Sexual development begins with the process by which the bipotential gonads of the embryonic urogenital ridge develop into either testes or ovaries. In the mouse, sex determination occurs at around 11.5 dpc and depends on the presence or absence of the Y chromosome and the associated activity of the testis-determining gene, Sry, in supporting cell precursors. The mutually antagonistic male and female developmental pathways are regulated by many cellular and molecular processes, disruption of which can lead to disorders of sex development (DSDs). However, many of the molecular mechanisms regulating the differentiation of the two gonads are still unknown. The boygirl (byg) mutant was identified in an ENU-based forward genetic screen for embryos with gonadal abnormalities. On the C57BL/6J background, XY byg/byg homozygotes exhibited complete embryonic gonadal sex reversal. The defective gene in byg, Map3k4, is a component of the mitogen-activated protein (MAP) kinase signalling pathway and provides the first evidence for a function of this pathway in sex determination. This thesis describes experiments aimed at investigating the cellular and molecular basis of the sex reversal phenotype associated with the XY Map3k^4byg/byg mutant. Cellular characterisations revealed a defect in male-specific proliferation at 11.5 dpc, which was attributed to a defect in Sry up-regulation. Elucidation of the downstream kinases activated by MAP3K4 during sex determination was attempted, with particular focus on identifying a role for p38α MAP kinase (MAPK). Using a conditional knockout approach, the function of p38α in Steroidogenic factor-1 (Sf1)-positive somatic cells was assessed. However, specific inactivation in these cells did not affect gonad development. Conditional inactivation of Map3k4 itself in these Sf1¬-positive cells also did not disrupt gonad development, suggesting that this pathway is either initiated in a different cell lineage or at an earlier stage than deletion driven by Sf1-Cre can disrupt. Conditional inactivation of p38α in the Müllerian duct mesenchyme and ovarian granulosa cells using Amhr2-Cre did reveal a function for p38α in female fertility, but did not disrupt embryonic sexual development. Gene knockdown in organ culture was attempted to determine a role for multiple p38 MAPKs in all cell types of the gonad. Therefore, this thesis details further characterisations of a novel signalling pathway important for the expression of Sry, focussing on the role of the p38 MAPKs.

Next-generation sequencing methods now allow rapid and cost-effective sequencing of DNA on a scale not previously possible. This offers great opportunities for the research of Mendelian disorders, but also significant challenges. The sequencing of exomes, or whole genomes, has emerged as a powerful clinical research tool, with targeted gene analyses generally being preferred in the clinical diagnostic setting. These methods have been employed here with the aim of identifying novel genetic causes of inherited heart disorders and to gain insights into the utility and limitations of these techniques for clinical diagnosis in these disorders. Data produced from the introduction of a targeted multi-gene next-generation sequencing test into clinical practice has been studied. Variation within the mitochondrial genome has been analysed to assess the importance of mitochondrial DNA variants in patients with hypertrophic cardiomyopathy. The m.4300A>G mutation is identified as an important cause of this disorder, with other previously cardiomyopathy-associated and novel variants also identified. Such multi-gene tests can facilitate interpretable and phenotype-relevant results, but at the expense of limiting more extensive data acquisition. Whole-genome sequencing has been performed in five families with different autosomal dominant inherited heart disease phenotypes of unknown genetic aetiology. In two of these likely pathogenic variants were identified, one in the gene encoding titin (TTN) and the other in the calcium channel subunit gene CACNA1C. In vitro studies were undertaken to support the pathogenicity of the TTN variant and understand the functional effects of this. In the other three families either multiple candidate gene variants were identified or no clear candidate variant was identified. This highlights the difficulties in interpreting these results, even in carefully selected families. Overall, although the research benefits of exome or genome studies are evident, the interpretation and validation of genetic variant data produced remains highly challenging for clinical diagnosis.

