Background The revised 2011 GOLD strategy presented a new classification and treatment of usual Chronic Obstructive Pulmonary disease (COPD) based on symptom assessment by CAT or mMRC and risk assessment based on exacerbations estimated from the spirometric grade or number of exacerbations in previous year (1). This new strategy has not previously been applied to patients with Alpha one antitrypsin deficiency (AATD). Aims To apply new GOLD strategy/categories in AATD and assess comparable symptom thresholds and predictability of mortality, future exacerbations and lung function decline (FEV1, Kco) and the role of comorbidities. Results The results have validated the strategy/classification in AATD with a suggested threshold of 13 rather than 10 for CAT to match with mMRC 1. Mortality and Kco decline was worse in the more severe category D which also had patients with more comorbidity. Applying COTE index to patients with AATD did not help in predicting mortality. Conclusion The new GOLD classification helps identify AATD patients who are at risk of poorer outcome based on lung function decline, mortality and exacerbation risk with patients in group D being most at risk. Presence of comorbidities does not appear to influence outcomes in AATD although they do tend to indicate a poorer quality of life. References 1. Vestbo J, Hurd SS, Agusti AG, Jones PW, Vogelmeier C, Anzueto A, et a!. Global strategy for the diagnosis, management, and prevention of chronic obstructive pulmonary disease: GOLD executive summary. American journal of respiratory and critical care medicine. 2013;187(4):347-65.

The Mixed-Lineage Leukaemia (MLL1) protein is a key developmental factor that acts to regulate genes via its histone methyl-transferase activity. This study aimed to examine how MLL1 and its associated complex contribute to gene regulation in a functionally relevant cell background. To assess dynamic processes involved, we developed a haematopoietic Stem Cell (hSC) -based system, in which Hoxa genes are down-regulated in a differentiation- induced manner. I characterised the histone modification distribution on two MLL-target genes showing the largest changes upon differentiation: Hoxa4 and Hoxa5. When active, these genes are associated with a peak of “activating” histone marks (H3K4me3, H3K9ac, H4K16ac) over the transcriptional start site, which are lost when the gene is repressed. This correlated with the recruitment of enzymes that deposit these marks, including components of the MLL complex (MLLC, MLLN and menin) as well as HATs that may be associated with the complex (CBP and MOF). Interestingly, the location of these proteins does not always correlate with the marks they deposit. We show that the dual mark H3K9acS10p is present on active Hoxa4 and Hoxa5 genes, and correlates with the presence of the histone kinase Msk1. We speculate that Msk1 contributes to regulating MLL1 HMT’ase activity on these genes.

There are over one million deaths from road traffic collisions. In Afghanistan, there have been 2005 UK battle injuries over 10 years. Advances in military trauma care have improved survival, resulting in more severely injured individuals entering the trauma care pathway. Improved understanding of immunoendocrine changes after severe trauma may facilitate novel interventions to improve outcomes. We prospectively recruited 102 severely injured patients at the QEH Birmingham; 52 military and 50 civilian patients with a mean Injury Severity Score of 27.2±13.9. Blood and 24-hr urine were collected at baseline (injury < 24h) and at regular intervals from while in hospital and at 3,4, and 6 months. Results demonstrated a reduced neutrophil function following a surge of DAMPs and cytokines that were released into the circulation. Both DHEA and DHEAS were significantly down-regulated (p < 0.0001). Serum testosterone was initially completely suppressed (p < 0.0001) but normalised after week 4. Protein and muscle loss followed a U-shaped curve; catabolism began to recovery 4-6 weeks following injury. In conclusion, the acute response to severe injury comprises increased glucocorticoid activation and down-regulation of adrenal and gonadal androgens. Delineation of whether the endocrine changes are beneficial or adverse will determine the potential for future intervention studies.

Nasal polyposis is a common disease affecting 2-4% of the general population. The aetiology and pathogenesis are far from clear. Recent publications have suggested up-regulation of several pro-angiogenic factors including VEGF. The aim of this study was to assess and quantify the degree of angiogenesis in nasal polyposis and to determine if angiogenesis was the driving force behind polyposis. We started by developing a novel triple stain to assess remodelling in the nasal mucosa. For the first time we were able to categorically refute the common belief of angiogenesis driven polyposis. We then carried out genomic studies and identified upregulation of genes controlling the cell cycle and apoptosis, suggesting cell turnover is an important part of the pathogenesis of nasal polyps. Our gene expression data was confirmed by TUNEL staining, indicating an increased level of apoptosis in nasal polyp tissue, counterbalancing the increased cell proliferation. Inflammatory genes are also upregulated, however the data collected so far cannot distinguish between different types of inflammatory response. We carried out proteomic studies using the lu minex system but this did not clarify the situation despite using matched samples that were used in the gene array. They highlight the protein differences occurring in the polyps themselves. We have shown chemoattractants for eosinophils & macrophages (which are found in polyps), and significantly in iNOS, which is novel.

