The Molecular Characterisation of Circulating Tumour Cells in Neuroendocrine Neoplasms

Identification of the molecular alterations that drive cancer is critical for precision oncology. Profiling of a single tissue biopsy is insufficient to interrogate the full spectrum of molecular heterogeneity that exists within a patient’s tumour, and is not without risk to the patient. The analysis of CTCs as part of a liquid biopsy circumvents this issue and allows single-cell analysis as well as longitudinal monitoring over time and in response to therapy. The aim of this thesis is to perform the first molecular characterisation of CTCs derived from NEN patients with a view to evaluating therapeutic targets and characterising tumour heterogeneity and evolution at the single-cell level. Firstly, I developed an assay to enable detection of the therapeutic targets SSTR2 and SSTR5 on individual NEN CTCs. Applied to a cohort of 31 metastatic NEN patients, I identified an SSTR+ subpopulation in 33% of patients and demonstrated significant intra- and inter-patient heterogeneity of SSTR expression. Next, I evaluated the size-based Parsortix platform for CTC enrichment against the gold standard EpCAM-dependent CellSearch in a pilot study of NEN patients, demonstrating that a higher number of CTCs could be isolated in a greater proportion of NEN patients using this technique. Furthermore, the presence of CTCs with low and absent EpCAM expression was observed for the first time in NEN alongside significant intra-patient heterogeneity in EpCAM expression. In order to fully dissect the heterogeneity observed in this early work, I developed DEPArraybased workflows to allow the single-cell evaluation of CTC copy number profiles using next-generation sequencing. The developed methodologies were subsequently tested in a representative cohort of NEN patients. By performing comprehensive copy number profiling of 125 single CTCs, I was able to identify recurrent and therapeutically relevant rearrangements, such as the amplification of CDK4/6, MET and BRAF and loss of BRCA2. Unsupervised hierarchical clustering demonstrated CTCs with distinct clonal lineages and significant heterogeneity was seen in CNV profiles between and within patient samples. In conclusion, this thesis describes successful workflows for the genomic analysis of CTCs at the single-cell level and is a step towards the implementation of precision oncology in neuroendocrine patients. This analysis has identified CTC heterogeneity at the single-cell level with implications for the identification of therapeutic targets, mechanisms of resistance to therapy, tracking of evolutionary change and biomarker refinement in NEN

Systematic Evaluation of the Immune Environment of Small Intestinal Neuroendocrine Tumours

BACKGROUND: The immune tumour microenvironment and the potential therapeutic opportunities for immunotherapy in small intestinal neuroendocrine tumours (siNET) have not been fully defined. METHODS: Herein, we studied 40 patients with primary and synchronous metastatic siNETs , and matched blood and normal tissue obtained during surgery. We interrogated the immune checkpoint landscape using multi-parametric flow cytometry. Additionally, matched FFPE tissue was obtained for multi-parametric immunohistochemistry (IHC) to determine the relative abundance and distribution of T-cell infiltrate. Tumour mutational burden (TMB) was also assessed and correlated with immune infiltration. RESULTS: Effector tumour infiltrating lymphocytes had a higher expression of PD-1 in the tumour microenvironment compared to the periphery. Additionally, CD8+ tumour infiltrating lymphocytes had a significantly higher co-expression of PD-1/ICOS and PD-1/CTLA-4 and higher levels of PD-1 expression compared to normal tissue. IHC revealed that the majority of cases have {less than or equal to}10% intratumoural T cells but a higher number of peritumoural T cells, demonstrating an "exclusion" phenotype. Finally, we confirmed that siNETs have a low TMB compared to other tumour types in the TCGA database but did not find a correlation between TMB and CD8/Treg ratio. CONCLUSIONS: Taken together, these results suggest that a combination therapy approach will be required to enhance the immune response, using PD-1 as a checkpoint immunomodulator backbone in combination with other checkpoint targeting molecules (CTLA-4 or ICOS), or with drugs targeting other pathways to recruit "excluded" T cells into the tumour microenvironment to treat patients with siNETs