Osteoarthritis (OA) is a common, multifactorial disease that is characterized by focal degeneration of the smooth articular cartilage in any of the synovial joints. Although the underlying molecular mechanisms for OA are still not fully understood, epidemiological studies have evidenced a significant genetic component to OA susceptibility. Genome-wide linkage scans and large-scale association studies have had success in unraveling the genetic architecture underlying OA with the identification of a number of susceptibility genes. In this work, functional analyses are reported of OA associated polymorphisms within two susceptibility genes: BMP5 and GDF5, both members of the TGF-β superfamily of secreted proteins. The extent of differential allelic expression (DAE) of BMP5 in human mesenchymal tissues was first examined with significant differences in BMP5 allelic output observed (allelic ratios exceeding 4:1 in the tissues of some donors). Significant variability in allelic expression within the different tissues of donors was also observed, suggesting that polymorphism in cis-regulation of BMP5 expression is common and that there is a considerable effect of tissue specific elements on BMP5 expression. DAE was then used as a phenotype to map tissue-specific cis-regulatory polymorphisms with the identification of a single nucleotide polymorphism (SNP) located downstream of BMP5 that was significantly associated with DAE as well as OA, suggesting that variability in cis-regulation of BMP5 is important in OA susceptibility. Moreover, the functional effect of a previously identified OA associated microsatellite within intron 1 of BMP5 was investigated using luciferase reporter assays and electrophoretic mobility shift assays (EMSAs) with significant differences observed both in the ability of various microsatellite alleles to modulate BMP5 promoter activity and to bind GATA-3 nuclear proteins, further suggesting a role for variability in BMP5 expression in OA susceptibility that may in part be due to altered GATA-3 binding. Finally, functional characterization of a previously reported OA associated SNP in the 5′ UTR of GDF5 is presented in which EMSAs show differential binding of nuclear factors between the two SNP alleles, strengthening the possible functional contribution of this SNP to OA susceptibility. Overall, this work demonstrates that polymorphism in cis-regulation is likely to play a role in OA susceptibility.

Heterozygous mutations in the glucocerebrosidase (GBA) gene represent the most common risk factor for Parkinson’s disease (PD), a disease in which midbrain dopaminergic neurons are preferentially vulnerable. However, the mechanisms underlying this association are still unknown, mostly due to the lack of an appropriate model of study. In this thesis, we aimed at elucidating the role of heterozygous GBA mutations in PD using a specific human induced pluripotent stem cell (hiPSC)-based model of disease. First we developed a protocol for the efficient differentiation of hiPSCs into dopaminergic cultures, and extensively characterized the derived dopaminergic neurons which expressed multiple midbrain relevant markers and produced dopamine. Next we screened a clinical cohort of PD patients to identify carriers of GBA mutations of interest. Using for the first time hiPSCs generated from PD patients heterozygous for a GBA mutation (together with idiopathic cases and control individuals) we were able to efficiently derive dopaminergic cultures and identify relevant disease mechanisms. Upon differentiation into dopaminergic neuronal cultures, we observed retention of mutant glucocerebrosidase (GCase) protein in the endoplasmic reticulum (ER) with no change in protein levels, leading to upregulation of ER stress machinery and resulting in increased autophagic demand. At the lysosomal level, we found a reduction of GCase activity in dopaminergic neuronal cultures, and the enlargement of the lysosomal compartment in identified dopaminergic neurons suggesting a decreased capacity for protein clearance. Together, these perturbations of cellular homeostasis resulted in increased release of α-synuclein and could likely represent critical early cellular phenotypes of Parkinson's disease and explain the high risk of heterozygous GBA mutations for PD.

