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Amyotrophic lateral sclerosis (ALS) is a rapidly progressing neurodegenerative disorder characterized by loss of upper and lower motor neurons. TDP-43 was identified as a major protein component of the characteristic neuronal inclusions and it has been detected in 90% of ALS cases. Furthermore, pathogenic mutations in the gene encoding TDP-43, TARDBP, were found in both sporadic and familial ALS cases. The aim of this study is to investigate the molecular mechanisms of cellular dysfunction and ultimately death caused by TDP-43 mutations in human cells using established cell lines and human motor neurons derived from induced pluripotent stem cells (iPSCs). We generated a novel in vitro cellular model using a fluorescently tagged human genomic TARDBP locus carrying three ALS-specific mutations, A382T, M337V or Y374X. In site specific bacterial artificial chromosome (BAC) human stable cell lines, TDP M337V mislocalized to the cytoplasm more frequently than wild-type TDP-43 (TDP Ypet) and TDP-A382T, an effect potentiated by oxidative stress. Cytoplasmic mislocalization was significantly higher in TDP M337V cells compared to TDP-Ypet and correlated with cell death. Cells expressing the mislocalized TDP M337V mutant spontaneously developed cytoplasmic punctae, while for TDP-A382T punctae were only revealed after endoplasmic reticulum (ER) stress induced by the calcium-modifying drug thapsigargin (TG). Lowering Ca2+ concentration in the ER of TDP-Ypet cells partially recapitulated the effect of pathogenic mutations by increasing TDP-43 cytoplasmic mislocalization, suggesting Ca²⁺ dysregulation as a potential mediator of pathology. Ca²⁺ signaling from the ER was impaired in cells carrying TDP-43 mutations, with a 50% reduction in the levels of luminal ER Ca²⁺ stores content and delayed Ca²⁺ release induced by carbachol compared to TDP-Ypet cells. The deficits in Ca²⁺ release correlated with upregulation of Bcl-2 and siRNA-mediated knockdown of Bcl-2 restored amplitude of Ca²⁺ oscillations in TDP-M337V cells. These results suggest that TDP-43 pathogenic mutations elicit cytoplasmic mislocalization of TDP-43 through Bcl-2 regulation of ER Ca²⁺ signalling. Preliminary work in iPSC-derived motor neurons transduced with genomic DNA expression TDP-43 vectors using Herpes Simplex Virus type 1 (HSV-1) amplicons showed cytoplasmic redistribution of TDP-43 under high oxidative stress, without significant differences between mutations and wild-type. TDP-43 mutations delivered by HSV-1 amplicons also did not affect survival of iPSC-derived motor neurons. In ALS patient-derived motor neurons carrying C9orf72 expansions, TDP-43 pathology was not detected. However, preliminary data indicate that C9orf72 MNs present ER Ca²⁺ dysregulation with significantly high intracellular Ca²⁺ concentration, which correlates with high protein levels of ER stress markers and low levels of Bcl 2. This work highlights a potentially pathogenic role for TDP-43 mutations in the dysregulation of Ca²⁺ homeostasis and explores the use of iPS technology to investigate the effects of ALS-associated mutations in healthy and patient-derived motor neurons.

