NIHRDataInsights/HRCSData huggingface dataset:
Title: Defining the role of ADP-ribosyltransferases in DNA repair and genome stability
Funder: Medical Research Council

Abstract: This work is concerned with increasing our understanding of how different ADP-ribosyltransferases (ARTs) maintain genome integrity through DNA repair. We have exploited genome editing technology to generate cell lines defective in the principle DNA damage responsive ARTs alone, or in combination. Using this unique set of reagents we have identified exciting and novel redundancy between ARTs in resolving DNA damage during S-phase. We will build on this work using genome editing technology, in combination with cutting edge biochemical and cell based assays, to define how the ARTs PARP1 and PARP2 regulate these processes. These approaches will also be extended to characterising a novel ART we have uncovered that allows cells deficient in PARP1 and PARP2 to tolerate DNA damage. Using state of the art screening facilities in Oxford, we will perform a genome-wide CRISPR/Cas9 based screen to identify novel genes and pathways that when disrupted suppress or enhance the sensitivity of PARP-deficient cells to DNA damage. Given inhibition of ARTs is being exploited to treat homologous recombination-defective tumours, we will assess how disruption of these genes impacts on these events. These experiments will lead to efforts in improving the efficacy of these agents in the clinic and identify new targets whose inhibition will overcome drug resistance.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Mesenchymal contribution to early oesophageal tumour formation
Funder: Medical Research Council

Abstract: Cancer has traditionally been thought to form and evolve as genetic mutations accumulate, altering cell behaviour and ultimately leading to invasion and death. Recent findings have shown that the contribution of non-cell autonomous components, such as the tumour microenvironment, also play an essential role in the etiopathology of the disease. Mesenchymal fibroblasts, the main cellular component of the stroma in most cancers, have not only been involved in tumour initiation and progression, but have also shown potential prospects for cancer therapeutics. Despite this, very little is known as to how mesenchymal cells regulate epithelial cell behaviour in the earliest stages leading to tumour formation, and the relevance of this cross-talk for cancer progression. Using diethylnitrosamine, a nitrosamine found in cigarette smoke, I have recently developed a model of early tumorigenesis in the mouse oesophagus (Alcolea, Nat Cell Biol 2014). This model recapitulates the appearance of sporadic mutations that accumulate in human carcinogenesis, and creates discrete tumoral lesions identifiable as early as 10 cells in size. In the current proposal I set up to exploit this unique system to dissect epithelial and mesenchymal cross-talk in early neoplasia. To answer this question, I will combine my expertise in in vivo single cell lineage tracing together with transcriptional network analysis to investigate spatio-temporal changes in mesenchymal cell behaviour, and how these changes correlate with alterations in epithelial cell fate during tumour formation. Further mechanistic insights and potential therapeutic relevance will be gained by using an organotypic culture system specifically designed to recapitulate oesophageal cell behaviour ex vivo. Outputs from these studies will provide druggable targets to test their translational potential in preclinical models.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Precision targeting of mTOR in conventional and MHC class I-restricted anti-tumour CD4+ T cells
Funder: Medical Research Council

Abstract: Although adoptive transfer of CD8+ T cells engineered to express tumour-specific TCR or chimeric antigen receptors can successfully induce remissions in patients with cancer, other patients fail to respond or respond only transiently. Recent work from the host laboratory has focused upon the concept that adoptive transfer of multiple T cell populations (heterogeneous in terms of subset, functional state and persistence) will better protect against immune escape than transfer of uniform populations of CD8+ T cells. In this proposal, I am seeking to extend this 'multiplex' T cell approach by exploring how gene modification of antigen recognition and functional state can be used to exploit the anti-tumour functions of CD4+ T cells. I will test the hypothesis that precision up- or downward tuning of mTOR complex 1 (mTORC1) in CD4+ T cells bearing conventional or MHC Class I-restricted TCR can be exploited (1) to enhance their effector functions within tumour microenvironments, and (2) to increase their potential for self-renewal, thus enabling long-term immune surveillance. By introducing positive or negative regulators of mTORC1 into tumour-specific murine CD4+ T cells and using tractable tumour models, I will determine the effects of mTORC1 tuning upon Th differentiation, functional plasticity and self-renewal. Knowledge regarding how mTORC1 up- or down-regulation will impact upon Th function and persistence will be used to devise appropriate delivery systems for manipulation of CD4+ T cells for future clinical use.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: MICA: Un-jamming the Ras switch - blocking Ras nucleotide exchange and promoting GTP hydrolysis
Funder: Medical Research Council

Abstract: We have developed modulators of Ras activity using novel artificial binding proteins, termed Adhirons (or commercially known as Affimer type II). Each Affimer constrains two nine amino acid variable loop regions for molecular recognition and our group has developed very high quality phage display libraries each comprising greater than 10^10 individual clones. Typically, reagents isolated using phage display have low nanomolar binding affinities and tend to bind in protein binding hot spots. In this project we aim to characterise a suite of Affimers already shown to inhibit Ras activity and Ras protein-protein interactions in vitro. Affimers have been isolated from phage display libraries that modulate Ras activation through 1) inhibiting nucleotide exchange caused by SOScat, 2) and promoting hydrolysis of GTP. These reagents will provide new mechanistic insights into the molecular regulation of Ras, providing novel therapeutic strategies to slow Ras-addicted tumour growth, and will develop our basic understanding of Ras biology and function


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: MICA: Immunotherapy for oral cancer prevention and treatment
Funder: Medical Research Council

Abstract: Oral cancer (OSCC) is common worldwide with more 220,000 deaths annually. Studies report that ~15-80% of OSCCs develop from pre-existing, premalignant precursor lesions (OPL), most commonly a white patch (leukoplakia). The global prevalence of leukoplakia is estimated to be 2.6%, with reported rates of malignant transformation of 3.5%. Immunotherapy is a highly promising new cancer therapy, with checkpoint inhibitors such as anti-PD1, predicated on boosting pre-existing anti-tumour immunity. Vaccines developed to generate immune responses against specific tumour antigens are also producing promising clinical results, notably in pre-malignant cervical dysplasia, suggesting a similar strategy could be used to target OPL. This project aims to identify shared antigens overexpressed in OPL and OSCC using transcriptomic microarrays. OPL transcriptome data will be compared with RNA sequencing datasets of OSCC (UoS & TCGA) to identify common antigens expressed across the disease process. For example, MAGED4B and FJX1 have already been shown by the CRM team to be overexpressed in both OPL and OSCC. The common antigens will be taken forward for vaccine construction using a novel plant viral particle platform developed by the UoS team. This safe single-strand RNA containing vaccine acts through engagement of TLR7/8 to activate immune mechanisms closely resembling those of a pathogenic viral infection, inducing a cytotoxic CD8 T-cell response of high magnitude and durability as well as tumour-specific CD4 T-cells. Vaccines will be tested in the HLA-A2 humanized mouse model (B6.Cg-Tg(HLA-A/H2-D)2Enge/J) using murine tumour cell lines (B16/F10 melanoma and 4NQO-derived oral cancer lines) expressing human HLA-A2 and transfected with selected target antigens).This study will establish proof-of principle of new prophylactic vaccines, which can be produced at low cost, to manage patients with OPL, and inform design of future immunotherapy trials for OSCC prevention.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Comparison of traditional vs. virtual simulation-enhanced training for scaling the cervical cancer surgery workforce in Zambia
Funder: Medical Research Council

Abstract: Phase 1 Specific Aims: 1. Develop a virtual reality simulation training platform for the surgical treatment of invasive cervical cancer. 2. Compare effectiveness of traditional surgical training (TS) (control condition) to traditional surgical training enhanced with virtual reality simulation (VR) (intervention condition) on the acquisition of surgical proficiency in treating cervical cancer. 3. Compare cost of achieving cervical cancer surgical proficiency using TS vs. VR training Six (6) surgical trainees will be randomly assigned to TS or VR-enhanced training, after the completion of which they will be evaluated as they perform (six) 6 cancer surgeries under the guidance of an expert, blinded to their initial training. Economic costs of achieving cervical cancer proficiency using TS vs. VR training will be estimated using the C4P-ST tool. Phase 2 Specific Aims: 1. Adapt remote real-time surgical supervision technology to resource-constrained surgical conditions 2. Evaluate the feasibility of virtual proctorship (real-time tele mentoring platform) to enhance and maintain the surgical proficiency of surgeons newly trained to perform cervical cancer surgery. Trainees from each of the study arms, deemed to be surgically proficient, will perform an additional three (3) cancer surgeries, with mentoring provided by an expert using tele mentoring from a remote location. Experts will be different than those used in Phase 1 and will be blinded to Phase 1 training. Potential Applications and Benefits: 1.Integration into surgical oncology education training curriculum in LMI countries a. Paradigm shift in cancer surgery training 2.Rapid scale up of cervical cancer surgery services in low income settings a. Decrease in cervical cancer morbidity and mortality 3. Evidence for effectiveness of technology-based surgery training a. Evidence-based policy making at the national and international levels b. Attract R&D investments from global fun


Research activity codes: 5.8 COMPLEMENTARY;5.4 SURGERY;6.4 SURGERY
Health categories: CANCER AND NEOPLASMS
Title: IMPC: Role of asparagine synthetase in anti-tumour T cell responses
Funder: Medical Research Council

Abstract: Background: T cells are white blood cells that have a key role in the immune responses that protect the body from the development and spread of cancer. Immune responses to tumours rely on the ability of T cells to specifically recognise components (antigens) of cancer cells that are not present on normal non-cancerous tissue. Upon encounter with a cancer antigen, a T cell undergoes a process of activation and division to generate a population of effector cells that then traffic through the body to the tumour site. This requires a lot of energy and nutrients to fuel the processes of cell growth, division and activation. In addition, within the tumour site, to maintain an effective immune response, T cells have to compete with tumour cells for nutrients. Indeed, nutrient deprivation within the tumour environment is thought to contribute to the failure of T cell immune responses in cancer. Aims: We are interested in determining how T cells cope with the energy demands required for effective anti-tumour responses. We wish to test the hypothesis that T cells increase their capacity to synthesize a key amino acid, asparagine, which serves as a building block for the generation of new proteins. We will determine the role of an enzyme called asparagine synthetase (AS) in this process by comparing the ability of control mice and mice lacking AS to generate T cell responses to tumour cells. Furthermore, we will compare the ability of control and AS-deficient T cells to undergo activation, growth and cell division in tissue culture to determine the role of asparagine synthesis in these fundamental processes. Output: These preliminary analyses will determine whether AS is important for T cell immune responses. By understanding the Fundamental mechanisms by which T cell responses are fuelled, in the future, we hope to use this knowledge to develop approaches to improve immune responses to cancer.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: From single cells to populations: generalized pseudotime analysis to identify patient trajectories from cross-sectional data in cancer genomics
Funder: Medical Research Council

Abstract: Longitudinal multiple tumour sampling studies are the ideal approach for the study of cancer evolution and its impact on patient outcome. However, such studies are logistically challenging and expensive to operate, and typically involve relatively smaller cohorts than a cross-sectional study involving the collection of a single tumour sample (or perhaps multiple samples obtained at the same time) from each patient. This project proposes novel statistical approaches to inferring (pseudo)temporal information by integrating cross-sectional studies involving whole genome sequencing and gene expression analysis of cancers along with clinical covariates. The model probabilistically assigns patients to a latent "pseudotime", which measures a marker of disease progression, based on their molecular and clinical profiles. The transformation from high-dimensional molecular observations to the one-dimensional pseudotime is implemented using a covariate-adjusted Gaussian Process Latent Variable Model that can model a different disease progression trajectory for each combination of the covariates. This will allow us to test if putative molecular mechanisms distinguish between patients, for example, whose disease progresses to metastatic status or become radio and/or chemotherapy resistant by looking for statistically significant differences in the trajectories of each phenotypic group. This project will also develop novel approaches for integrating methods that can predict the functional annotation of somatic mutations and their impact on cellular programming. These models will provide probabilistic genome annotations that can be used as input into the pseudotime ordering algorithms. We will integrate all this work and apply about application to the Genomics England 100,000 Genomes Project.


Research activity codes: 1.4 METHODOLOGIES AND MEASUREMENTS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: Assessing new therapeutic opportunities linked to TCR signalling in mature T-cell lymphomas with unmet need
Funder: Medical Research Council

Abstract: Comprehensive insights into genetic changes in a variety of malignancies over the past decade have provided a basis for identification of new targets and personalized treatments. Lagging behind some of the more prevalent cancer types, mutations associated with T-cell lymphomas, including those with limited treatments, have only been described within the last two years. We now propose to extend structural insights into some of the key components mutated in these cancers (such as PLCgamma) using latest developments in cryoEM and methods for mapping molecular interactions (HDX-MS) as well as to establish the exact contribution of genetic alterations to pathogenesis. Our approaches will be based on the expertise and available clinical material for two related CD4+ T-cell malignancies with different aetiology, CTCL and ATL which is virally (HTLV-1) transformed. In addition to already acquired data for bioinformatics, we also have access to primary cells from individual patients from longitudinal studies of these malignances and we obtained cell lines from ATL patients with PLCG1 mutations; for comparison, we also have Btk-inhibitor resistant cell lines with PLCG2 mutations. In these systems, we plan to assess broader genetic changes and apply gene editing (CRISPR modification) and pharmacological inhibitors to a range of components involved in TCR signalling and establish those that are critical as well as their links in pathology. Overall, we aim to identify mechanisms that contribute to oncogenesis and maintenance of malignancy and key components that can be therapeutic targets. PLC and/or other components that we identify will guide new routes to treatment. Use of pharmacological inhibitors is important in assessing potential drug targets. However, there is no reliable inhibitor that specifically targets PLC enzymes. To address this limitation, we have established a collaboration with a GSK team that will provide us with relevant material.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: The MUC1-ST/Siglec-9 innate check point axis in cancer: prevalence, prognostic significance and potential therapeutics.
Funder: Medical Research Council

Abstract: Tumour-associated macrophages are some of the most abundant immune cells found in tumours, their presence correlating with metastasis and poor prognosis. Changes in the post-translational modification glycosylation, is a hallmark of cancer and the glycosylation of MUC1 is dramatically altered in breast cancer. We have shown that a tumour-associated glycoform of MUC1 (MUC1-ST) binds to the lectin Siglec-9 expressed by monocytes and macrophages. This interaction results in the release of factors associated with tumour growth, modulation of the microenvironment and the induction of a tumour-associated macrophage (TAM) phenotype. In this project we will confirm our in vitro data in vivo using primary breast cancers, define the transcriptome of the MUC1-ST induced macrophages and apply it to public databases to determine prognostic significance, and investigate therapeutic applications of blocking the MUC1-ST/Siglec-9 interaction using human in vitro models We will phenotype macrophages infiltrating into breast cancer by 1) immunohistochemistry and RNAscope 2) flow cytometric analysis, and correlate this with the MUC1 glycoform (MUC1-ST) that binds Siglec-9. Using matched sera and tumour samples we will also determine if there is a correlation between MUC1-ST expressed by the tumours and the presence of factors secreted by myeloid cells after binding to MUC1-ST. The transcriptome of macrophages differentiated from monocytes by MUC1-ST will be determined by RNAseq allowing us to develop a 'MUC1-ST macrophage' signature, which we will apply to large tumour datasets to understand the impact of these cells on disease. We will also study the therapeutic potential of using antibodies to Siglec-9 to block the migration of labelled monocytes induced by MUC1-ST educated monocytes using in vitro assays and an organotypic breast cancer culture model. The effect on angiogenesis will also be investigated in vitro.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: MICA: The network of class I PI3K interacting proteins is dramatically rewired in a PTEN-/- mouse model of prostate cancer. What are the implications?
Funder: Medical Research Council

Abstract: Mutations in many components of the class I PI3K signalling pathway support tumour progression and this has led to major investment in the development of PI3K inhibitors. Despite this focus and the vast body of data that has defined the proteins that CAN regulate class I PI3Ks, the network of molecules that actually DO perform this role in vivo, either in healthy tissues or in cancers, remains largely unknown. Loss of the tumour-suppressor and PIP3-phosphatase, PTEN, leads to chronic activation of class I PI3K signalling and is a common occurrence in human cancers generally (11.8% of analysed tumours) and prostate cancer specifically (13.6%, early and over 60% late, stage). We have unpublished proteomic data, obtained from mice expressing endogenously-tagged class I PI3K components, that for the first time reveals the proteins that interact with the class I PI3K regulatory subunits in healthy compared to PTEN-null mouse prostate (3 month, Hi-grade PIN stage). We find evidence of substantial rewiring upstream of PI3K activation in the PTEN-null tissue, including; a dramatic decrease in association of IRS1 (Insulin Receptor Substrate 1) and increases in interactions with the poorly characterised molecules AFAP1L2 (XB130) and PLEKHS1, but little change in association with cell surface receptors. We hypothesise that these events drive reduced insulin responsiveness/dependency and, through the molecular properties of AFAP1L2 and PLEKHS1, increased receptor-independent, PIP3-driven 'feed-forward' augmentation of PIP3 signalling and tumour progression. We aim to investigate the mechanisms that lead to this rewiring and its implications for prostate cancer.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Cellular plasticity and senescence at the origin of lung cancer
Funder: Medical Research Council

Abstract: Our main objective is a better understanding of the mechanisms and processes that lay at the origin of lung cancer. In other tumour models, it is known that, upon damage and/or oncogenic stress, differentiated cells may undergo de-differentiation (gain of plasticity) acquiring malignant phenotypes. Since cell senescence is a response to damage and stress, and senescent cells can secrete pro-inflammatory and pro-tumorigenic factors, we hypothesize these cells can also induce in nearby cells de-differentiation processes favouring lung cancer initiation. Our specific aims are: (i) To induce lung de-differentiation processes upon damage (urethane treatment) and/or oncogenic stress (K-Ras activation). To do so, we will employ a regrogrammable mouse model transiently expressing the four Yamanaka factors. We will determine whether reprogramming-induced de-differentiation is an oncogenic promoter. (ii) To capture early tumour cells expressing transiently or stably de-differentiation markers by using a lineage tracing mouse strain and FACS approaches. Cells will be subjected to RNAseq analyses and epigenetic techniques such as chromatin immunoprecipitation. (iii) To address the interplay between cell senescence and de-differentiation processes during lung tumorigenesis. Senescence will be manipulated both genetically and chemically during lung cancer initiation. Lineage tracing approaches will allow us to perform longitudinal studies on the activation of pluripotency markers and how it relates to senescence. We will determine if senescence-induced plasticity is an important oncogenic promoter. (iv) To identify factors secreted by senescent cells able to induce de-differentiation of nearby cells and/or malignant transformations. Microdissected sections of tumours from control and senescence-manipulated mice will be subjected to gene expression and protein arrays. Conditioned media from cultured senescent cells will be subjected to SILAC analyses.


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