Vascular disease is the leading cause of global disease burden, but substantial gaps in our knowledge regarding family history of vascular disease, peripheral arterial disease (PAD) and acute aortic disease persist. Prospective, population-based data in these neglected areas may be useful in diagnosis, risk prediction, prognosis and clinical management of vascular disease. The Oxford Vascular Study (OXVASC) is an ongoing prospective, population-based study of vascular disease in all territories in Oxfordshire, UK, which started in 2002. The study population comprises all 91,106 individuals registered with nine general practices. Multiple overlapping methods of “hot” and “cold” pursuit are used to identify all patients with acute vascular events. I have shown that patients with acute coronary syndromes (ACS) and a history of myocardial infarction (MI) in both parents are 6 times more likely to have siblings with MI than those ACS patients with no parental history of MI, whereas, parental stroke does not predict stroke in siblings among TIA/stroke patients. Maternal history of MI is more common in women than men with ACS. Premature maternal MI is strongly associated with premature MI in females and males. I have also shown that maternal stroke is more common than paternal stroke in female ACS patients, and that family history of stroke is as common in patients with ACS as in patients with TIA/stroke. However, I showed that these associations between family history and MI or stroke cannot be explained by disease localisation or disease severity on coronary angiography. In both primary and secondary prevention settings, PAD indicates a high risk of future events. I have shown that, although acute PAD events account for only 7% of acute vascular events at 1 year, they account for 12% of acute vascular deaths. Acute peripheral arterial events are more aggressive in terms of risk factor profile, mortality and morbidity than other vascular disease. Half of patients with incident PAD had history of vascular disease. Incidence and severity of PAD events generally increases with age, and severity of disease predicts mortality. I have shown that incidence of ruptured abdominal aortic aneurysm (RAAA) and aortic dissection increased steeply with age, and 5-year mortality rates were 74% and 65% for RAAA and aortic dissection respectively. I have also shown that the true population-based incidence of acute aortic dissection is similar to previous estimates of incidence, implying that it is accurately diagnosed and coded, and that retrospective data analysis produces valid estimates of incidence.

Common mycobacterial diseases, including tuberculosis and leprosy, contribute to major mortality and morbidity worldwide. Despite evidence of an important role of host genetic factors in susceptibility to these infections, few compelling genetic associations have been identified with previous candidate gene and linkage approaches. This thesis investigates the genetic factors of human immunity to these mycobacterial diseases using a high-throughput approach of association testing. To assess genetic susceptibility to tuberculosis, I have conducted a genome-wide association study in the Gambian population as part of the Wellcome Trust Case Control Consortium (WTCCC). The study reveals the region flanking CADM1 as a potential susceptibility locus. Combining this study with a Ghanaian cohort further implicates two genetic loci at chromosome 18q11.2 (P = 9.2x10⁻⁹) and PARD3B (P = 1.4x10⁻⁶). For leprosy, I have performed a gene-centric association study in the New Delhi Indian population. Evidence of significant association was observed in the HLA-DRB1/DQA1 (P = 4.9x10⁻¹⁴) and TLR1 (P = 1.7x10⁻⁹) loci. These studies identify important genomic regions that may be involved in immunity to tuberculosis and leprosy. Further analysis revealed a significant immunogenetic overlap between tuberculosis and leprosy. This provides proof-of-principle for the subsequent aggregate analysis for mycobacterial susceptibility, which suggests that the steroid biosynthesis pathway may be important in anti-mycobacterial immunity. This thesis represents one of the largest studies to identify the genetic factors for human immunity against mycobacteria. These novel findings will further enhance vaccine and pharmaceutical efforts into prevention and treatment of these mycobacterial diseases.

