NIHRDataInsights/HRCSData huggingface dataset:
Title: New insights into the cellular response to complex DNA damage induced by proton beam therapy
Funder: Medical Research Council

Abstract: Proton beam therapy (PBT) is a cutting-edge precision technique for cancer treatment that specifically targets the tumour and spares the surrounding normal tissues. The therapeutic effect of PBT is largely attributable to DNA damage, particularly complex DNA damage (CDD) where several DNA lesions are generated in close proximity by a single radiation track. Since PBT is not monoenergetic and energy is deposited via the Bragg peak, the amount and complexity of CDD can vary which can have a significant impact on the biological response to PBT. However little is known of the molecular and cellular mechanisms that recognise and process CDD in cells. Recent evidence published by the Principal Investigator has demonstrated that a specific cellular DNA damage response is triggered in response to CDD induced by PBT, and that specific enzymes (e.g. USP6 and PARP-1) control cell survival under these conditions. Utilising PBT at different energies (and thus linear energy transfer; LET) which creates CDD in different proportions, in combination with various biochemical, molecular and cellular biology techniques, this proposal aims to expand on this knowledge by focusing on the specific DNA repair pathways and enzymes, particularly of the base excision/single strand break repair pathways, that are critical for resolving of PBT-induced CDD sites. Furthermore, data provided from recent comprehensive siRNA screening has identified proteins in the cellular DNA damage response (e.g. OGG1 and PARG), and ultimately utilised novel inhibitors against these enzymes (TH5487 and PDD00017273) that can enhance cellular radiosensitivity in response to CDD-induced by PBT, which require further detailed investigation. The overall goal is to improve our understanding of the radiobiology of PBT linked to CDD and repair, and ultimately in the identification of novel strategies using targeted drugs/small molecule inhibitors that may enhance the efficacy of PBT in cancer treatment.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Steroid-producing immune cells promote metastatic dissemination of cancer cells
Funder: Medical Research Council

Abstract: Metastasis is the leading cause of death in cancer patients. Immune cells play a dual role during this process. They can destroy the cancer cells, as well as, can promote the metastasis. We are only beginning to understand the mechanisms of immune cell promotion of metastasis. I observed that T cell-mediated steroidogenesis promotes metastasis. Yet, how T cell steroidogenesis contributes to the cancer cell metastasis is unknown. Therefore, this project has been designed to investigate the role of steroid-producing T cells in the promotion of cancer metastasis and how this may be exploited therapeutically. Our first aim is to define the immune cell-mediated steroid biosynthesis during metastasis. In mice models of lung metastasis, we will functionally characterise steroid-producing immune cells, profile and quantify the steroids, and reveal the signalling cues that induce steroidogenesis in T cells. Next, we will determine the mechanisms of how do steroid-producing T cells promote metastasis. I observed that ablation of T cell steroidogenesis restricts lung colonisation of cancer cells. We will test whether the restriction of metastasis is because of stimulation of the anti-tumour immunity. Alternatively, we will examine whether the steroids directly promote metastatic dissemination of cancer cells to the lung. Finally, we will reveal the steroid regulatory mechanisms that drive metastasis. Our ultimate aim is to exploit this newly created knowledge to innovate therapeutic strategy for metastatic cancer. The first approach is to restrict metastasis by pharmacologic inhibition of the steroidogenesis pathway in mice model. The next innovative approach is to develop steroid-resistant T cells for adoptive cell therapy, both in human and mice. We will genetically engineer the T cells to make them steroid-resistant, and test their tumour cell killing efficacy in the preclinical mice model and by co-culturing them with the tumour spheroids.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: The structural basis of transcription factor 3C recruitment by N-myc
Funder: Medical Research Council

Abstract: Myc proteins function as a transcriptional regulators that recruit other proteins such as transcription factors (e.g. TFIIIC), protein kinases (e.g. CDK9) and chromatin-modifying adaptors and enzymes (e.g. STAGA), which act at multiple regulatory steps to activate transcription. This proposal focuses on the interaction between N-myc and TFIIIC, which leads to activation of RNA Polymerase II (Pol II) transcription of a subset of genes important for cellular proliferation. In preliminary work we have identified a small region of the N-myc sequence that interacts directly with a subcomplex of TFIIIC. We have also demonstrated that we can express and purify this minimal interaction module. Most of the work outlined in the proposal is dedicated to understanding the N-myc:TFIIIC interaction at a structural level using three orthogonal approaches: X-ray crystallography, cryo-electron microscopy, and structural mass spectrometry. Additionally, we aim to validate the structure using mutation and protein:protein interaction assays, initially in vitro using biophysical approaches (ITC, FP), then in cultured cells (co-IP, PLA). Finally, we aim to extend the validated structural observations and mutations to determine how the complex relates to other N-myc interactions involved in transcriptional activation and its regulation. We will use mutation combined with affinity tag proteomics to determine which interactors are dependent on the N-myc:TFIIIC interaction. This will enable us to identify other proteins that associate with the complex. Additional analysis by cell XL-MS will help us understand the basic architecture of the higher-order complex. Results can be applied to work by molecular oncologists performing synthetic lethality screens of important oncogenic pathways. They can also be exploited by the cancer drug discovery community, using structural and computational methods to block protein:protein interactions.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Tailored monitoring of patients with monoclonal gammopathy to improve early detection of myeloma and monoclonal gammopathy of clinical significance
Funder: Medical Research Council

Abstract: Earlier detection is a high priority for patients and improves survival: 84% of people with myeloma survive for >5 years if diagnosed at the earliest stage, compared with only 26% if diagnosed at advanced stage. Myeloma is most frequently diagnosed late (>3-6 months post symptom presentation) and has the longest diagnostic delay of any cancer, with emergency presentations in >30% of newly diagnosed myeloma patients who have shortened survival. Because MGUS precedes all myelomas, an early diagnosis strategy of monitoring all MGUS patients for progression to myeloma, is impractical. Progression risk is ~1%/year in the MGUS population, with a prevalence of 3.2% in individuals >50 years. In addition, over the last few years, well defined clinical association of organ damage secondary to monoclonal protein in a MGUS setting has been described. This has been grouped under single diagnosis category of MGCS. Lack of optimal risk stratified monitoring for MGUS patients makes screening inefficient. Therefore, research is required to develop better monitoring/ tools. Exploring clinical characteristics of MGUS patient populations from primary care records (CPRD database) who remain in MGUS state versus those who transformed to myeloma will enable understanding of clinical predictors of disease progression. In addition, we will attempt to quantify the burden of undiagnosed MGCS patients in primary care. Oxfordshire CCG has funded an OxCom MGUS monitoring service to enable streamlined monitoring of MGUS patients in Oxfordshire. Prediction model from CPRD data will be validated in this database of 3000 MGUS patients with annual increment of 1000 patients per year. A recent observation that aberrant glycosylation of light chain drives MGUS to MGCS and/ or myeloma transition, has generated a new hypothesis. We can test this hypothesis using longitudinal excess diagnostic serum samples in a prospective MGUS to myeloma cohort vs controls, run alongside OxCoM MGUS patient pathway


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: Defining precision medicine in laryngeal cancer: developing an enhanced clinical cohort
Funder: Medical Research Council

Abstract: Laryngeal cancer is diagnosed in 2400 new patients each year in the UK and disproportionately affects those who are socioeconomically disadvantaged. Half of patients present with advanced disease and have poor survival. Treatment can render a patient permanently nil by mouth or in need of a permanent tracheostomy. Progress has stalled over the past 30 years with survival has remaining at best static, and at worst it has declined. Currently, we have no method of prognosticating how a specific tumour or patient will respond to treatment We require an understanding of how an individual patient with laryngeal cancer responds to treatment. This project aims to inaugurate an enhanced clinical cohort of patients with laryngeal cancer, to define precision medicine in this disease: Workstream 1: The head and neck 5000 cohort recruited 1065 patients with laryngeal cancer; these patients have three year oncological and quality of life follow up data. Initial analysis of these data will allow some information on outcome and inform development of the enhanced cohort. Workstream 2: We will pilot processes to establish this cohort in two cancer centres and maximise recruitment and retention of patients and data collection. Analyses will assess data quality and provide a demonstration of the value of the cohort. We have opportunity to roll out the cohort to The Northern Head and Neck Cancer Alliance: this is a group of seven head and neck cancer centres, committed to improving outcomes. Workstream 3: We will explore inclusion of radiomics and tissue biomarkers within the patient cohort. This workstream will establish governance and processes for collection of biological samples and radiological data to the cohort. "Proof of principle" pilot studies will be undertaken. Following the fellowship, the ambition is to roll the cohort out nationally. In time, the cohort will have the potential to revolutionise progress in laryngeal cancer


Research activity codes: 6.4 SURGERY;6.5 RADIOTHERAPY AND OTHER NON-INVASIVE THERAPIES
Health categories: CANCER AND NEOPLASMS
Title: Evaluation of a novel in vitro model of sonic hedgehog medulloblastoma by single cell transcriptomics
Funder: Medical Research Council

Abstract: RESEARCH OBJECTIVES: The childhood malignant brain tumour, medulloblastoma (MB), which originates in the cerebellum has devastating consequences. The lack of tumour models that capture treatment-relevant tumour heterogeneity and model tumour microenvironment has hampered treatment advances. I will develop a novel human model of a major MB subtype, sonic hedgehog (SHH)-MB, whose prognosis is negatively affected by additional mutations, in particular in the tumour suppressor gene, TP53. I will test whether TP53 wild-type (WT) and TP53 mutant SHH-MB can be better modelled by co-culture with wild type (WT) cerebellar organoids (CBOs), to mimic the tumour micro-environment. Conversely, I will also determine whether tumour cells induce permissive changes in the CBO. METHODOLOGY: I willl analyse the transcriptomes of tumour spheroids from the human SHH-MB TP53 WT cell line (ONS76) and a TP53 mutant cell line (DAOY) in co-culture with WT CBOs, at single cell level using the 10X Genomics Chromium platform. The R toolkit, Seurat will be used to visualise cell identities, and identify differentially expressed genes. Tumour heterogeneity will be determined by identifying cell subsets defined by distinct 'gene signatures'. I will compare the two cell lines to each other and to published single cell and bulk transcriptome profiles of human MB biopsies to establish similarities and differences. Pathway analysis will be applied to test whether specific biochemical pathways are upregulated in tumour cells and/or the WT CBOs. APPLICATION/EXPLOITATION: Patient-specific tumour models could be developed by growing biopsy samples ex vivo in WT CBOs to test personalised therapies. The effects of drug treatments on tumour and wild-type cerebellar cells can be concurrently analysed to assess treatment toxicity.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Liquid biopsy for aggressive T-cell lymphoma
Funder: Medical Research Council

Abstract: Peripheral T-cell lymphoma (PTCL) is characterised by early treatment failure and poor clinical outcomes in many patients. However, existing tools to predict early treatment response are inadequate. This project will develop a robust and quality assured circulating tumour DNA (ctDNA) test. Subsequently, the project will leverage a unique sample repository available through the UK PTCL Biobank to explore the hypothesis that ctDNA analysis predicts clinical outcomes in patients receiving standard first-line chemotherapy. Furthermore, by interrogating serial ctDNA data from patients who experience early relapse this project will identify molecular drivers of chemoresistance in PTCL. The project is divided into three main work packages (WP): a) WP1 will develop a robust, quality assured test, to detect and track ctDNA mutations in PTCL. This work will advance our existing PTCL ctDNA assay by incorporating molecular barcoding and error suppression bioinformatics to improve test sensitivity and specificity. Test validation will be performed to UKAS accreditation standards. b) WP2 will use this test to determine the utility of ctDNA analysis as a predictor of clinical outcomes in PTCL. These data will provide evidence that ctDNA-based clinical outcome prediction is a tool that can support precision medicine approaches in PTCL. c) WP3 will focus on uncovering molecular dynamics of chemoresistance in PTCL by tracking phased variants to discover clonal shifts and identify molecular drivers underpinning drug resistance. Reverse translating these clinically informed mechanistic insights will accelerate preclinical studies testing therapeutic strategies that overcome chemoresistance. Collectively, this project aims to demonstrate that ctDNA analysis can act as a precision medicine catalyst in PTCL and lead to improved outcomes in these difficult-to-treat diseases.


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: The impact of antibody isotype on patient monocyte and macrophage functions and activation states to manipulate anti-tumour responses in melanoma
Funder: Medical Research Council

Abstract: Aims: To assess the ability of anti-melanoma antigen antibodies drive anti-tumour response by polarising macrophages and monocytes away from tumour-promoting, immunomodulatory subsets and towards tumour-inhibiting subsets. Objectives: 1. Investigate the subsets, polarisation states and FcR expression of patient-dervied monocytes and macrophages extracted from melanoma lesions. 2. Engineer antibodies of different IgG isotypes, the most common isotypes used in antibody therapeutics, and the IgE class, to recognise a melanoma-associated antigen. 3. Determine whether the engineered antibodies can promote anti-tumour effector functions when applied to patient-derived monocytes and macrophages, using in vitro and in vivo models Methodology: 1. Flow cytometric analysis of monocytes from a large in-house biobank of blood samples from patients with differences in stage of melanoma, exposure to treatment modalities and response to treatment, will be compared to age and gender matched healthy volunteers. In addition, analysis of macrophages extracted from melanoma tissue using multiparameter flow cytometry, including phenotype subset evaluation, ex vivo immune mediator and transcriptomic analyses and multiple in vitro assays assessing the impact of macrophages on melanoma growth, invasion and migration 2. Analysis of how phenotypic and functional characteristics of tumour associated macrophages outlined above can be altered with the engagement of FcRs by different antibody isotypes 3. Explore the ability of antibodies to induce infiltration of macrophages with enhanced anti-tumour effector function and restrict tumour growth in in vivo melanoma xenograft models and models of checkpoint inhibitor resistant melanoma. Scientific and Medical Opportunity: This study will provide greater insights into the role of monocytes and macrophages in malignant melanoma, including in treatment-resistant disease and how anti-cancer antibodies may enhance macrophage function.


Research activity codes: 2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: CANCER AND NEOPLASMS
Title: Towards a CAR T-cell therapy approach for Calreticulin-mutated Myelofibrosis
Funder: Medical Research Council

Abstract: We wish to develop a chimeric antigen receptor-T cell (CAR-T) therapy for patients with Myelofibrosis (MF). MF is a bone marrow disorder caused by a disordered megakaryocyte progenitor cell clone and results in early death and acute myeloid leukaemia. It is an unmet clinical need as the only available curative option is a stem cell transplant which carries high mortality and it is unfeasible for most patients. Mutations in Calreticulin (CALR) have been identified as a disease driving mutation with oncogenic properties in 25% of MF cases. CALR mutations mutations cause a +1bp frame shift which results in an alternative reading frame translated into a novel C-terminus which includes the sequence 'SPARPRTSCREACLQGWTEA'. Also, the endoplasmic reticulum signal (KDEL motif) is no longer present which allows mutCALR to escape ER. This mutated CALR is translocated to the cell surface, where it leads to constitutive JAK2/STAT5 signaling via activation of the Thrombopoietin receptor (MPL/TpoR). Therefore, CALR may be an excellent target for CAR-T therapy. Initially, we will develop an array of monoclonal antibodies against the novel sequence found in mutCALR by initiating a rat vaccination campaign. We will then validate its surface expression in HSCs and progenitor cells and measure its serum concentration. Once a successful monoclonal antibody has been developed, we will incorporate it into a CAR-T construct. The optimal CAR-T cell construct in terms of the co-stimulation and other cytokine release will be determined by performing in vitro experiments and testing their efficacy against mutCALR MF HSCs. Successful CAR-T constructs will then be tested in vivo in MISTRG murine models who will be transduced with mutCALR HSCs from MF patients.


Research activity codes: 2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: CANCER AND NEOPLASMS
Title: Defining and targeting mitochondrial dysfunction in cellular models of succinate dehydrogenase (SDH)-mutated tumours
Funder: Medical Research Council

Abstract: Phaeochromocytoma and paraganglioma (PPGL) are tumours that arise from chromaffin cells of the adrenal medulla or autonomic nervous system. 40% of PPGL are associated with a germline mutation in susceptibility genes; of these, succinate dehydrogenase B (SDHB) mutations have the highest rate of malignancy (~10%). SDH dysfunction leads to accumulation of the oncometabolite succinate, which drives tumorigenesis through mechanisms including pseudohypoxic signalling and impaired homologous recombination DNA repair. It is unknown what is unique to SDHB-deficient tumours that would explain why SDHB mutations are more likely to give rise to metastatic disease than other SDHx mutations. SDH functions in mitochondria and I hypothesise that comparative analysis of the mitochondrial consequences of loss of each SDH subunit will reveal unique consequences of SDHB functional loss that drive malignancy. To test this hypothesis, I have generated an isogenic series of cell lines by CRISPR/Cas9 genome editing, where individual SDH subunits are deleted. I will analyse abnormalities in mitochondrial structure and network dynamics, metabolic function, and stress responses in the knockout cells and also cells with clinically occurring SDH point mutations re-expressed. I will investigate therapeutic strategies in my cellular models of SDH disease. Treatment will target previously shown impaired DNA repair and mitochondrial defects identified through this fellowship - a unique combination based on synthetic lethality and crosstalk between DNA damage and altered metabolism investigated in other cancer models. Outcomes of this fellowship will be a comprehensive comparison of the mitochondrial consequences of loss of SDH subunits and specific clinical mutations, as well as the potential identification of targets for therapeutic development. The fellowship will provide me bespoke training towards development as a clinician scientist.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Deciphering immune signalling changes and the influence of irradiation in SWI/SNF deficient cells
Funder: Medical Research Council

Abstract: The interplay between the cellular response to ionising radiation and immune signalling has important therapeutic consequences, but the responses are complex and not yet fully understood. We established that the SWI/SNF chromatin remodelling complex is important for both normal immune pathway signalling and radiation responses, but the mechanistic basis for these changes remains obscure. Irradiated cells also show changes in their immune signalling pathways. Moreover, in both irradiated cells and SWI/SNF deficient cells, there are alterations to the composition of the proteasome. Here, we propose to investigate the mechanistic basis for altered immune signalling and proteasome composition in SWI/SNF deficient cells, and how this is influenced by irradiation. We will also investigate how altered proteasome composition impacts on proteasome activity, and how these changes influence the population of cell surface antigens (the immunopeptidome). Understanding these cellular pathways and their regulation by SWI/SNF and/or irradiation at a molecular level is important because SWI/SNF is defective in about 25% of human cancers, and radiotherapy is widely used in the clinic. The results obtained will yield important insights into normal and tumour responses to irradiation, and provide a mechanistic framework for guiding new developments in immunotherapy and radiotherapy.


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