Nicotinic acid (NA) has been clinically used for over 50 years to regulate lipid plasma levels. It is the only drug in current clinical use that significantly raises HDL cholesterol and reduces inflammatory markers. However, mechanistic understanding into its wide range of actions remains unclear. The recent identification of the Gi-coupled protein receptor HCAR2, for which NA is a potent agonist, provides intriguing insight due to its anti-lipolytic action and restricted, yet specific, expression in adipose tissue and immune cells. The HCAR2 gene is 96% homologous to HCAR3, but the HCAR3 receptor shares neither the specificity for NA, nor the range of functional effects. Moreover, the close homology makes it difficult to separate the genetic variability and regulation of the two genes. To this end, I resequenced HCAR2 and HCAR3 in a selected population to characterize the variability of the two genes and to inform the subsequent design of specific genotyping assays. The Oxford Biobank, which is a random population-based collection of 30-50 year old men and women in Oxfordshire with a wide range of collected phenotypes, was used to explore genetic associations. A preliminary trend with HDL and rs7314976 in HCAR2 motivated the further search associations. However after increasing the sample size, the HDL association did not reach significance. When looking at inflammatory phenotypes, a 20% lower level of systemic hsCRP was found in males with a promoter region variant in HCAR3 (N=1808, p=0.007 for rs55718746). Replication of this finding in two relevant cohorts (NPHS-II, N=2185 and Whitehall, N=4228) resulted in conflicting findings. After optimising the specific detection of both HCAR2 and HCAR3 transcripts, I characterized gene expression in human AT biopsies. This revealed an 18% increase in HCAR2 expression in the female abdominal depot (N=106, p<0.0001) and a reduction in abdominal HCAR2 in both males (β=-0.37, p<0.001, N=107) and females (β=-0.251, p=0.005, N=106) with increasing adiposity. The rs55718746 variant in HCAR3 was also seen to influence expression of both HCAR2 (N=182, p=0.018 in the abdominal depot) and HCAR3 (N=198, p=0.005) but surprisingly in opposite directions, establishing it as the first cis-eQTL for this genomic region. Finally, I used human adipocyte in vitro culture systems to setup a pilot to study the anti-inflammatory effects of NA. The gene expression of HCAR2 and HCAR3 increased significantly with adipocyte differentiation in vitro. NA led to a drop in IL-6 transcript abundance in two out of three of the in vitro differentiated human adipocytes. In conclusion, genetic variability in HCAR2 and HCAR3 shows weak associations with cardiovascular disease risk phenotypes relating to their respective pathways. The relevance of HCAR2 and HCAR3 gene expression and the role of the receptor in the control of inflammation will require further studies.

Type 2 diabetes (T2D) has a genetic component which is only partially understood. The majority of genetic variance in disease susceptibility is unaccounted for, whilst the precise transcripts and molecular mechanisms through which most risk variants exert their effect is unclear. A complete understanding of T2D susceptibility mechanisms could have benefits in risk prediction, and in drug discovery through the identification of novel therapeutic targets. Work presented in this thesis aims to define relevant transcripts and disease mechanisms at known susceptibility loci, and to identify disease association with classes of genetic variation other than common single nucleotide polymorphisms (SNPs). KCNQ1 contains intronic variants associated with T2D susceptibility and β-cell dysfunction, but only maternally-inherited alleles confer increased disease risk. It maps within an imprinted domain with an established role in congenital and islet-specific growth phenotypes. Using human adult islet and foetal pancreas samples, I refined the transcripts and developmental stage at which T2D susceptibility must be conferred by demonstrating developmentally plastic monoallelic and biallelic expression. I identified a potential risk mechanism through the effect of T2D risk alleles upon DNA methylation. The disease-associated regions identified through genome-wide association (GWA) studies often contain multiple transcripts. I performed mRNA expression profiling of genes within loci associated with raised proinsulin/insulin ratios in human islets and metabolically relevant tissues. Some genes (notably CT62) were not expressed and therefore excluded from consideration for a risk effect, whilst others (for example C2CD4A) were highlighted as good regional candidates due to specific expression in relevant tissues. GWA studies for T2D risk have focused predominantly upon common single nucleotide polymorphisms. As part of a consortium conducing GWA analysis for copy number variation (CNV) and T2D risk, I optimised and compared alternative methods of CNV genotyping, before using this information to validate two signals of disease association. I genotyped three rare single nucleotide variants emerging from an association study with T2D risk based on imputed data, providing an indication of imputation accuracy and more powerful disease association analysis. These data underscore the challenge of translating association signals to causal mechanisms, and of identifying alternative forms of genomic variation which contribute to T2D risk. My work highlights candidates for functional analysis around proinsulin-associated loci, and makes significant progress towards uncovering risk mechanisms at the KCNQ1 locus.

