Lowering LDL-cholesterol with statin therapy produces substantial reductions in cardiovascular events, and larger cholesterol reductions may produce larger benefits. Rarely, myopathy occurs with statins, especially at higher doses and in combination with certain medications. Similarly strong associations might exist between myopathy with high-dose statin regimens and genetic variants, especially those affecting blood statin levels. This study aimed to find genetic variants associated with statin-induced myopathy. A feasibility study was completed to assess whether plausible effect sizes of 5 to10-fold higher risks per genetic variants could be detected among 50-100 cases with statin-induced myopathy and to consider the best study design. A genome-wide association study was then carried out using approximately 300,000 genetic markers (and additional fine-mapping) in 85 people with definite or incipient myopathy and 90 controls, who were all taking 80mg simvastatin daily in a 12,000 participant trial of 80mg vs 20mg simvastatin daily. The cases were also compared to 2,300 additional controls who had not been exposed to intensive-dose statin therapy. Replication of the myopathy result and lipid-lowering associations were tested in a 20,000 participant trial of 40mg simvastatin daily versus placebo. The genome-wide scan yielded a single strong association (p = 4x10^-9) of myopathy with the rs4363657 single nucleotide polymorphism (SNP) located within the SLCO1B1 gene on chromosome 12. This non-coding SNP was in nearly complete linkage disequilibrium (r²=0.97) with the non-synonymous rs4149056 SNP. The population prevalence of the rs4149056 C allele was 15%, and the odds ratio for myopathy was 4.5 (95% confidence interval 2.6 to 7.7) for each copy of the C allele and 16.9 (4.7 to 61.1) for CC vs TT homozygotes. Over 60% of these myopathy cases could be attributed to the C variant. The SLCO1B1 gene encodes the organic anion transport polypeptide OATP1B1, which has been shown to regulate hepatic uptake of statins. In literature reports, rs4149056 reduced statin transport and was associated with 37% (31% to 44%) higher systemic statin acid levels per C allele. The association of rs4149056 with myopathy was replicated in the trial of 40mg simvastatin daily, which also showed that it was associated with the cholesterol-lowering effects of simvastatin. No SNPs in any other region were clearly associated with myopathy (although comparison of the myopathy cases with the 2,300 controls identified a region of chromosome 1p12 that warrants further study). This study identified common variants in SLCO1B1 that influence the risks of statin-induced myopathy substantially. Genotyping these variants may be useful for tailoring both the statin dose and safety monitoring. More generally, such studies of the genetic determinants of serious adverse reactions with other drug classes may help to improve the balance between treatment efficacy and safety.

Epidermal growth factor receptor (EGFR) is frequently overexpressed in the majority of triple negative breast cancer patients (TNBC). However, the molecular determinants behind their limited response to EGFR-targeted therapies are poorly understood. Here, both the acute and chronic responses of TNBC to the EGFR-targeted therapy, cetuximab (CTX), have been investigated. The expression of EGFR has been analyzed in a cohort of 2000 breast cancer tumours from the public dataset as well as in a panel of breast cancer cell lines. Furthermore, the response of TNBC cell lines to CTX has been investigated using conventional biochemical methods. Finally, a comprehensive transcriptomic profiling of an acquired CTX-resistant TNBC model by RNA sequencing has been performed to understand the molecular determinants of acquired CTX resistance. The results confirmed that EGFR is highly expressed in TNBC in comparison to non-TNBC breast cancer tumours and cell lines, which was associated with adverse clinical outcomes. Targeting EGFR in TNBC cell lines using CTX failed to completely inhibit the EGFR signalling pathway and was associated with an increase in ADAMs-mediated release of endogenous EGFR ligands, EGF and TGFα. Inhibition of ADAMs (ADAM10 and ADAM17) significantly enhanced the anti tumour efficacy of CTX both in vitro and in vivo. Furthermore, transcriptomic profiling of the acquired CTX-resistant TNBC cell line (MDA-MB-468CR) revealed an activation of several key oncogenic pathways and genes, including the TGFβ/BMP pathway. Blocking BMP receptors (BMPRs) restored the sensitivity of resistant cells to CTX treatment. Collectively, current findings offer alternative strategies that could enhance the CTX response in TNBC. We further reported that simultaneous targeting of both EGFR and BMPR pathways could overcome CTX resistance, which might have important implications for the treatment of TNBC.