Chronic otitis media (OM) is an archetypal complex disease, which is particularly prevalent in childhood. Epidemiological data suggest high heritability for disease susceptibility, but previous genetic association studies have had methodological flaws, and none have specifically focused on chronic OM phenotypes. Mouse models represent one way to ascertain candidate loci for human association testing. A number of mouse models of middle ear inflammation have been reported, but many susceptibility loci remain undiscovered. I demonstrate that oto-endoscopy is a robust and scalable phenotyping platform for OM in the mouse, and discuss its value in new model discovery. Chronic OM is also a feature of trisomy HSA21 (Down Syndrome). Through an interrogation of the mouse library of segmental trisomy models of Down Syndrome, I identify a critical trisomic region for chronic otitis media. This region may underlie OM susceptibility in Down Syndrome, but could also contribute to disease susceptibility in non-syndromic disease. Mouse models can also be used to interrogate disease mechanisms. Our previous work has shown that the chronically inflamed middle ear is hypoxic, and that hypoxia signalling is a potential therapeutic target. Exploiting the Junbo mouse model, I demonstrate that surgical ventilation of the Junbo ear improves inflammation, and that this is associated with loss of hypoxia signalling. I present preliminary results from transcript analyses of human middle ear effusions showing marked upregulation of hypoxia signalling. A systematic review of existing mouse models suggests that the loci FBXO11, EVI1, SMAD2, and TGIF1 are good candidates genes for human association testing. I detail recruitment and collection of DNA from families in the UK where a child is undergoing grommet insertion. Association testing using a variant of the transmission disequilibrium test shows susceptibility associated with polymorphisms at FBXO11, and possibly also SMAD2 and TGIF1.

Maturity-onset diabetes of the young (MODY), due to hepatocyte nuclear factor 1 alpha mutations (HNF1A-MODY), is the most common form of monogenic diabetes presenting in young adults. An accurate genetic diagnosis of HNF1A-MODY has therapeutic implications for the patients and their family members. However, the majority of people with HNF1A-MODY are not referred for genetic testing and remain misdiagnosed as type 1 or type 2 diabetes. As part of measures to address this misdiagnosis, over the last few years there have been efforts to define clinical features and biomarkers that can be used to identify those at high risk of HNF1A-MODY. Secreted hepatic proteins regulated by HNF1A are attractive candidates for diagnostic biomarkers that would be specific for this form of diabetes. Apolipoprotein M (apoM), C-reactive protein (CRP) and plasma glycan profile have all been investigated as biomarkers to improve selection of suspected MODY cases for genetic testing. In my thesis, I have addressed questions about the variation in apoM between different forms of diabetes and assessed the performance of hsCRP and plasma glycan profile to identify HNF1A-MODY in previously uninvestigated individuals with young-onset diabetes and in a non-European population. Additionally because CRP and plasma glycans are both important components of an acute inflammatory response, I examined the effect of haploinsufficiency of HNF1A in a standardised model of inflammation. When investigating apoM, I showed that serum apoM levels are lower in HNF1A-MODY than controls, and have demonstrated for the first time that serum apoM provides good discrimination between HNF1A-MODY and type 1 diabetes. CRP and plasma glycan profile both performed well in identifying HNF1A-MODY cases in unselected young adults with diabetes. The results also suggested that both biomarkers have value for assessing the functional impact of novel HNF1A variants. I went on to examine the use of a low CRP for selecting those at risk of HNF1A-MODY in South Asian subjects with young-onset diabetes. This study suggests that the overall population prevalence of HNF1A-MODY is similar in South Asians to Europeans, but that MODY represents a lower proportion of those with diabetes (due to the higher prevalence of type 2 diabetes in South Asians). The specific selection strategy employed in this study was not successful in identifying subjects at high risk of HNF1A-MODY (only 3% of those sequenced had mutations), suggesting that additional clinical and biochemical features will be required in addition to CRP to distinguish South Asians at high risk of HNF1A-MODY. Lastly, using endotoxaemia as a standardised model of acute inflammation for the first time in HNF1A-MODY, I have shown that despite low baseline levels, subjects with HNF1A-MODY had peak stimulated CRP levels comparable to non-diabetic controls. An attenuated cytokine response was observed in HNF1A-MODY, which requires further investigation. This is also the first report of inflammation-associated changes in plasma and white cell membrane glycan profile in diabetes. This research work adds substantially to current understanding of performance of HNF1A-MODY biomarkers, a critical step before their clinical translation. The work presented also provides novel insights into the regulation of the acute inflammatory response in HNF1A-MODY.

