NIHRDataInsights/HRCSData huggingface dataset:
Title: Evolutionary Predictions In Colorectal Cancer (EPICC)
Funder: Wellcome Trust

Abstract: We aim to make prognosticating cancer like forecasting the weather. Weather forecasting combines detailed measurement of the current atmospheric state with a mechanistic understanding of atmospheric evolution that can be ‘played forward’ using a mathematical model to give accurate predictions. In oncology, we have the capability to make detailed measurements of the current state of a cancer, but critically lack a mechanistic understanding about how tumours will evolve over time. The shortfall in knowledge presents a major hurdle to accurate prognostication and is the focus of our proposal. We will perform a uniquely high-resolution molecular analysis of human colorectal cancers, and via mathematical modelling of these data, derive an unprecedented quantitative understanding of the ‘evolutionary laws’ that underpin colorectal carcinogenesis. We will evaluate the prognostic value of these laws, and then use them to construct and test models that mechanistically forecast disease evolution. The proposal builds upon our previous work demonstrating the predictability of cancer genomic alterations (Williams et al., Nature Genetics, 2016) as a direct consequence of physical constraints on tumour evolution (Sottoriva et al., Nature Genetics, 2015). This research will represent a major step towards the replacement of correlation-based prognostication with a new paradigm of accurate mechanistic forecasting.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: Using behavioural science to maximise the impact of cervical cancer control policies
Funder: Cancer Research UK

Abstract: Background The success of cancer prevention and early diagnosis programmes depends critically on human behaviour; high participation is essential to reducing cancer incidence and mortality. I will use the cervical cancer context to develop an approach to understanding participation that can be applied to other cancer fields. Every year ~3,000 women in the UK are diagnosed with cervical cancer and 900 die of the disease; and many of these diagnoses and deaths are potentially preventable by screening and vaccination against oncogenic types of human papillomavirus (HPV). Almost 1 in 4 women in England do not take part in screening and around 1 in 6 girls offered the HPV vaccine remain un-/under-vaccinated. In addition, cervical cancer disproportionately affects women from more socioeconomically deprived backgrounds; largely because of underuse of screening. Aims This work brings together approaches from health psychology, social marketing and behavioural economics to develop a sophisticated understanding of non-participation, segment non-participants into distinct types, and develop and evaluate targeted interventions designed to increase informed uptake of HPV vaccination and cervical screening. Methods In Stage 1, I will use qualitative and quantitative methods to develop and validate a non-participant typology, with markers to allow identification. Interviews will provide in-depth understanding of non-participation. A population-based survey will be used to assess discriminant validity and distribution of types within the population. Stage 2 will develop theory-driven targeted interventions to increase informed uptake of vaccination and screening within the different groups. I will draw on theoretical approaches from a range of disciplines including social marketing and behavioural economics (e.g. so-called ‘nudge’ approaches). Acceptability and feasibility of a series of interventions will be established using focus groups, surveys and experimental studies. Stage 3 will include randomised controlled trials of the most acceptable and promising interventions to evaluate their impact. The fellowship will build on my existing expertise in cervical cancer prevention and allow me to develop new collaborations and skills to progress my career in this field. How the results of this research will be used This work has the potential to influence the delivery of cervical screening and HPV vaccination, increasing uptake to reduce the cervical cancer burden. The methods to be developed will also have application in other cancer prevention programmes where there is a need to increase informed participation.


Research activity codes: 4.4 POPULATION SCREENING;3.4 VACCINES;4.3 INFLUENCES AND IMPACT;3.1 PRIMARY PREVENTION INTERVENTIONS TO MODIFY BEHAVIOURS OR PROMOTE WELL-BEING
Health categories: CANCER AND NEOPLASMS
Title: Investigating the role of gland phenotype in the evolution of Barrett’s oesophagus to dysplasia
Funder: Cancer Research UK

