliferation fraction, apoptotic levels, and tumor histopathology, as well as responses to doxorubicin treatment. Microarray analysis was also performed to profile gene expression.The MMTV-ras/p53-/- and MMTV-ras/p53R172H/R172H mice display similar properties in age of tumor onset, tumor growth rates, and tumor histopathology, as well as response to doxorubicin. However, a subset of genes show differential expression between the two groups of tumor , and do not appear to be regulated by wild-type p53. At the same time, the MMTV-ras/p53R172H/R172H and MMTV-ras/p53+/+ tumors share similar expression levels of a group of genes that are differentially expressed in the MMTV-ras/p53-/- tumors. Thus, the gain-of-function effects may be caused in part by perturbed regulation of genes not normally regulated by wild-type p53, in addition to imbalances in the regulation of normal p53 target genes.

Aging is an intrinsic process that is independent of obvious disease. In contrast to normal aging, age-related diseases are conditions that typically manifest at advanced ages, are associated with explicit pathology and cause disability and premature death. We used Drosophila as a model to investigate the molecular-genetic mechanisms associated with aging and age-related disease. Age-related locomotor impairment (ARLI) is a serious condition for the elderly and greatly impacts their quality of life. Toward identifying genes and mechanisms that influence ARLI, we performed a forward genetic screen using Drosophila mutants. This screen identified a loss of function mutant in PDK1, a component of the insulin signaling pathway. Additional loss of function mutants in the insulin signaling pathway genes PI3K Dp110, and AKT also delayed ARLI. These results suggest a role for insulin signaling in ARLI. Wolfram Syndrome (WFS) is a progressive neurodegenerative disease that is caused by mutations in the genes WFS1 and CISD2. The function of CISD2, the most recently identified gene has not been fully resolved. We used RNAi to knockdown wfs2, the fly ortholog of CISD2 to identify genes and pathways associated with wfs2 that will provide insight into the normal function of this gene. Through a targeted genetic screen in the Drosophila eye we identified that wfs2 interacts with two lysosomal storage disease genes PPT1 and CLN3. These results suggest that WFS and lysosomal storage diseases may be influenced by common molecular-genetic mechanisms. Furthermore, wfs2 may play a role in the neurodegenerative pathways associated with lysosomal storage disease. Oxidative stress is associated with aging and age-related disease. To identify genes that can protect against endogenous oxidative stress we performed a candidate suppressor screen. This screen revealed that expression of wild-type Ataxin-3 suppressed the short lifespan of Sod2 knockdown flies. The ubiquitin associated function of Ataxin-3 was determined to be important for this suppression. Interestingly, Ataxin-3 expression also extended the short lifespan due to knockdown of thioredoxin reductase in muscle. These results suggest that Ataxin-3 expression may play a protective role against enhanced endogenous oxidative stress due to reduced function of a number of antioxidant enzymes.

The primary aim of this study was to determine the effectiveness of array-based technology for detecting and quantifying the presence of mosaicism. This aim was achieved by studying individuals having mosaicism for Down syndrome. SNP arrays were performed on 13 samples from individuals with mosaicism for trisomy 21, 13 samples from individuals with normal chromosome 21complements (negative controls) and 5 samples from individuals with full or partial trisomy 21 (positive controls). In addition, BAC arrays were processed on 6 samples from individuals with mosaicism for trisomy 21, 3 negative controls and 1 positive control. These studies have shown that array-based technology is effective for detecting mosaicism that is present in 20% or more cells with the results being consistent for both platforms. We also demonstrated the strength of array-based technology to identify previously unrecognized chromosomal mosaicism. A second aim of this study was to gain insight regarding the effect that trisomy 21 has on telomere attrition and the frequency of chromosomal instability. This study provides the first reported measure of both chromosome-specific telomere lengths and the frequency of acquired chromosome abnormalities in trisomic cells and isogenic euploid cells obtained from the same individuals. A chromosome-specific telomere length assay was performed on lymphocytes obtained from 24 young individuals with mosaicism for Down syndrome. While differences in overall telomere signal intensities were observed between the euploid and trisomic cells within a person, strikingly similar profiles for chromosome-specific telomere intensities were observed between the cell types within a person. Analyses were also completed on lymphoblast samples obtained from 8 older individuals with mosaicism for Down syndrome, including 5 individuals without dementia and 3 individuals with dementia. In the older study subjects, a significant inverse correlation was observed between telomere length and the frequency of micronuclei, suggesting that telomeric shortening is leading to an increased frequency of chromosomal instability, possibly through dicentric chromosome formation. However, further studies of more individuals, especially additional analyses of older individuals, are needed. These future studies may help to identify genomic regions of interest and serve to inform investigators of potential candidate genes in the etiology of dementia.