Individuals reporting chronic respiratory symptoms without airflow obstruction (AFO) were originally classified as “at risk” stage (GOLD Stage 0) of Chronic Obstructive Pulmonary Disease (COPD). However, this stage was removed due to lack of evidence regarding its progression to diagnosed COPD. There remain many such individuals in the population, including some already misdiagnosed with COPD despite not meeting required criteria. This thesis aims to clarify the uncertainty around the relevance of “GOLD Stage 0”. There are three systematic reviews examining the risk of developing COPD amongst GOLD Stage 0 patients, their prognosis and the prognostic factors. The independent effect of respiratory symptoms versus AFO on quality of life is examined using data from the Health Survey for England. Baseline data from the Birmingham COPD Cohort Study are used for two cross-sectional analyses, (1) comparing GOLD Stage 0 patients with those recently identified with COPD and (2) examining the characteristics of those “overdiagnosed” with COPD. GOLD Stage 0 patients showed a similar pattern of poor health outcomes to those diagnosed with COPD. Overdiagnosis of COPD was common, particularly among GOLD Stage 0 patients. Obesity and restrictive disease were potential explanations for some overdiagnosed. The presence of chronic respiratory symptoms has a negative impact on patients’ health, regardless of the presence of diagnosed AFO.

Background: Saudi Arabia is an affluent nation faced with steep population increase (~75% in just over 10 years) and a young population (63% aged under 30) in the context of globalized dietary habits and food supply leading to increase the trend of consumption junk food use. However, there are no national dietary surveys to give more accurate details. With existing high prevalence of obesity, it is foreseeable that Saudi Arabia (SA) will face a significant increase in the burden of non-communicable diseases (NCDs) in a short space of time. Reducing the behavioural and environmental risk factors associated with NCDs (physical activity, alcohol overuse, exposure to tobacco smoke, and low nutritionally balanced diet including high salt and energy intake and low intake of fruit and vegetables) requires cross-community sectors, including health, education, agriculture, and planning. Early detection and intervention also require reliable and cost effective tools. The relationship between chronic high salt intake and CVDs has already been established. This thesis examines the relationship between body composition and nutrition, and NCDs using techniques from the full breadth of Human Nutrition Research. Methods: The first cross-sectional study focused on developing and validating a culture-specific FFQ for salt intake against 24-h urinary outputs and repeated 24-h dietary recall, to identify relationships between salt intake, socio-economic factors and blood pressure (BP); and explore dietary sources of salt intake. In the second study, a secondary analysis of integrated data from five Saudi National Surveys assessed the performance of different anthropometric measures (body mass index (BMI), waist circumference (WC), waist to hip ratio (WHR) and waist to height ratio (WHtR)) and body composition indices (estimated skeletal muscle mass (SMM), the percentage of skeletal muscle mass to body weight (%SMM) and Skeletal Muscle Mass Index (SMI)) in predicting metabolic diseases. Saudi nationals only were included in the study. ROC analysis was used to explore the best predictor of metabolic diseases and develop new thresholds. To assess the agreement and misclassification of overweight and obesity using BMI and WC measurements, BMI in combination with WC measurements were used to classify participants as [High-Risk Adiposity by BMI and WC], [High-Risk Adiposity by BMI only], and [High Risk Adiposity by WC only] based on the action levels. Each anthropometric and muscle mass indices were categorised to deciles. Additionally calculated were age-adjusted odds ratios by applying logistic regression models of the different metabolic risk factors in case of an increase of one decile of the respective anthropometric and estimated SMM parameter. In the third study, a cross-sectional survey was developed using the Theory of Planned Behaviour to provide a holistic understanding of factors that may influence food choices and behaviours, and in particular, intentions of adopting a nutritionally-balanced diet. External variables including age, gender, socio-economic status, and being aware of health and nutrition policies and others were included into the model as they were potentially related to TPB constructs. Attitude toward behaviour, subjective norms, perceived behavioural control and knowledge as actual barriers to behaviour were assessed. Results: In the first study, the newly developed Saudi FFQ was found to be of moderate validity in ranking people based on their estimated salt intake, and performed as well as other salt FFQ developed for other nations. The Riyadh population used in this survey consumed 8.7 g salt per day (estimate), higher than the recommended level of salt ( > 5 g/d for salt). A minority (18%) met the recommended level. The main