Glucose-6-phosphate dehydrogenase (G6PD) deficiency, a common heritable trait whose prevalence mirrors geographic patterns of historic malaria endemicity, is thought to confer a selective advantage owing to partial protection conferred against malaria. Direct evidence supporting this malaria protection hypothesis in the form of clinical association studies remains controversial, however, as conflicting results have been reported with respect to the strength and specificity of a protective effect, if any, conferred to carriers of G6PD deficiency-associated alleles. This thesis examines genetic diversity at the G6PD locus, and then considers how such variation impacts both immediate molecular phenotypes and multifactorial clinical phenotypes. First, Chapter 3 presents a survey of variation at G6PD in several malaria-endemic areas, while Chapter 4 describes a novel technique for polymorphism discovery using pooled massively parallel sequencing. Next, in Chapters 5 and 6, I evaluate the link between genetic variation at the locus and G6PD enzyme activity, identifying major and minor determinants of G6PD deficiency state in an association study conducted in Kenya, and demonstrating a new technique for assaying G6PD deficiency at the level of an individual erythrocyte in a pilot project in Mali. Finally, Chapter 7 addresses the malaria protection hypothesis directly by conducting a fine-mapping case-control association study of severe malaria in the Gambia, where I found that G6PD deficiency alleles exhibited differential direction of association with respect to two important clinical syndromes-- trending towards risk conferred to severe malarial anemia, and protection with respect to cerebral malaria. Overall, these findings suggest that future clinical association studies should consider heterogeneity at the genetic level, as well as at the level of molecular and clinical phenotypes in order to achieve a better mechanistic understanding of the relationship between G6PD deficiency and severe malaria.

FBXW7 encodes the substrate recognition component of an SCF E3 ubiquitin ligase complex. This complex regulates the degradation of multiple targets, such as Notch1, c-Jun, c-Myc and cyclin E, that function in critical developmental and cancer pathways. FBXW7 mutations are found in cancers of diverse tissue origins, with one of the highest mutation rates in the colorectrum. FBXW7 mutations are typically missense mutations that disrupt the substrate recognition domain at critical arginine propellor-tips. Mutations are often mono-allelic suggesting that FBXW7 is not a typical tumour supressor gene. Despite this, most of the evidence on FBXW7 function to date comes from null systems. Several Fbxw7 -null mouse models have been generated and suffer homozygous embryonic lethality due to disrupted vascular development. Conditional Fbxw7-null mice have been created but do not in general reflect the mutation spectrum found in human tumours. In order to analyse the functional effects of Fbxw7 propellor-tip missense mutations, mice carrying a commonly-occurring Fbxw7 R482Q mutation were generated. This propellor-tip mutation was knocked-in constitutively and whilst heterozygous mice developed normally in utero, they died perinatally due to defective lung development. Cleft palate and eyelid fusion defects were also observed with incomplete penetrance. Fbxw7 substrates were screened in embryonic lungs and significantly elevated protein levels of Klf5 and Tgif1 were observed. The Fbxw7 R482Q mutation was also conditionally knocked-in in the gut. In the heterozygous state, large adenomas in the small intestine were observed at a low multiplicity, in approximately 30% of mice at an age greater than 300 days. Upregulation of Wnt signalling and Ctnnb1 mutations have been identified in a selection of these tumours. Breeding the Fbxw7^R482Q allele onto Apc-mutant backgrounds led to accelerated morbidity, in which compound R482Q/Apc-mutant mice exhibited polyps of increased number and size. Elevated protein levels of Fbxw7 substrates Klf5 and Tgif1 were observed in adenoma and normal intestinal tissue from these mice. In vitro work using epitope-tagged murine wildtype and propellor-tip mutant Fbxw7 proteins showed that they were capable of dimerising, opening the prospect of investigating a dominant negative mechanism of action. To conclude, an Fbxw7 propellor-tip mutation studied in vivo resulted in both disrupted embryonic development and intestinal tumorigenesis and was distinct from Fbxw7 -null alleles.