Clic proteins influence ethanol-related behavior in flies and other species and also mediate TGF-β signaling. These findings suggest that Clics and the TGF-β signaling pathway might work together to modulate behavioral responses to ethanol. I used the Drosophila model to address the hypothesis that TGF-β signaling is important for ethanol sensitivity. Ethanol sensitivity was blunted by multiple transposon insertions in the TGF-β receptor gene thickveins. Collectively, however, I found no consistent correlation between expression of thickveins and altered ethanol sensitivity in flies harboring transposons. I therefore also assessed ethanol sensitivity in flies with loss of function point mutations in thickveins. Ethanol sensitivity was not altered in these additional thickveins genotypes, contrary to my major hypothesis. My analysis of thickveins suggests that TGF-β signaling might influence ethanol sensitivity, but if so there must be a complex relationship between the function of this pathway and sensitivity to alcohol.

Decades of work has led researchers to believe that risk for complex behavioral phenotypes, such as alcohol use disorders, is likely influenced by multiple genes of small effect acting in conjunction with each other and the environment. Currently, the field of psychiatric genetics is developing methodologies for the identification of genetic risk variants that predispose individuals to the development of complex behavioral disorders. Several challenges related to the complex and polygenic nature of these phenotypes, must be considered. This dissertation study attempts to address these important challenges in the context of alcohol use disorders and related phenotypes. A rich twin and family study literature has indicated that 40-70% of the variance in alcohol use disorders (AUDs) is influenced by genetics. Recent attempts to identify specific x genetic risk variants associated with AUDs have been met with limited success. Meanwhile, evidence of the moderating effects of the environment on AUDs has been mounting, providing a strong rationale for examining gene-environment interaction. In the following chapters several studies will be described that integrate established twin methodologies into gene identification projects in an effort to reduce heterogeneity (both phenotypic and genotypic), elucidate environmental constructs that moderate genetic influences, and to enhance statistical power to detect the subtle genetic influences on alcohol related phenotypes.

Family-based and genome-wide association studies (GWAS) of alcohol dependence (AD) have reported numerous associated variants. The clinical validity of these variants for predicting AD compared to family history has not yet been reported. These studies aim to explore the aggregate impact of multiple genetic variants with small effect sizes on risk prediction in order to provide a clinical interpretation of genetic contributions to AD. Data simulations showed that given AD’s prevalence and heritability, a risk prediction model incorporating all genetic contributions would have an area under the receiver operating characteristic curve (AUC) approaching 0.80, which is often a target AUC for screening. Adding additional environmental factors could increase the AUC to 0.95. Using the Collaborative Study on the Genetics of Alcoholism (COGA) and the Study of Addiction: Genes and Environment (SAGE) GWAS samples, we used several different sources to capture genetic information associated with AD in discovery samples, and then tested genetic sum scores created based on this information for predictive accuracy in validation samples. Scores were assessed separately for single nucleotide polymorphisms (SNPs) associated in candidate gene studies and in GWAS analyses. Candidate gene sum scores did not exhibit significant predictive accuracy, but SNPs meeting less stringent p-value thresholds in GWAS analyses did, ranging from mean estimates of 0.549 for SNPs meeting p<0.01 to 0.565 for SNPs meeting p<0.50. Variants associated with subtypes of AD showed that there is similarly modest and significant predictive ability for an externalizing subtype. Scores created based on all individual SNP effects in aggregate across the entire genome accounted for 0.46%-0.57% of the variance in AD symptom count, and have AUCs of 0.527 to 0.549. Additional covariates and environmental factors that are correlated with AD increased the AUC to 0.865. Family history was a better classifier of case-control status than genetic sum scores, with an AUC of 0.686 in COGA and 0.614 in SAGE. This project suggests that SNPs from candidate gene studies and genome-wide association studies currently have limited clinical validity, but there is potential for enhanced predictive ability with better detection of genetic factors contributing to AD.