Abstract: Background: Barrett’s oesophagus (BO), the premalignant precursor condition to oesophageal adenocarcinoma, occurs in 3-5% of the adult UK population. BO patients are offered periodic endoscopic surveillance in an effort to detect progression early. There are currently no biomarkers that triage patients at increased risk of disease progression. For this reason many patients are unnecessarily burdened by surveillance, most of whom (95%) will never develop clinical symptoms. It is imperative that we improve our ability to accurately assess progression risk in BO patients. BO is a glandular metaplasia that evolves through extensive clonal competition to esophageal adenocarcinoma. Microscopically BO displays a rich phenotypic diversity of morphologically distinct gland phenotypes. Whilst studies have suggested that genotypic diversity can predict progressing risk in BO, the phenotypic diversity in BO has not been appreciated. For this reason, it remains unresolved whether genotypic progression in BO is restricted to a singular phenotype or whether all phenotypes are at risk of progressing to cancer. Indeed, whether phenotypic diversity reflects genotypic diversity (i), and whether this diversity can be used as a biomarker for progression risk (ii), is unknown. Aims: In this project I propose to: 1) investigate whether BO gland phenotypes co-evolve with genotypic clonal expansions; 2) investigate whether phenotypic diversity in surveillance biopsies can be used as a cancer risk indicator 3) determine the phenotypic origins of Barrett’s dysplasia 4) investigate the origins of recurrent BO post ablative treatment and determine whether phenotypic diversity can predict recurrence risk Methods: Here I propose to couple phenotyping of Barrett’s mucosa with high resolution sequencing within Barrett’s metaplasia and dysplasia. I will also study the evolution of gland phenotype in relation to clonal evolution using SNP array data obtained from biopsies taken from a longitudinal cohort of patients that have shown progression versus those that have not. I propose to develop quantitative evolutionary models from these data to predict risk of progression. How the results will be used: This is an innovative approach where tissue architecture and genotype are analysed in concert to provide an effective means to measure evolution in BO and therefore a more effective cancer risk stratification. Data obtained from this proposal form the framework for developing evolutionary biomarkers as a model for cancer risk.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: Spatial Prostate Assessment and Circulating Environment (SPACE) Study
Funder: Cancer Research UK

Abstract: Background Establishing a comprehensive genomic map incorporating mechanism, biology and risk stratification is a fundamental goal of translational prostate cancer science. Although we already undertake clinical risk stratification in prostate cancer and have made some progress in defining molecular groups, there has been little success in fusing these approaches. Prostate cancer, as with other solid tissue pelvic malignancies, sheds cells into the lymphatics and blood of the pelvis and abdomen and yet little is known about the micrometastatic potential of such cells, nor their genomic status, particularly in high risk ‘localised’ disease. Aims I aim to discover whether molecular stratification approaches previously published on prostatectomy specimens can be applied accurately to diagnostic biopsies. I will then determine the distinctive contribution of tumour and environmental niche factors to tumour cell development and progression by multifocal sampling by targeted biopsy and RP cut-up. Finally, I will isolate prostate cancer cells from blood and lymphatic tissue and fluid, determine the tumour focus of origin by genomic interrogation, and identify essential factors for metachronous disease recurrence. Methods Our approach to preparation of prostatectomy specimens for genomic study has been published (Warren et al 2013). The Multi-Parametric Magnetic Resonance Imaging (MRI) protocol forms part of the Ginsberg group consensus statement (Kuru et al 2013). Nucleic acids will be extracted by standard approach (AllPrep, Qiagen); library preparation and genomic profiling performed by our core facility. The Risbridger Group approach to patient derived xenografting is established (Lawrence et al, Nature Protocols 2013). Collaborations to be established with Joakim Lundeberg’s team for spatial transcriptomics (Stahl et al, Science 2016). How the results will be used This could underpin decision making in prostate cancer within the next 5- 10 years providing the evidence needed to help urologists and the men they treat to decide whether they need invasive surgery or radiotherapy and, ultimately, which drug they need if their disease does relapse. This approach could save lives.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: Elucidating and Treating Chromosome 1q (MCL-1) Amplified Prostate Cancer
Funder: Wellcome Trust