Identification of additional risk loci for stroke and small vessel disease: a meta-analysis of genome-wide association studies

BACKGROUND: Genetic determinants of stroke, the leading neurological cause of death and disability, are poorly understood and have seldom been explored in the general population. Our aim was to identify additional loci for stroke by doing a meta-analysis of genome-wide association studies. METHODS: For the discovery sample, we did a genome-wide analysis of common genetic variants associated with incident stroke risk in 18 population-based cohorts comprising 84 961 participants, of whom 4348 had stroke. Stroke diagnosis was ascertained and validated by the study investigators. Mean age at stroke ranged from 45·8 years to 76·4 years, and data collection in the studies took place between 1948 and 2013. We did validation analyses for variants yielding a significant association (at p<5 × 10(-6)) with all-stroke, ischaemic stroke, cardioembolic ischaemic stroke, or non-cardioembolic ischaemic stroke in the largest available cross-sectional studies (70 804 participants, of whom 19 816 had stroke). Summary-level results of discovery and follow-up stages were combined using inverse-variance weighted fixed-effects meta-analysis, and in-silico lookups were done in stroke subtypes. For genome-wide significant findings (at p<5 × 10(-8)), we explored associations with additional cerebrovascular phenotypes and did functional experiments using conditional (inducible) deletion of the probable causal gene in mice. We also studied the expression of orthologs of this probable causal gene and its effects on cerebral vasculature in zebrafish mutants. FINDINGS: We replicated seven of eight known loci associated with risk for ischaemic stroke, and identified a novel locus at chromosome 6p25 (rs12204590, near FOXF2) associated with risk of all-stroke (odds ratio [OR] 1·08, 95% CI 1·05-1·12, p=1·48 × 10(-8); minor allele frequency 21%). The rs12204590 stroke risk allele was also associated with increased MRI-defined burden of white matter hyperintensity-a marker of cerebral small vessel disease-in stroke-free adults (n=21 079; p=0·0025). Consistently, young patients (aged 2-32 years) with segmental deletions of FOXF2 showed an extensive burden of white matter hyperintensity. Deletion of Foxf2 in adult mice resulted in cerebral infarction, reactive gliosis, and microhaemorrhage. The orthologs of FOXF2 in zebrafish (foxf2b and foxf2a) are expressed in brain pericytes and mutant foxf2b(-/-) cerebral vessels show decreased smooth muscle cell and pericyte coverage. INTERPRETATION: We identified common variants near FOXF2 that are associated with increased stroke susceptibility. Epidemiological and experimental data suggest that FOXF2 mediates this association, potentially via differentiation defects of cerebral vascular mural cells. Further expression studies in appropriate human tissues, and further functional experiments with long follow-up periods are needed to fully understand the underlying mechanisms

Discursive psychology and emotion

Discursive psychology (DP) offers a window onto the way emotion and cognition play out in everyday interaction. As one of the pioneers of DP, Edwards has been instrumental in shaping this approach, and his work on emotion and interaction has been particularly inspiring. In this chapter we consider this impact by providing an understanding of the concerns that motivated Edwards, the contributions of the paper and the lasting impact that his research has had on how emotion is conceptualized. Edwards developed a discursive psychology of emotion that examined two things: the ways in which emotion categories can be threaded through everyday talk, and how people use ascriptions and avowals of emotion to perform actions in talk. This focus on how wonderfully useful emotion categories and descriptions can be for speakers had never been done, and still sits in stark contrast to classic individualist studies that characterize the discipline of psychology

MCR: Open-Source Software to Automate Compilation of Health Study Report-Back

Sharing individualized results with health study participants, a practice we and others refer to as “report-back,” ensures participant access to exposure and health information and may promote health equity. However, the practice of report-back and the content shared is often limited by the time-intensive process of personalizing reports. Software tools that automate creation of individualized reports have been built for specific studies, but are largely not open-source or broadly modifiable. We created an open-source and generalizable tool, called the Macro for the Compilation of Report-backs (MCR), to automate compilation of health study reports. We piloted MCR in two environmental exposure studies in Massachusetts, USA, and interviewed research team members (n = 7) about the impact of MCR on the report-back process. Researchers using MCR created more detailed reports than during manual report-back, including more individualized numerical, text, and graphical results. Using MCR, researchers saved time producing draft and final reports. Researchers also reported feeling more creative in the design process and more confident in report-back quality control. While MCR does not expedite the entire report-back process, we hope that this open-source tool reduces the barriers to personalizing health study reports, promotes more equitable access to individualized data, and advances self-determination among participants

The costs of human-induced evolution in an agricultural system

Pesticides have underpinned significant improvements in global food security, albeit with associated environmental costs. Currently, the yield benefits of pesticides are threatened as overuse has led to wide-scale evolution of resistance. Yet despite this threat, there are no large-scale estimates of crop yield losses or economic costs due to resistance. Here, we combine national-scale density and resistance data for the weed Alopecurus myosuroides (black-grass) with crop yield maps and a new economic model to estimate that the annual cost of resistance in England is £0.4bn in lost gross profit (2014 prices), and annual wheat yield loss due to resistance is 0.8 million tonnes. A total loss of herbicide control against black-grass would cost £1bn and 3.4 million tonnes of lost wheat yield annually. Worldwide, there are 253 herbicide-resistant weeds, so the global impact of resistance could be enormous. Our research provides an urgent case for national-scale planning to combat further evolution of resistance, and an incentive for policies focused on increasing yields through more sustainable food-production systems rather than relying so heavily on herbicides

Design and Validation of the GI-NEC Score to Prognosticate Overall Survival in Patients with High-Grade Gastrointestinal Neuroendocrine Carcinomas

BACKGROUND: Prognostic markers for risk stratification of patients with gastrointestinal high-grade neuroendocrine carcinomas (GI-NECs) are lacking; we designed and validated a prognostic score for overall survival (OS). METHODS: Consecutive patients diagnosed in five neuroendocrine specialist European centers were included. Patients were divided into three cohorts: a training cohort (TC), an external validation cohort (EVC), and a prospective validation cohort (PVC). Prognostic factors were identified by log-rank test, Cox-regression, and logistic regression analyses. The derived score was internally and externally validated. All statistical tests were two-sided. RESULTS: Of 395 patients screened, 313 were eligible (TC = 109 patients, EVC = 184 patients, and PVC = 20 patients). The derived prognostic score included five variables: presence of liver metastases, alkaline phosphatase (ALK), lactate dehydrogenase (LDH), Eastern Cooperative Oncology Group performance status (ECOG PS), and Ki67. In multivariable analysis, the score was prognostic for OS (hazard ratio [HR] = 1.86, 95% confidence interval [CI] = 1.47 to 2.35, P < .001) and had good discrimination (C-index = 0.76) and calibration (mean error = 0.021, 90th percentile = 0.037) in the TC. These results were validated in the EVC and PVC, in which our score was able to prognosticate for OS when adjusted for other prognostic variables in the multivariable analysis (HR = 1.85, 95% CI = 1.27 to 2.71, P = .001; and HR = 4.51, 95% CI = 1.87 to 10.87, P = .001, respectively). The score classified patients into two groups with incremental risk of death: group A (0-2 points, 181 patients [63.9%], median OS = 19.4 months, 95% CI = 16.1 to 25.1) and group B (3-6 points, 102 patients [36.1%], median OS = 5.2 months, 95% CI = 3.6 to 6.9). CONCLUSIONS: The GI-NEC score identifies two distinct patient cohorts; it provides a tool for clinicians when making treatment decisions and may be used as a stratification factor in future clinical trials