sources of salt were, surprisingly, vegetables and un-processed foods, and a positive relationship between income and salt intake was observed. Meanwhile, salt intake, defined by FFQ, was associated with systolic BP only (R=0.089, p=0.036), an association which disappeared when adjusted for age, WC and gender. The second study highlighted that a majority of Saudi adults could be categorized as overweight or obese (72%). Worryingly, short of half of those with a normal BMI (18.5–25) aged over 45 also had a large waist. Combining WC and BMI did not improve their value as predictors of metabolic diseases and WC was the best overall predictor of metabolic diseases while BMI was the poorest. This study suggests new cut-off points for WC in SA, in a context of metabolic diseases, ranging between 90 to 92 cm (women) and 94 to 99 cm (men). The newly developed WC cut-offs are higher than the cut-offs for Asian men and women (90 and 80 cm, respectively). The new WC cut-off for women is higher than the cut-off for Caucasian women (88 cm); and the WC cut-off for men is lower than the cut-offs for Caucasian men (102 cm). The obesity prevalence based on BMI and WC also increased proportionately with both SMM (kg) and SMI (kg/m2) increase while the obesity decreased proportionately with %SMM increase. SMI was a poor predictor of metabolic diseases while %SMM was the best, having the highest AUC levels. New (defined) cut-off points for %SMM for metabolic diseases were defined, ranging from 29 to 32% for men and 26 to 28% for women. The third study highlighted that very few SA adults have been exposed to national nutrition and health guidelines (18%). Awareness of these was the strongest predictor of attitude toward behaviour, social norms and knowledge of nutritionally-balanced diet whilst perceived social pressure to engage in behaviour toward a more nutritionally balanced diet (SN) was the strongest predictor of subjects’ intention. Conclusion: Study 1 added a new and unexpected source of salt intake including vegetables and unprocessed foods. These findings raise a concern regarding the encouragement to increase intake of vegetables without including advice regarding cooking advice, in light of the risk of higher salt intake in SA. It would be worthwhile to consider education strategies towards the use of alternative ingredients or dressings in salad and cooked vegetables. Study 2 added an evidence about the weakness of BMI and SMI in predicting metabolic diseases and misclassifying the population. The study suggests using WC and %SMM as alternative measures and adopting the newly developed cut-offs. Study 3 sheds the light on possible avenues for policies, health promotions and nutrition interventions to focus on Saudi adults, in order motivate the population to adopt nutritionally balanced diet by increasing population knowledge and awareness.

Governments, funding agencies, academic institutions, and health care policy makers are increasingly investing in the design, development, and dissemination of systematic reviews (SRs) to inform clinical practice guidelines, ethical guidance of clinical research, and health care practice and policy. SRs need to be sensitive to the dynamic nature of new evidence, such as published papers. The emergence of new evidence over time may undermine the validity of conclusions and recommendations in any given SR and subsequent practice guideline. This issue has only started to be more seriously considered during the last decade or so. Now it is clear that the use of out-dated evidence can lead to a waste of resources, provision of redundant, ineffective or even harmful health care. The author of this dissertation and his colleagues conducted and published three empirical studies and two conceptual articles (in six peer-reviewed journal publications), which addressed the methodologic aspects of when and how to update SRs. This PhD project provides a summary of these publications. The work described herein has had a significant impact on raising awareness and initiating new research efforts for keeping SRs up-to-date. Publication 1 proposed the first formal definition of what constitutes an update of a SR. The article presented distinguishing features of an updated vs. not updated or a new review. Publication 2 (or Publication 3) systematically reviewed methods, techniques, and strategies describing when and how to update SRs (Study #1). Publication 4, an international survey (Study #2), identified and described updating practices and policies of organisations involved in the production and commission of SRs. Publication 5 reviewed the knowledge and efforts in updating SRs and provided guidance for authors and SR groups as to when and how to update comparative effectiveness reviews produced by the Agency for Healthcare Research and Quality’s (AHRQ) Evidence-based Practice Centres (EPCs) throughout North America. Publication 6 (Study #3) described the development, piloting, and feasibility of a surveillance system to assess the need for updating comparative effectiveness reviews produced by the AHRQ’s EPC Program. This surveillance method has proved to be an efficient approach for prioritising SRs with respect to updating need.

In patients with a particular disease or health condition, prognostic factors are characteristics (such as age, biomarkers) that are associated with different risks of a future clinical outcome. Research is needed to identify prognostic factors, but current evidence suggests that primary research is of low quality and poorly/selectively reported, which limits subsequent systematic reviews and meta-analysis. This thesis aims to improve prognostic factor research, through the application, development and evaluation of statistical methods to quantify the effect of potential prognostic factors. Firstly, I conduct a new prognostic factor study in pregnant women. The findings suggest that the albumin/creatinine ratio (ACR) is an independent prognostic factor for neonatal and, in particular, maternal composite adverse outcomes; thus ACR may enhance individualised risk prediction and clinical decision-making. Then, a literature review is performed to flag challenges in conducting meta-analysis of prognostic factor studies in the same clinical area. Many issues are identified, especially between-study heterogeneity and potential bias in the thresholds (cut-off points) used to dichotomise continuous factors, and the set of adjustment factors. Subsequent chapters aim to tackle these issues by proposing novel multivariate meta-analysis methods to ‘borrow strength’ across correlated thresholds and/or adjustment factors. These are applied to a variety of examples, and evaluated through simulation, which show how the approach can reduce bias and improve precision of meta-analysis results, compared to traditional univariate methods. In particular, the percentage reduction in the variance is of a similar magnitude to the percentage of data missing at random.

Immunotherapies signify a major development in the fight against increasing cancer morbidity and mortality. However, they have been limited by a lack of tumour-specific targets. MHC class I associated phosphopeptides represent a novel class of potentially tumour-specific targets, since dysregulation of signalling in cancers leads to aberrant phosphorylation. Using an autologous model of cancer, in healthy individuals, it was shown that a significant proportion of all anti-tumour cytotoxic memory T cell responses target phosphopeptides. In colorectal cancer (CRC), there is an established association between memory CD8+ T cell infiltration and survival. CRC and oesophageal adenocarcinoma tumours and cell lines were used to identify 134 tumour-associated phosphopeptides. Approximately 65% of these derive from well-defined cancer pathways and are thus markers of malignancy. Multifunctional tumour-infiltrating lymphocytes were present in primary and metastatic tumours that recognised these phosphopeptides. Furthermore, healthy donors have pre-existing memory T cell responses to many CRC-associated phosphopeptides. Phosphopeptide-specific T cells were readily expanded ex vivo and killed CRC cell lines. Therefore, MHC class I associated phosphopeptides are ideal immunotherapeutic targets, as immunity must spare healthy tissue. Immunity to tumour-associated phosphopeptides represents a biological strategy for distinguishing tumour from healthy tissue. These phosphopeptides are potential sHLA-associated cancer biomarkers and immunotherapeutic targets.

Aim: To gather, analyse and present the views of personnel currently working within pharmaceutical companies relating to factors influencing drug diffusion (market penetration), using case studies to determine how their perspective relates to diffusion curves and literature-based timelines describing the same phenomenon. Methods: Qualitative study based on semi-structured interviews with marketing, market access or senior management personnel from eight major UK R&D pharmaceutical companies. Case studies were selected through expert consultation. Diffusion curves were produced for all potential case study drugs (n=21) and timelines constructed from the literature and augmented with clinical expert input. Results: Thematic analysis of 15 interviews conducted across four case studies: bisphosphonates; atypical anti psychotics; phosphodiesterase type 5 inhibitors and statins revealed 10 diffusion themes: clinical need; clinician/patient experience; clinical evidence; health service/policy environments; adopter attitudes; communicating relative advantage; market development; opinion leaders; company culture/ heritage and pricing. Triangulation with diffusion curves and literature-based timelines demonstrated a high level of convergence between accounts. Points of divergence revealed unique pharmaceutical industry insights. Conclusion: Eliciting diffusion knowledge from this under-researched stakeholder group largely confirmed issues previously outlined in the literature, but importantly has revealed the significance of less tangible social interactions that inform perceptions of new pharmaceuticals that can significantly influence adoption and diffusion.