Abstract: Prostate cancer (PC) is a leading cause of cancer-related death in men globally. Advanced PC responds to androgen receptor blockade but inevitably remains lethal. Novel therapeutic strategies are urgently required, incorporating disease molecular stratification. I have acquired data demonstrating that a gene cassette on chromosome (ch) 1q, incorporating the anti-apoptotic gene MCL-1, is amplified in 16% of lethal PC. Furthermore, patient-derived tumour models with ch1q (MCL-1) amplification are resistant to established treatments but respond to MCL-1 inhibition. I hypothesize that, interrogation of MCL-1 biology will elucidate superior strategies to target MCL-1. Consistent with this, RNA splicing factor SF3B1 knockdown drives expression of its pro-apoptotic isoform MCL-1S, and deubiquitinating enzyme UCHL3 knockdown degrades MCL-1 protein, inhibiting PC growth. Furthermore, UCHL3 is deleted in 7-13% of lethal PC which may reduce MCL-1 expression and sensitise to BCL-XL/BCL-2 inhibition. I will therefore: (1) evaluate the impact of ch1q (MCL-1) amplification on PC cellular processes and response to standard therapies; (2) develop novel strategies to target MCL-1 (and other BCL-2 family members) in PC; and (3) identify novel targets to deliver innovative therapeutic strategies for ch1q (MCL-1) amplified PC. I envision that this work will improve outcome from this commonest of male cancers.

Lay abstract: New treatments for lethal prostate cancer Current drugs available for treating lethal prostate cancer (PC) eventually stop working. This is because PC cells become resistant. Approximately 16% of patients have a certain rogue gene pattern, which leads to high levels of some proteins. I hypothesise these increased protein levels may cause the drug resistance. I will test each such protein in PC models and patient tumour samples to find out which ones most lead to PC cell growth. I will then identify existing or novel drugs that block these proteins from working, thereby stopping PC cells from growing. Finally, we will test how these drugs could treat patients with this gene pattern. These studies will help identify novel therapeutic strategies to improve the outcome of lethal PC patients. This approach could also work with other common cancers: breast and lung cancer cells, for instance, often show the same gene pattern.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Basal extrusion: a new mechanism for metastasis initiation
Funder: Cancer Research UK

Abstract: Our studies on epithelial cell number homeostasis identified a fundamental cell death mechanism that oncogenic mutations hijack to drive cancer cell invasion. When epithelia become too crowded, they trigger some cells to seamlessly extrude out of the layer and eventually die. Several driver mutations of aggressive cancer types (pancreatic, lung, and colon) disrupt extrusion signaling, instead causing cells to amass at sites where they typically extrude, disrupt barrier function, and lead to an aberrant type of extrusion—basal cell extrusion (BCE)—that enables their invasion into the underlying tissue. Cells invading by BCE pinch off their entire apexes, permanently removing their epithelial determinants and enabling new plasticity. Using the transparent zebrafish epidermis as a model for epithelia where carcinomas develop, we can visualize KRas-transformed cells invading, migrating, and seeding new metastatic sites. This unprecedented resolution revealed other surprising findings: i) GFP-KRasV12 cells invade at sites distinct to the primary masses and ii) adopt neuron-like or mesenchymal-like morphologies or become enlarged. iii) While many GFP-KRasV12 cells divide, migrate, and circulate in the blood, only those also carrying a common collaborating mutation in p53 survive and form large metastases in the head. Although there are intrinsic caveats to using zebrafish to model cancer, our findings may shed new insight into metastasis mechanisms in humans. In this grant, we aim to identify mechanisms driving BCE, how it impacts the fate and survival of invading cells and if this mechanism can drive invasion of transformed cells in other tissues and animals. To achieve these goals, we have divided our aims into three work packages: 1) What is the fate of cells invading by BCE? 2) What factors impact the identity and fate of invading cells? 3) What controls BCE? For WPs 1&2, we will live image invasion in zebrafish, ex vivo mouse tissue slices, and human organoids, and use comparative transcriptomics and imaging to identify and follow the fates of invading cells. For WP3, we will use cell culture monolayers and cysts to identify mechanisms and signalling driving basal extrusion and assess if other cancers use this mechanism. We expect that the proposed studies will establish hallmarks of cells resulting from BCE and determine if it can initiate metastasis in human cancers. If so, our studies could pave new avenues for diagnosing and preventing metastatic cancer.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Novel mechanisms of FAK-dependent immune evasion in Pancreatic Cancer
Funder: Cancer Research UK

Abstract: Background: Immunotherapy continues to show promise in the treatment of a number of cancers. However, similar results have not been forthcoming in patients with pancreatic cancer, and prognosis remains poor. Hence, there is a real and urgent need to identify the key molecular drivers of resistance to immunotherapy, in order to develop new therapeutic strategies for this cancer of unmet need. I recently identified a novel function for Focal Adhesion Kinase (FAK) in regulating the anti-tumour immune response in a mouse model of skin Squamous Cell Carcinoma (SCC). Specifically, FAK-dependent regulation of chemokines and cytokines in cancer cells, including Ccl5 and TGF2, was required to drive elevated levels of regulatory T-cells (Tregs) into tumours, resulting in suppression of the anti-tumour CD8+ T-cell response. This was mediated through nuclear FAK signalling, and treatment with a small molecule FAK kinase inhibitor resulted in immune-mediated tumour regression. Similar findings have since been reported using genetic and transplantable mouse models of pancreatic cancer. There, FAK inhibition resulted in broad reprogramming of the fibrotic and immuno-suppressive pancreatic tumour microenvironment. However, that was not sufficient to drive immune-mediated pancreatic tumour regression, instead resulting in prolonged survival. I have identified additional FAK-dependent mechanisms of immune regulation in pancreatic cancer cells in response to either stimulation with IFN-gamma or supernatants conditioned using activated CD8+ T-cells, including regulation of antigen processing/presentation, metabolic immune checkpoints, intercellular adhesion molecules, and other inflammatory mediators. These findings imply that we do not yet understand the full extent and complexity of FAK’s role in regulating the immune response to pancreatic cancer. Aims: 1. Define the function of cancer-cell-intrinsic, IFN-induced immune regulators in the anti-tumour immune response to FAK-depleted and FAK inhibitor treated pancreatic tumours, and identify novel strategies for FAK / immunotherapy combinations. 2. Use human patient derived pancreatic cancer cells to gain insights into which pancreatic cancer patients are most likely to benefit from targeting FAK-dependent reprogramming of the IFN-response alone or in combination with immunotherapy. Methods: I will use a combination of CRISPR gene editing, flow cytometry, proteomics, nanostring gene expression analysis, in vivo tumour growth studies, and advanced intravital imaging to investigate novel mechanisms of FAK-dependent immune regulation in pancreatic cancer. How the results will be used: This project will deliver an advanced understanding of FAK-dependent immune regulation, to accelerate the development of new therapeutic strategies for the treatment of pancreatic cancer.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Understanding the Roles of ERphagy during Epithelial-to-Mesenchymal Transition
Funder: Cancer Research UK