Since the initial description of cancer stem cells (CSCs) as a self-renewing subpopulation of malignant cells with tumor-initiating capacity, a growing body of evidence has supported the existence of CSCs in virtually every tumor type. Our previous work in colorectal cancer has identified the transcription factor CDX1 as a key regulator of colorectal CSC differentiation. CDX1 expression is frequently lost in colorectal cancer, resulting in more aggressive, poorly differentiated tumors with higher proportions of CSCs. Many miRNAs have been implicated in tumor suppression and carcinogenesis, but the roles of miRNAs in differentiation, particularly in colorectal cancer, remain poorly understood. We began by identifying miRNAs downstream of CDX1 by using high-throughput small-RNA sequencing to profile miRNA expression in two pairs of colorectal cancer cell lines with stable CDX1 overexpression or knockdown. Validation of candidates identified by RNAseq in a larger cell line panel revealed miR-215 to be most significantly correlated with CDX1 expression. ChIP-qPCR and promoter reporter assays confirmed that CDX1 directly transactivates miR-215 transcription. MiR-215 is depleted in FACS-enriched CSCs compared to unsorted samples. Overexpression of miR-215 in poorly-differentiated, highly clonogenic cell lines causes growth arrest and a dramatic decrease in colony formation. miR-215 knockdown using a miRNA sponge causes an increase in clonogenicity and impairs differentiation in CDX1-high cell lines. Indeed, the effects of CDX1 expression on both gene expression and colony morphology can be attenuated by miR-215 inhibition, indicating that miR-215 is a functional mediator of CDX1. Microarray studies following miR-215 overexpression indicate that miR-215 induces terminal differentiation-associated growth arrest, due in part to direct silencing of BMI1 expression and de-repression of BMI1 target genes including CDKN1A. Our work situates miR-215 as a link between CDX1 expression and BMI1 repression that governs differentiation in colorectal cancer. We further characterize another miRNA-transcription factor axis in colorectal cancer, and we identify the novel miR-3189-3p as a potent effector of cell death with potential therapeutic implications.

Human Artificial Chromosomes (HACs) have been confirmed as viable gene expression vectors and a potential tool for gene therapy. However, standard lipid-based delivery methods pose a developmental barrier. The work presented in this thesis includes the development of a novel and efficient HAC vector system for gene delivery into human cells using Herpes Simplex Virus-1 (HSV-1) amplicon technology. The development of HSV-1 amplicons for HAC delivery is a major step forward in the HAC field. In this study, utilising the technology allowed the generation of HACs at a high efficiency in a range of human cell types, which is a significant step in the development for HAC gene expression systems. Further work also showed a significant difference in HAC stability between cell lines. Real-time PCR analysis determined that Aurora B was over expressed in cell lines in which the HACs were unstable. This correlated with high levels of chromosomal instability and was confirmed by western blot analysis. Since Aurora B is a kinase involved in at least two cell cycle checkpoints, cellular phosphorylation levels were perturbed to mimic that observed in the unstable cells, using okadaic acid, which is both a protein phosphatase inhibitor and activates Aurora B. Treatment of cells showed an increase in both HAC and overall chromosomal instability and an increase in histone H3 Serine 10 and Serine 28 phosphorylation. The project also focussed on the development of a gene expression system using HSV-1 amplicons. Two different strategies were explored. Firstly, one approach involved engineering the HPRT genomic locus into an HSV-HAC vector, by Red mediated recombination for complementing the HPRT deficiency in HPRT- HT1080 cells. As an alternative approach, co-infection of two different HSV-1 HAC amplicons for generating a single HAC gene vector was investigated. Initial experiments utilising the latter approach were the most successful and show promise for generating HAC containing genes via this strategy.

Genome-wide association studies (GWAS) exploit the correlation in ge- netic diversity along chromosomes in order to detect effects on disease risk without having to type causal loci directly. The inevitable downside of this approach is that, when the correlation between the marker and the causal variant is imperfect, the risk associated with carrying the predisposing allele is diluted and its effect is underestimated. This thesis explores four different facets of this risk dilution: (1) estimating true effect sizes from those observed in GWAS; (2) asking how the context of a GWAS, including the population studied, the genotyping chip employed, and the use of im- putation, affects risk estimates; (3) assessing how often the best-associated SNP in a GWAS coincides with the causal variant; and (4) quantifying how departures from the simplest disease risk model at a causal variant distort the observed disease risk model. Using simulations, where we have information about the true risk at the causal locus, we show that the correlation between the marker and the causal variant is the primary driver of effect size underestimation. The extent of the underestimation depends on a number of factors, including the population in which the study is conducted, the genotyping chip employed, whether imputation is used, and the strength, frequency, and disease model of the risk allele. Suppose that a GWAS study is conducted in a European population, with an Affymetrix 6.0 genotyping chip, without imputation, and that the causal loci have a modest effect on disease risk, are common in the population, and follow an additive disease risk model. In such a study, we show that the risk estimated from the most associated SNP is very close to the truth approximately two-thirds of the time (although we predict that fine mapping of GWAS loci will infrequently identify causal variants with considerably higher risk), and that the best-associated variant is very often perfectly or nearly-perfectly correlated with, and almost always within 0.1cM of, the causal variant. However, the strong correlations among nearby loci mean that the causal and best-associated variants coincide infrequently, less than one-fifth of the time, even if the causal variant is genotyped. We explore ways in which these results change quantitatively depending on the parameters of the GWAS study. Additionally, we demonstrate that we expect to identify substantial deviations from the additive disease risk model among loci where association is detected, even though power to detect departures from the model drops off very quickly as the correlation between the marker and causal loci decreases. Finally, we discuss the implications of our results for the design and interpretation of future GWAS studies.

Genetic polymorphism in Plasmodium falciparum is a considerable obstacle to malaria intervention. Parasites have repeatedly evolved to overcome every front-line antimalarial deployed throughout history, and artemisinin resistant populations are expanding in Southeast Asia. Promising vaccine candidates routinely fail when challenged by the genetic diversity of natural parasite populations, and a recent trial using a blood-stage antigen showed immunity was allele specific. Modern sequencing technologies have revolutionized our understanding of parasite genomics and population genetics by providing access to single nucleotide variation, but characterizing more complex polymorphism remains a key challenge. Solving this problem is important because the selective pressures from drugs and host immunity often create complex polymorphism in the most clinically relevant genes that is missed using standard genotyping methods. In three sections, this thesis is a narrative about 1) encountering complex variation, 2) overcoming it with novel tools, and then 3) innovatively applying those tools to old and new questions. I first show examples of complex variation in a vaccine candidate (EBA-175) and a drug resistance gene (pfcrt) while reporting SNP based analyses of Kenyan and Tanzanian field isolates. While introducing this complex variation I also describe biological insights discovered in these populations. In Kenya I show evidence that chloroquine resistance selects for parasites that are primaquine sensitive, use a GWAS approach to discover new drug resistance loci, and catalogue variation in known resistance genes. In Tanzania I describe the population structure and allele frequencies of parasites from two geographic regions. In the second section of the thesis I develop methods for accessing complex variation and demonstrate their utility by producing de novo assemblies of eba-175, pfcrt, ama1, and msp3.4 from thousands of sequenced samples. Finally, in the third section I apply these tools in depth to eba-175. I comprehensively characterize the SNP and structural variation in eba-175 using an alignment of 1419 de novo assemblies. I use this resource to illustrate the profiles of positive selection across the gene, and corroborate these signals of balancing selection by showing the geographic distribution of the F/C indels and a lesser known 6bp indel positioned between the DBL domains. I then use the alignments to design Sequenom genotyping assays that facilitate a genome wide association study, testing for human associations with the eba-175 indels in the infecting parasite. I close by reporting a potential association on human chromosome 14 with the 6bp indel in eba-175.

By undertaking a number of different experimental approaches at the genetic, cellular/ molecular and integrative physiology levels, I investigated functional variation in the Hypoxia-Inducible Factor (HIF) transcription pathway in humans. My studies focused on Tibetan natives. Tibetan highlanders are adapted to life in a hypoxic environment and exhibit distinct physiological traits at high altitude. Recent studies identified positive selection at two genetic loci, EPAS1 (HIF2α) and EGLN1 (PHD2), in Tibetan highlanders and demonstrated an association of EGLN1/EPAS1 genotype with haemoglobin concentration. Both are genes of the HIF pathway, which coordinates an organism’s response to hypoxia. Patients living at sea level with genetic diseases of the HIF pathway have characteristic phenotypes at both the integrative physiology and cellular levels. I investigated whether Tibetans living at sea level also possess distinct phenotypic characteristics, and whether these may be related to underlying variation within the HIF pathway. I compared Tibetans living at sea level with Han Chinese, their most closely-related major ethnic group, and found that Tibetans possess a significantly different integrative physiology phenotype. Tibetans had a lower haemoglobin concentration and haematocrit, a higher pulmonary ventilation relative to metabolism, and blunted pulmonary vascular responses to both acute (minutes) and sustained (8 hours) hypoxia. Regarding genotype- phenotype relationships within the Tibetans, I found a significant correlation between both EPAS1 and EGLN1 genotype and the induction of erythropoietin by systemic hypoxia. At an intermediate cellular level, the relative expression and the hypoxic induction of HIF- regulated genes were significantly lower in peripheral blood lymphocytes from Tibetans compared with Han Chinese. I also investigated whether the genetic variation in EPAS1 selected for in Tibetans may be functional at the molecular level by affecting transcription of EPAS1 in cells and whether certain coding variants in <e,>EGLN1 found in Tibetans affect protein (PHD2) activity in cells and in vitro. A small supplementary study was undertaken in patients with idiopathic erythrocytosis, who have elevated or inappropriately normal erythropoietin levels, to investigate if they have genetic alterations in the HIF system.