Tumour tissue is characterised by fluctuating oxygen concentrations, decreased nutrient supply, and acidic pH. Angiogenic signalling pathways that drive a certain metabolic 'configuration' may give endothelial cells a selective advantage in the tumour environment. Previously it has been shown that glycolysis drives proliferation, migration and tip cell formation during sprouting of endothelial cells (De Bock, Georgiadou et al. 2013), and is increased by VEGFA. DLL4-NOTCH has been shown to limit angiogenesis and slow down proliferation of endothelial cells, and promote stalk cell formation during angiogenic sprouting, leading to sprout elongation. DLL4-NOTCH is implicated in tumour angiogenesis, and its overexpression is a potential mechanism of resistance to anti-VEGFA therapy (Li, Sainson et al. 2011). This thesis aimed at investigating the effect of the DLL4-NOTCH signalling pathway on endothelial metabolism and its implications in angiogenesis. Firstly, it was found that DLL4-NOTCH decreases the glycolytic rate and mitochondrial respiratory parameters in endothelial cells. When given exogenous fatty acids, DLL4-NOTCH activation caused increased fatty acid uptake, storage and oxidation. This shows that the induction of DLL4-NOTCH signalling results in increased fatty acid utilisation. Secondly, this research identified fatty acid oxidation as a target metabolism pathway for angiogenic therapy. More specifically, inhibition of fatty acid oxidation decreased proliferation of endothelial cells, decreased sprout elongation in the sprouting assay, and decreased sprouting from the axial vein in the zebrafish model. ATP production was not affected. Therefore, it was hypothesised that DLL4-NOTCH activation promotes and maintains the stalk cell phenotype through an increase of fatty acid oxidation, thereby promoting biomass production for endothelial cell proliferation and growth during angiogenic sprout elongation. Thirdly, a key fatty acid metabolism gene, fatty acid binding protein 4 (FABP4), was identified, that is positively regulated by NOTCH at its promoter region. FABP4 is a candidate for mediating increased fatty acid flux in endothelial cells in response to DLL4-NOTCH. This study shows that FABP4 is induced by VEGFA in a manner dependent on DLL4-NOTCH, and the insulin-responsive transcription factor FOXO1 was required for FABP4 expression in response to DLL4-NOTCH. FABP4 is pro-angiogenic and implicated in tumour angiogenesis in ovarian cancer omental metastasis. Taken together, this study shows for the first time that DLL4-NOTCH signalling increases FABP4 induction, contributing to a key pro-angiogenic pathway, and also fatty acid utilisation in endothelial cells, and thereby contributes to the formation of blood vessels.

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.

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.

Genome-wide association studies in multifactorial diseases have contributed to our understanding of genetic risk and defined specific disease-associated loci in particular populations. However, risk cannot be fully explained by genetics and evidence points to both genetic and environmental factors being important in causation and pathophysiology. The role of vitamin D in calcium homeostasis is well established. Over the last 30 years it has become clear that vitamin D has a wider role in physiology and disease, notably in autoimmune, cancer and infectious conditions. However, the molecular mechanisms and possible causal role of these associations are poorly understood. Here I propose that the role of vitamin D in immune and inflammatory responses is significant, that genetic variation partly determines the response to vitamin D and that integrative analysis can yield important insights for disease mechanisms. For this I investigate the relationship between vitamin D and genetic risk involving the immune system by focusing on multiple sclerosis and sepsis, conditions classically defined as autoimmune and inflammatory respectively. I describe data resolving genetic variation associated with autoimmune diseases in vitamin D receptor binding sites; the association to multiple sclerosis of a genetic variant lying within a VDR binding site; the correlation of plasma vitamin D with genotype and cell specific transcriptomes in healthy volunteers; and the extent of vitamin D deficiency in severe sepsis and septic shock, its association with survival, correlation with gene expression and use in sub-classification to identify patients at higher risk of death. The limitations of each study and future work are discussed. Integrating epidemiological and clinical observations with genetic and functional genomics techniques has the potential to reveal interactions in population specific disease susceptibility that may lead to an improved understanding of disease mechanisms and clinical translation. The work I present here bridges molecular analysis, candidate and genome- wide, with phenotypic observations that are important in our understanding of disease.

Yersinia pestis is a human pathogen and the causative agent of bubonic plague, responsible for causing three massive pandemics, resulting in hundreds of millions of deaths in the 14th century alone. Yersinia’s virulence stems from its ability to overcome host immune defences by the injection of six Yersinia outer proteins (Yops) into the host cells via its Type III secretion system. One of these Yops, YopO specifically disables the actin polymerization machinery, leading to the crippling of phagocytosis. YopO consists of a GDI domain which sequesters Rac and Rho, and a kinase domain, the activity of which is dependent on host actin. Little is known about the targets of the kinase domain and the mechanism of function of YopO remains incomplete. In this work, YopO was crystallized in complex with actin, revealing that YopO binds to actin on subdomain 4, away from the 'hotspot’ between subdomains 1 and 3 which is involved in binding most actin-binding proteins. The structure reveals how recruitment of YopO-bound actin monomers stalls actin polymerization by steric hindrance. The structure also demonstrates how YopO uses actin for self-activation and suggests that actin is being used by YopO as bait for recruitment into actin machineries. Using SILAC mass spectrometry, actin cytoskeletal machineries within macrophages that recruit YopO are identified and these include, amongst others: VASP family proteins, gelsolin family proteins, formins and WASP. Of these, VASP, EVL, diaphanous1, WASP and gelsolin have been identified to be phosphorylated by YopO and were validated by in vitro phosphorylation. This work demonstrates that YopO uses actin as a scaffold for selection of kinase substrates, enabling targeted phosphorylation of the actin machinery and provides insight into the regulation of the actin cytoskeleton by phosphorylation under non-pathogenic conditions.

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