Abstract: Background: Cancer metastasis remains one of the biggest hurdle in cancer therapy. Intracellularly, cancer metastasis is triggered by epithelial-to-mesenchymal transition (EMT) which is a drastic transcriptional and translational reprogramming that drives the loss of cell-cell adhesion and polarity in favour of cell migratory and invasion properties. Current EMT and metastasis research focuses on the upstream transcriptional changes but very little is known about the post-transcriptional mechanisms that relay the upstream EMT signal to the eventual mesenchymal transition. In the quest to identify genes that mediate the endoplasmic reticulum-specific autophagy (ERphagy) using a genome-wide CRISPR screening approach, I unexpectedly found that ERphagy is antagonistically regulated by EMT- and MET (mesenchymal-to-epithelial transition)- transcription factors (TFs) across several cancer types. This suggests that ERphagy could be epistatic to EMT-TFs during mesenchymal transition and might play a role in cancer metastasis. Aims: My lab will focus on fundamentally explore this novel observation of EMT-activated ERphagy and its impact on mesenchymal transition summarised in the following three major aims: AIM1: Defining the generalisability of EMT signal in ERphagy activation AIM2: Characterise the mechanism of selective ERphagy during EMT AIM3: Determine the impact of ERphagy on mesenchymal phenotypes Methods: We will use various cancer cell types and EMT-inducing cytokines to define the properties and extent of conservation for EMT-activated ERphagy. Quantitative proteomics will be used to define the cargoes that are specifically targeted for ERphagy during EMT activation. We will use transcriptomic approaches (RNAseq and CUT&RUN) to identify the ERphagy effectors that are direct transcriptional targets of the EMT- and MET-TFs. Based on the ERphagy effectors and cargoes, several mechanistic hypotheses (e.g., ER stress resolution and cellular remodeling via ERphagy) will be biochemically explored using qRT-PCR, Western Blotting and confocal microscopy to further characterise the intracellular events during EMT-activated ERphagy. We will also use various EMT assays to examine the effect of perturbed or hyper-activated ERphagy on various mesenchymal properties. Outcome: Pharmacological intervention on EMT-TFs is currently elusive. Our proposed fundamental work will serve as a first step in exploring the feasibility of targeting the downstream ERphagy instead as a strategy to prevent mesenchymal transition. Warranted by the outcome of this proposal, we intend to perform in vivo mouse work to explore the feasibility of inhibiting ERphagy to prevent tumour metastasis. We will also perform small molecule screens for inhibitors of the identified ERphagy factors as potential therapeutic approach in cancer metastasis.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Identification of tumour-specific spliced epitopes to target large cohorts of cancer patients by immunotherapy
Funder: Cancer Research UK

Abstract: Identification of tumour-specific spliced epitopes to target large cohorts of cancer patients by immunotherapies Background Targeting CD8+ T cells to recurrent tumour-specific mutations can profoundly contribute to cancer treatment. To promote this, I advocate targeting tumour-specific spliced epitopes (TSSEs), which overcome limits on antigen sequence diversity, thereby potentially treating a substantially larger patient cohort. Spliced epitopes are naturally produced by proteasomes through reshuffling the antigen sequence and although they have been increasingly studied in infection and autoimmunity, they have been largely neglected in cancer immunotherapy. Aims My Aim is to identify and validate TSSEs as targets of anti-cancer immunotherapies for large numbers of patients. I shall employ a multi-disciplinary approach including: (i) the systematic identification and characterisation of TSSEs derived from selected recurrent mutation; (ii) the generation and validation of TSSE-specific T cells and TCRs suitable for adoptive T cell therapy (ATT); (iii) the quantitation of TSSE antigenicity in cancer patients. Our preliminary results show that we can almost triple the potential melanoma and pancreatic cancer population treatable with ATT by targeting TSSEs identified in this project. Methods TSSE identification and characterisation will be studied at a biochemical and cellular level by combining in silico and in vitro methods which I have co-developed over the last decade. Specific CD8+ T cell clones and their TCRs will be isolated from the peripheral blood of patients with melanoma and pancreatic cancer, and the lymphocyte responses to spliced epitopes compared between patients and controls. Thereupon, the efficacy of TSSE-specific CD8+ T cell clones to selectively recognise and eradicate cancers will be tested in vitro and in xenograft tumour models. How the results of this research will be used The project will: 1. generate a computer-based method for the prediction of spliced peptide generation. 2. identify spliced epitopes carrying selected tumour-specific mutations that can be employed in different immunotherapeutic strategies; 3. define the features of naturally-occurring adaptive immune responses against TSSEs in cancer cells, potentially impinging upon the efficacy of immunotherapies such as checkpoint blockade; 4. isolate CD8+ T cell clones and their TCRs reactive to TSSEs, which can be used in adoptive T cell therapies (ATTs); 5. build a foundation for clinical trials using ATTs against melanoma, pancreatic adenocarcinoma, colon carcinoma and other tumours carrying mutations that are presented as spliced epitopes.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS