NIHRDataInsights/HRCSData huggingface dataset:
Title: Investigating anti-tumour T cell responses in nasopharyngeal carcinoma to refine vaccine-based immunotherapies
Funder: Medical Research Council

Abstract: We have developed a therapeutic vaccine, known as MVA-EBNA1/LMP2, that expresses a fusion protein encoding almost all known CD4 T-cell targets in EBNA1 and multiple CD8 T-cell epitopes from LMP2. This vaccine has already been shown to be safe and to exhibit promising therapeutic activity in early phase clinical trials. Knowledge of the factors in the blood and tumour tissues of NPC patients that might limit T cell responses will be required not only to maximize the therapeutic efficacy of our vaccine, but also to identify biomarkers of likely treatment response for eventual patient stratification. To address these gaps in knowledge we will first use multiplex immunohistochemistry to provide a detailed characterisation of the immune micro-environment of NPC, including the expression of immune checkpoints. We will use our established EBV-specific T cell clones and NPC cells, including lines we have recently established that more faithfully recapitulate primary disease, to explore the activity of these checkpoints, initially focusing on those mediated by fibroblasts. Finally, we will use next generation sequencing to describe how the TCR repertoire in the blood of NPC patients varies throughout the course of disease, and how it compares to the TCR repertoire we observe in tumour tissues. Importantly, using our cultured immune assays we will be able to interrogate these data to define T cell responses to relevant EBV and cellular tumour antigens.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: Immunotherapy for Head and Neck Cancer
Funder: Medical Research Council

Abstract: Worldwide, head & neck cancer (HNSCC), is the sixth most common cancer (annual estimated incidence >400,000) and is a significant health burden in both Malaysia and the UK. HNSCC is often difficult to treat; surgery & radiotherapy, remain standard treatments, but despite improvements, are associated with significant morbidity and a relatively static 5-year survival rate of around 50-60%. Immunotherapy is the most promising new cancer therapy for several decades; immune checkpoint inhibitors against CTLA4 and PD1/PDL1 have shown efficacy across cancer types, including HNSCC. To improve response rates there is significant interest in combining checkpoint inhibitors with other immunotherapeutics including costimulatory receptor agonists (eg. CD27) and therapeutic vaccines against tumour-associated antigens (TAA). Few common TAA are described in HNSCC however, the Cancer Research Malaysia (CRM) team has identified MAGED4B and FJX1 as highly expressed in both Malaysian and UK patients; these represent excellent targets for vaccine development. The project aims to develop and test the efficacy of DNA vaccines encoding full length MAGED4B and FJX1 antigens. These will be integrated into the clinically-tested University of Southampton vaccine design that incorporates the tetanus toxin domain (Dom) to provide linked CD4 T-cell help for optimal CD8+ T-cell induction. Vaccines will be tested in a humanised syngeneic cancer mouse model in combination with antibodies targeting anti-PD1 and anti-CD27. Tissues from UK and Malaysian HNSCC patients (all HLA class I and II genotyped) will be analysed for the presence of MAGED4B and FJX1 antigen-specific CD8+ T-cells, and specific antigenic peptides identified. New murine syngeneic HNSCC models will also be developed for use in future immunotherapy studies. This will establish proof-of-principle of a new therapeutic vaccine concept to manage HNSCC patients, and inform design of future immunotherapy HNSCC trials


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: The identification of genetic vulnerabilities in head and neck cancers for the development of novel therapies.
Funder: Medical Research Council

Abstract: The global cancer burden is expected to double by the year 2030 and this will disproportionately affect the Asian continent. Head and neck squamous cell carcinoma (HNSCC) is endemic in Asia, and it is one of the top 3 cancers in Malaysia. Long-term survival of less than 50% and limited approved therapies for HNSCC underscore the urgent need for the development of novel and effective therapies. While the mutational landscape of HNSCC is now well established, the ability to identify the targetable component of the cancer genome will accelerate translation of these knowledge into clinical benefit. A major focus in the development of new cancer therapies has been the identification of essential genes that are critical for the survival of cancer cells, and where loss or inactivation of these can result in cell death or growth arrest. This project will use state-of-the art biological models, genome-wide CRISPR/Cas9 lethality screens and next-generation sequencing, to address this major health problem in Asia. We will use experimental and computational approaches to identify essential genes for HNSCC and specific pharmacologic inhibitors that could target these genes. The successful completion of this project will form the basis of developing novel targeted drugs for HNSCC as well as re-purposing existing therapies currently used to treat other cancer types.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: Promoting Awareness of Cancer and Early Detection (PACED) Initiative in Malaysia
Funder: Medical Research Council

Abstract: The incidence of cancer in Malaysia and cancer-related deaths are increasing. The relatively high cancer mortality rate accounted for 10% of medically certified deaths. Research indicates clearly that there is a low level of cancer awareness in Malaysia and that low awareness delays help seeking, late presentation is high and detection rates are poor. In addition, there were strong misbeliefs about cancer and several emotional barriers to seeking help. The project comprises four phases. Phase 1 - 'Development of a culturally sensitive cancer Awareness Raising Programme (CARP)' - the main aim of this phase is to develop the content of the CARP including the key messages and design and test mode(s) of delivery. The CARP will focus on the three most prevalent cancers in Malaysia - lung, breast and colorectal. Phase 2 - 'Design the evaluation framework', - a workshop will be held to discuss and finalise the evaluation framework and metrics particularly regarding the identification of the outcomes of the CARP and the assessment tools in the context of the Malaysian infrastructure and health system. The evaluation framework will ascertain changes in awareness including recognition, attitudes, beliefs and knowledge about cancer and early diagnosis. Phase 3, 'Undertaking formative research' - qualitative and quantitative methods will be used to test the appropriateness, acceptability and feasibility of the CARP and assessment tools. Phase 4, 'Evaluate the impact of the CARP' - a large scale pilot evaluation study will be conducted in the Federal Territory of Kuala Lumpur and Selangor state. Pre-and post-campaign surveys will be carried out to evaluate the performance of campaign in term of awareness of signs and symptoms, beliefs and attitudes towards cancer and early diagnosis and attendance at primary care physicians with the symptoms highlighted in the campaign. Finally, we will develop a protocol for the roll-out of a national level CARP.


Research activity codes: 4.3 INFLUENCES AND IMPACT;8.3 POLICY, ETHICS AND RESEARCH GOVERNANCE
Health categories: CANCER AND NEOPLASMS
Title: Understanding the regulation of cytotoxic T lymphocyte signalling and activity through single-cell genomics
Funder: Medical Research Council

Abstract: Cytotoxic T lymphocytes (CTLs), which develop from naïve CD8+ T cells, are one of the central players in immune defence against cancer. In recent years, these cells have become a key target for therapies that enhance the anti-tumour immune response. T cell activation is a highly regulated but rapid process, requiring a multitude of coordinated signalling events to ensure fast, specific responses to antigen. While the transcriptomics of these early signalling processes have been studied in bulk cellular populations, many events in early activation are obscured by averaging across a heterogeneous cell pool. We here propose to use single-cell sequencing technologies to examine the transcriptome and coordinated protein expression during activation of CD8+ T cells. Specifically, we aim 1) to construct a fine-grained time-course of signalling during early T cell activation, 2) to understand how TCR affinity affects pathway usage and intercellular heterogeneity in early responses, 3) to understand how check-point molecules and their inhibitors affect the CTL transcriptome, 4) to create a pipeline for integrated analysis of transcriptomic and surface protein expression data from single cells. We will use a murine model of transgenic CD8+ T cells specific for a chicken ovalbumin peptide to have fine-tuned control over T cell activation. Single cells will be index sorted into lysis buffer by fluorescence-activated cell sorting to record surface protein information. Transcriptomic profiles will be generated by RNA sequencing. Starting from existing analysis methods for differentially distributed genes, we will develop tools to integrate flow cytometry and transcriptomic data to better characterise activation states and signalling pathways. This work will shed light on signalling events in T cell activation and response to environmental stimuli. Such information is crucial to finding targets for novel therapeutics.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Lethal renal cell carcinoma sub-clones: Defining mechanisms of tumour evolution, treatment resistance and immune escape.
Funder: Medical Research Council

Abstract: Aim: To study the evolutionary dynamics of clear cell renal cell carcinoma (ccRCC), focusing on the subpopulations of tumour cells (subclones) that evolve to become metastatic, resistant to immune response, treatment resistant and ultimately "lethal". Objectives: 1) To determine the features of lethal ccRCC sub-clones. 2) To develop novel scalable methods to detect lethal sub-clones. 3) To characterise the immune landscape of ccRCC and the mechanisms of lethal sub-clone immune escape. 4) To investigate the heterogeneity of immune gene expression in ccRCC sub-clones. Methodology: Patients (n=320) will be recruited through the renal TRACERx study (PI=Prof. C. Swanton) with primary, metastatic & autopsy tumour tissue, together with circulating cfDNA, collected. High-throughput DNA sequencing will be conducted on a multi-region basis, combined with computational image analysis of tumour slides and statistical methods, to identify recurrent features unique to lethal sub-clones. Immunogenic profiling will be conducted using multiplex immunohistochemistry to phenotype tumour-infiltrating lymphocyte sub-types, RNA-seq for expression analysis and bioinformatics techniques combined with experimental validation (tetramer assay) to identify tumour-specific neoantigens. The functional mechanisms of immune gene expression will be investigated using methylation profiling and Capture Hi-C. Scientific Impact: It is anticipated novel biological mechanisms of ccRCC tumour progression and treatment resistance will be identified. In addition new cost-effective methods, providing detail on tumour clonal architecture, will be piloted. Finally an increased understanding of ccRCC anti-tumour immunity, and how this is impacted by intratumour heterogeneity, is expected. Medical Impact: i) biomarkers to guide ccRCC treatment, ii) novel diagnostic to identify patients with high tumour diversity, iii) immunogenic insights to support ccRCC immunotherapy development.


Research activity codes: 4.2 EVALUATION OF MARKERS AND TECHNOLOGIES;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: CANCER AND NEOPLASMS
Title: Exploring the Teachable Moment for Alcohol Reduction in Breast Clinics: Formative Work to Inform Intervention Design, Development, Process Evaluation
Funder: Medical Research Council

Abstract: Existing research on alcohol brief interventions (ABI) has yet to examine the potential for suspected breast cancer clinics and breast screening mammography as a 'teachable moment'. We propose an early phase study to assess: (i) women's information needs regarding effects of alcohol on cancer risk, (ii) the nature of tailored feedback required, and (iii) the potential of a digital ABI to develop alcohol awareness into a long-term intrinsic motivation to reduce alcohol consumption. We will also investigate the potential to involve their social network, with the hypothesis that friends and family may also experience a 'teachable moment' due to the anxiety surrounding a suspected breast cancer referral or screening appointment. Early phase work will finalise a comprehensive review of the literature on alcohol intervention and behaviour change techniques in health care settings and efficacy of digital lifestyle interventions, and complete our draft logic model, started in preparation for this application. This knowledge will feed into a person-based approach to intervention development to involve patients in the design of an ABI. A continuous electronic clinic survey will measure determinants of readiness to change, intrinsic motivation, participants' demographic and clinical characteristics and level of alcohol consumption. Semi-structured interviews and focus groups will comment on currently available applications, and help design personalised feedback and optional web-based modules helping participants maintain awareness and motivation over time. Acceptability and feasibility will finally be measured in real-world conditions by testing the intervention prototype in clinics (using the LifeGuide digital behaviour change design software platform). Patients, clinicians, public health specialists, and commissioners, will be involved throughout to co-create the planned intervention.


Research activity codes: 3.1 PRIMARY PREVENTION INTERVENTIONS TO MODIFY BEHAVIOURS OR PROMOTE WELL-BEING;5.6 PSYCHOLOGICAL AND BEHAVIOURAL
Health categories: CANCER AND NEOPLASMS
Title: Understanding the oncogenic mediated pro-inflammatory environment in stem cell driven hypothalamic pituitary tumours
Funder: Medical Research Council

Abstract: Craniopharyngiomas (CPs) are tumours thought to arise from embryological remnants that form the pituitary. Two subtypes exist; adamantinoumatous associated with oncogenic B-catenin (ACPS) and papillary associated with mutations in BRAF (PCPs). Treatment of these aggressive tumours consists of neurosurgical resection and radiotherapy. There are no licenced pharmacological treatments for CPs. The association between inflammation and cancer is well established, however, this has not been investigated in CPs. My preliminary data highlights an up-regulation of pro-inflammatory markers in both mouse and human ACPs. I hypothesize that some of the first genes up-regulated after oncogenic activation in CPs are pro-inflammatory and that their inhibition will slow development and progression. I have developed a unique mouse model of CPs which allows activation of oncogenes at a specific time point within pituitary stem cells. To identify early up-regulated pro-inflammatory genes, RNA-seq will be performed on mouse pituitaries harvested up to 1 week after oncogene activation. Simultaneously, cells from pituitaries will be cultured and the secretome analysed via lipidomics, ELISA and IHC. To investigate inhibition of pro-inflammatory markers on CP development, mice and cultured cells will be treated with anti-IL6. In parallel, two pro-inflammatory genes will be genetically ablated within a new mouse model. I have one of the largest cohorts of human CPs consisting of over 200 samples. IHC for inflammatory markers within human CPs will be quantified and correlated with clinical phenotypic data to investigate an association between the degree of inflammatory infiltrate and incidence of tumour recurrence. Confirming a pivotal role of pro-inflammatory genes in the early development of CPs could lead to clinical trials using anti-inflammatories as adjuvant or neoadjuvant therapies, thereby reducing rates of recurrence and improving the quality of life for patients with CPs.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Identifying new approaches to the treatment of endocrine resistant breast cancer
Funder: Medical Research Council

Abstract: Aims: ESR1 mutations, as demonstrated in MCF7-Y537S cells, are associated with estrogen independent function and resistance to anti-estrogens. Gene expression profiling demonstrates that many ER target genes are upregulated in MCF7-Y537S cells. We aim to establish whether these key genes associated with ER function have utility as therapeutic targets in metastatic, ESR1 mutant breast cancer. Objectives: 1. Confirm the upregulation of identified nuclear receptors and EGF family members in MCF7-Y537S cells. 2. Investigate whether nuclear receptors and kinase cascades overexpressed in MCF7-Y537S cells are also upregulated in CRISPR-Cas9 engineered metastatic breast cancer cell lines expressing other ESR1 mutations. 3. Determine mechanisms of action of these overexpressed nuclear receptors and kinase cascades in breast cancer cell lines. 4. Investigate whether modulation of the identified nuclear receptor and signaling cascades using synthetic agonists/antagonists provide treatment strategies for this setting. Methodology: A range of techniques will be utilised including RT-qPCR, Western blotting, growth assays, RNA-Seq and ChIP-Seq, which are performed frequently by the host laboratory. Scientific and Medical Opportunities: The host laboratory have published extensively on ESR1 mutations and possible means of overcoming resistance. Recently published work includes the generation of breast cancer cell line models for ESR1 mutant metastatic disease, including MCF7-Y537S cells, using CRISPR-Cas9, providing a valuable model for assessing the mechanism of action of ESR1 mutations. We will now extend this work to investigate the function of upregulated ER target genes and evaluate potential therapies in mutant ESR1 cell lines. As clinically evaluated modulating drugs for many of these nuclear receptors and signaling pathways already exist, they could readily be repurposed. We propose that these upregulated genes may be useful therapeutic targets.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: Imaging DNA damage repair during radionuclide therapy
Funder: Medical Research Council

Abstract: Peptide Receptor Radionuclide Therapy (PRRT) is a most effective therapy for the treatment of somatostatin receptor expressing neuroendocrine tumours (NETs). NETs, although rare, present a significant clinical challenge, especially where surgery is impossible. PRRT, often administered as 177Lu- or 90Y-labelled somatostatin peptide analogues dotatate or dotatoc, directs these beta-emitting radionuclides to receptors on tumour cells, irradiating the tumour locally, causing DNA damage and tumour cell death. Since these radiolabelled peptides do not distribute significantly to other parts of the body, radiotoxicity to non-target tissues is limited to the kidneys, because of renal clearance, and some bone marrow toxicity. PRRT has demonstrably good obective response rates of up to 80%. Despite its frequent and successful use in the clinic, little or no dosimetry or radiobiological considerations are taken into account at the time of PRRT treatment planning or delivery, and treatment is usually administered as a standard dose and time scale, without any considerations for peptide uptake in the tumour, radiosensitivity, DNA damage effects, or dosimetry. Here, we propose to combine SPECT imaging of 177Lu-dotatoc distribution with DNA damage imaging, developed in our group. We showed that low amounts of 111In-anti-yH2AX-TAT, targeting the DNA damage repair protein yH2AX allows to visualise and quantify the extent of DNA double strand break damage. Combining dosimetry based on 177Lu imaging with visualisation of its radiobiological effects with 111In-anti-yH2AX-TAT will provide information about PRRT efficacy, at the time of treatment administration, allowing for an adaptive treatment regimen, which we hypothesise will increase complete response rates. Additionally, we will evaluate combination of 177Lu-dotatate PRRT with Auger electron treatment with 111In-anti-yH2AX-TAT, using larger therapeutic doses of 111In. We hypothesise that the combination will be superadditive.


Research activity codes: 5.5 RADIOTHERAPY AND OTHER NON-INVASIVE THERAPIES
Health categories: CANCER AND NEOPLASMS
Title: The role of macrophage-derived granulin in pancreatic cancer metastasis - mechanisms and therapeutic opportunities
Funder: Medical Research Council

Abstract: We have recently observed that pancreatic cancer liver metastasis critically depends on macrophage-derived granulin (Nielsen et al., Nature Cell Biology, May 2016). However, the molecular mechanisms by which granulin promotes the formation of a hospitable metastatic niche, and the therapeutic potential of targeting pro-metastatic functions of stromal cells at the metastatic site remain unknown. Aim: The here proposed study aims to identify and target signalling pathways that promote the pro-metastatic functions of stromal cells at the metastatic site in PDAC. Objectives and planned methodologies: This study will: 1. Generate and use primary hepatic stellate cells and primary macrophages in co-culture assays to characterise the interaction between these two stromal cell types. 2. Use a proteomic approach to identify how macrophage-derived granulin induces pro-metastatic functions of hStCs. 3. Evaluate in vitro and in vivo the identified pro-metastatic factors for their ability to sustain metastatic cancer cell growth and tumour immunity. 4. Use pre-clinical pancreatic tumour metastasis models in combination with genetic tools to ablate stromal cell populations (i.e. MAMs and activated hStCs) to characterize their role in tumour immunity. 5. Test in pre-clinical metastatic PDAC models the therapeutic potential of combining stroma-targeted therapies with a T cell checkpoint inhibitor. Results: The pre-clinical testing of potential therapies will identify treatment options that can be translated into clinical trials. In using both genetic and pharmacological approaches, this programme of work maximises the likelihood of successfully identifying key targets for metastatic pancreatic cancer treatment.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS