NIHRDataInsights/HRCSData huggingface dataset:
Title: The Cancer Cell Cycle: Control of pRb and p53 tumour suppressor proteins
Funder: Cancer Research UK

Abstract: 1) Background: Cancer is a term that describes over one hundred different diseases which share the common property of abnormal cellular proliferation. Despite enormous efforts the disease, for the most part, remains clinically unmet. In order to design new therapies that are effective against the disease it is essential to decipher the molecular details and interplay between the key pathways which control proliferation, and the molecular defects that occur in tumour cells. In normal cells, the G1 to S phase transition is a point of control which is tightly regulated, whereas tumour cells progress liberally in an unrestrained fashion into S phase. The retinoblastoma protein pRb and p53 are tumour suppressor proteins that act to negatively regulate the G1 to S phase transition. pRb principally affects growth control as a transcriptional regulator of the E2F family of transcription factors. In contrast, p53 is a stress-responsive transcription factor that interfaces with proliferation by activating genes involved with a variety of cell fates including cell cycle arrest and apoptosis. Significantly, tumour cells very frequently harbour mutations that alter pRb and p53 activity; loss of pRb deregulates early cell cycle control and loss of p53 causes insensitivity to checkpoint control. _x000D_ _x000D_ 2) Aims and Objectives: The primary objective of this programme is to clarify the functional and biochemical significance of new levels of post-translational control that impact on pRb and p53, and understand the importance of these events for cancer. The binding proteins that recognise the modifications will be investigated, together with the enzymes that are responsible for depositing and removing them. _x000D_ _x000D_ 3) Methods: We will employ molecular and cellular tools together with proteomics and genomics based technologies to pursue the investigation. A range of cell and biochemical assay systems will be utilised to explore the significance of the post-translational modifications on pRb and p53 and binding proteins for cancer cell proliferation. _x000D_ _x000D_ 4) How the results of this research will be used: Because the inactivation of pRb and p53 are regarded as hall marks of tumourigenesis and recognised to be critical events in attaining the malignant phenotype, the information arising from this study will not only advance our understanding of the molecular basis of cancer but also illuminate new pathways for therapeutic intervention. An underpinning translational platform allows results generated in the laboratory to be bridged with and evaluated in the clinical setting.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Identification of Myc-dependent apoptotic effectors
Funder: Cancer Research UK

Abstract: The highly pleiotropic Myc transcription factor plays a dual role in the potentiation of cellular proliferation and apoptosis – specifically, Myc-induced apoptosis acts as an intrinsic tumour suppressor mechanism. Suppression of apoptosis is a requirement in Myc-driven cancers and in many, perhaps all, other types of tumour. In transgenic mouse tumour models in which apoptosis is constitutively suppressed, Myc activation results in rapid and sustained cell proliferation concomitant with rapid evolution of diverse tumour attributes. Importantly, subsequent Myc deactivation leads to complete tumour regression, indicating that Myc is required both to initiate and sustain the tumour phenotype. Likewise, re-instating the capacity for apoptosis in Myc-driven tumours elicits their rapid regression. Restoring the link between growth deregulation and apoptosis therefore represents a powerful approach to the effective treatment of cancer. However, the precise molecular mechanisms coupling Myc activation to the apoptotic machinery are poorly understood. This proposal seeks to determine the nature of this coupling and how it becomes severed in cancers. Mitochondria play the pivotal role in apoptosis. Existing evidence supports the hypothesis that Myc’s ultimate apoptotic effectors are components of the outer mitochondrial compartment. We will employ quantitative proteomics techniques combined with our own, unique, switchable Myc technology, to (1) identify mitochondrial proteins that change following acute Myc activation with the same rapid kinetics as apoptotic induction, (2) determine how Myc elicits such changes, and (3) validate the roles of candidate effectors in mediating Myc-dependent apoptosis. Myc’s thousands of target genes are functionally very diverse and the mechanism by which it promotes apoptosis is likely to be indirect. Hence, defining Myc’s apoptotic mechanisms through inspection of its target genes is unlikely to be straightforward. Instead, we will isolate the outer mitochondrial compartment from cells before and at various times after acute Myc activation and determine which proteins change in abundance or post-transcriptional state over the course of apoptotic induction, using stable isotope labelling of amino acids in cell culture (SILAC). In conjunction with peptide separation and tandem mass spectrometry, SILAC yields relative quantitative data of protein changes. Proteins identified as candidate Myc apoptotic effectors will be subject to rigorous validation using a variety of cell and molecular biological techniques. Our preliminary data clearly indicate identifiable Myc-induced alterations to proteins within purified mitochondria. The unambiguous importance of the mitochondrial pathway in Myc dependent apoptosis makes it highly likely that we will identify significant and relevant effector proteins.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Polygenic susceptibility to prostate cancer and implications for personalised screening in population setting
Funder: Cancer Research UK

Abstract: Background _x000D_ Population screening for prostate cancer using serum prostate specific antigen (PSA) may prevent death from the cancer for a subset of men, but at a cost of considerable overdiagnosis (detection by screening of tumours which would not otherwise have arisen symptomatically in a person’s lifetime) and overtreatment. _x000D_ It is not known yet if stratifying population according to absolute risk that is dependent on age and polygenic profile and targeting screening to a sub-population with risk above a certain threshold would improve the benefit to harm ratio of screening for prostate cancer. _x000D_ _x000D_ Aims_x000D_ To study the clinical and public health utility of incorporating polygenic risk-profiling into a screening strategy for prostate cancer screening, particularly in reducing overdaignosis and mortality from prostate cancer, improving cancer detection, and reducing unnecessary biopsies. _x000D_ _x000D_ Methods_x000D_ Analysis will be based on clinicopathological and genotyping data from the ongoing Prostate Testing for Cancer and Treatment (ProtecT) study and the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort on screen-detected and clinically detected cancers respectively. _x000D_ The study populations will be stratified by absolute risk score that accounts for age and polygenic risk. Estimates of overdiagnosis will be derived from the observed and expected prevalence of screen-detected cancer across the different risk strata. _x000D_ Using multi-state models of the natural history of prostate cancer, the likely effect of the screening on mortality will be modelled. _x000D_ Compared to the approach of screening based on PSA test only, the validity and accuracy of approach that uses PSA test and absolute risk score simultaneously (parallel testing) and consecutively (serial testing) will be studied using Receiver operating characteristic (ROC) curves. _x000D_ _x000D_ How the results of this research will be used_x000D_ This project relating polygenic risk to overdiagnosis and severity of disease will elucidate the potential of polygenic risk to assist in detection of potentially life-threatening prostate cancer as opposed to indolent, possibly overdiagnosed, disease, and therefore ameliorate the benefit-harm balance of PSA screening. The natural history modelling, estimating disease progression rates, will give an estimate of the likely effect of different screening regimens on mortality from prostate cancer. The assessment of the predictive value of polygenic risk in biopsied subjects will indicate its potential, if any, in improving sensitivity or specificity of PSA test. The findings will have implications on clinical practice and on screening policy development.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.4 POPULATION SCREENING
Health categories: CANCER AND NEOPLASMS
Title: The Promyelocytic Leukaemia protein as a target in cancer therapy
Funder: Cancer Research UK

Abstract: The Promyelocytic Leukaemia protein as a target in cancer therapy._x000D_ _x000D_ Arsenic trioxide therapy for Acute Promyelocytic Leukaemia (APL) is mediated by SUMO-dependent degradation of Promyelocytic Leukaemia (PML)-Retinoic Acid Receptor a (RAR) oncogenic fusion protein. We demonstrated that ubiquitin mediated proteolysis of PML requires RNF4 E3 ubiquitin ligase. This allows terminal differentiation of tumour cells and cures disease. Our objective is to establish the molecular basis for the remarkable specificity of arsenic in APL and to determine if it can be employed therapeutically in other situations. Key questions to be addressed are:_x000D_ _x000D_ 1. How does arsenic "activate" PML. A YFP-PML expressing cell line will be used in a high content siRNA screen for gene products required for arsenic induced degradation of PML. Using TAP-tagged PML we will define post-translational modifications on PML induced by arsenic by time-resolved, SILAC based, mass spectrometry. Correlation between gene products required for arsenic induced degradation of PML and modifications that appear on PML in response to arsenic will allow us to elaborate the pathway of activation. _x000D_ _x000D_ 2. How does arsenic induce SUMO modification of PML. Proteomic analysis indicates that arsenic induced SUMO modification of PML is highly specific. Accounting for this we find that PML is a SUMO E3 ligase. The hypothesis we will test is that arsenic activates a SUMO E3 ligase activity of PML inducing an autoSUMOylation reaction._x000D_ _x000D_ 3. What is the role of SUMO-PML in stem cell maintenance. PML plays a role in stem cell maintenance and its degradation, induced by arsenic, leads to stem cell differentiation. Thus arsenic treatment could induce differentiation of inherently resistant "cancer stem cells" into cells that are susceptible to chemotherapeutic drugs. We will test this and follow arsenic treatment with SUMO proteome analysis in human stem cells (collaboration) and in RNF4-/- mouse ES cells. In an siRNA screen for SUMO-dependent transcriptional repressors, we identified many epigenetic regulators that are SUMO modified, contain SUMO interaction motifs and are important in stem cell maintenance. Our hypothesis is that this represents a SUMO-dependent transcriptional repression network, recruited onto promoters by SUMO modified transcription factors We will identify sites of modification and introduce forms that cannot be SUMO modified back into stem cells and assess endogenous gene expression and use ChIP analysis to monitor promoter occupancy, to establish SUMO dependence. _x000D_


Research activity codes: 5.1 PHARMACEUTICALS;4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: Structural studies of uridylating enzymes involved in RNA turnover controlling S-M checkpoint control
Funder: Cancer Research UK

Abstract: _x000D_ Cid1 is a cytosolic uridylating enzyme, first identified in Schizosaccharomyces pombe, which catalyses addition of uridines to 3’ ends of poly-adenylated mRNAs, targeting them for degradation via recruitment of the 5’ decapping machinery. Once decapped, the mRNAs are degraded exonucleolytically by cytosolic RNases. Cid1 is a member of the polß family of polymerases but is distinctive in (i) having RNA uridyl transferase activity and (ii) being cytosolic. Cid1 was discovered through its re-imposition of the S-M cell cycle checkpoint when hydroxyurea-mediated arrest is overridden by caffeine. Cid1 homologues have been identified in human cells where they are also involved in responses to cell cycle perturbation, as well as antagonising miRNAs that regulate cytokine production and differentiation. Human Cid1 homologues therefore represent interesting targets for small molecule inhibitors, which would potentially have anti-proliferative and/or anti-inflammatory properties. _x000D_ _x000D_ We intend to build on our existing solution of the structure of Cid1 at 3.4Å resolution by determining the full structure at enhanced resolution, especially in complex with reactants and reaction intermediates including UTP and DNA/RNA. We will study the human Cid1 homologues ZCCHC6 and ZCCHC11 using the same approaches. _x000D_ _x000D_ We will use X-ray crystallography to determine atomic structures. We will use E. coli to express Cid1 and a variety of systems to express the human proteins both full-length and as subdomains. We have already achieved significant success with Cid1 itself and wish to capitalise on this now to derive an atomically detailed description of uridyl transferase activity. _x000D_ _x000D_ Overall the insights we gain from either part of our work – that on Cid1 and that on its homologues – will be of direct relevance to the search for chemotherapeutics against cancer because they will allow us to provide a description of how the reaction partners are recognised, integrated and bound together by Cid1 and related proteins. Our collaborators have initiated the design of small molecules inhibiting Cid1 and we will also determine structures for the enzyme bound with these, to help in the refinement of their design. The insights we gain from an atomic resolution structure of Cid1 will in this way allow us to construct a model for its mechanism, and to describe the basis of its specificity whereby it regulates RNA function. These insights will be of direct relevance for the design of molecules modulating uridyl transferase function as therapeutic leads.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: CANCER AND NEOPLASMS
Title: Role of Fc gamma receptor II in the immunostimulatory and therapeutic activity of anti-CD40 mAb
Funder: Cancer Research UK

Abstract: Anti-cancer monoclonal antibodies (mAb), such as rituximab, are effective first line therapeutics for a limited number of mainly lymphoid cancers. They work primarily by binding directly to the cancer cells and recruiting effector cells via activatory Fc receptors (FcR), resulting in ADCC and phagocytosis. As such, mAb isotypes that interact well with activatory FcR are crucial for the activity of this class of reagent with human IgG1 and mouse IgG2a being the most active. Another exciting type of anti-cancer mAb in development is immunomodulatory mAb, as exemplified by the marked increase in survival of metastic melanoma patients recently demonstrated in a phase III trial of the anti-CTLA-4 mAb, ipilimumab. Immunomodulatory mAb appear to work indirectly by stimulating the immune system to overcome tumour-induced immune tolerance. In contrast to direct binding mAb, the influence of mAb isotype and FcR interaction on the efficacy of these agents is unknown._x000D_ Our own work on immunomodulatory mAb has focussed on anti-CD40, an effective anti-cancer agent in pre-clinical models that also shows promise in early phase clinical trials. In this project, we will examine the role of isotype in anti-CD40 activity. We will use a number of in vitro and in vivo experimental approaches involving genetically engineered anti-CD40 mAb, along with specific FcR knockout mice and mice transgenic for human CD40, to determine: _x000D_ 1) the role of mAb isotype and FcR interaction in anti-CD40 activity and whether enhancing anti-CD40-FcR interaction can increase efficacy;_x000D_ 2) whether anti-human CD40 mAb show similar FcR dependence to anti-mouse CD40 for activity._x000D_ Taken together these studies will provide critical understanding of the role of isotype and FcR interactions in the activity of an immunomodulatory anti-cancer mAb that may have general implications for this class of therapeutic and which is crucial for the design of more effective clinical reagents.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.2 CELLULAR AND GENE THERAPIES
Health categories: CANCER AND NEOPLASMS
Title: Characterisation of the role of PARP-3 during DNA double-strand break repair
Funder: Cancer Research UK

Abstract: Background and Relevance to Cancer: _x000D_ DNA double-strand breaks (DSBs) are a major threat to cell survival and genetic integrity, as indicated by the increased radiation sensitivity and cancer incidence (particularly leukaemia) in individuals with defects in the response to these lesions. An emerging but poorly understood aspect of the response to DSBs is protein ribosylation, a post-translational modification catalysed by a superfamily of ADP-ribosyl transferases. Currently, the members of this superfamily implicated in DNA damage responses are the poly (ADP-ribose) polymerases PARP-1 and PARP-2. These enzymes have received much attention because inhibitors of their activity are promising candidates for monotherapeutic treatment of specific cancers. Here, we find that PARP-3, a largely uncharacterised ADP-ribosyl transferase of unknown function, is stimulated by DSBs in vitro and functions co-operatively with aprataxin-and-PNK like factor (APLF) to accelerate the rate of DSB repair in human cells. These data identify PARP-3 as a putative novel 'sensor' of chromosomal DSBs and uncover a novel and unanticipated aspect of DSB repair. _x000D_ _x000D_ Based on our data we present the following model. We suggest that PARP-3 binds to and is activated by chromosomal DSBs, resulting in ribosylation of histone H1 in the vicinity of the break. We propose that APLF is then recruited to DSBs via its ability to bind ADP-ribose and that APLF renders chromosomal DSBs 'permissive' for DNA ligation by promoting access and/or retention of the DNA ligase complex XRCC4/Lig4. We suggest that APLF achieves this by anchoring the DNA ligase at the break and/or by modifying chromatin structure directly. _x000D_ _x000D_ Aims and Objectives: _x000D_ To address our model we will characterise, _x000D_ [1] The DSB substrate specificity and protein targets of PARP-3 ribosylation. _x000D_ [2] The role of PARP-3 in APLF recruitment and the role of APLF in promoting DNA ligation in chromatin. _x000D_ [3] The impact of PARP-3 and APLF on chromatin structure. _x000D_ [4] The importance and mechanism of PARP-3/APLF-mediated DSB repair for cell survival and genetic stability. _x000D_ _x000D_ Methods: _x000D_ We will employ a variety of biochemical and cellular approaches to dissect the role of the PARP-3/APLF axis. _x000D_ _x000D_ How the results will be used: _x000D_ This work will progress our understanding of DSB repair and its influence on genetic stability and cancer, and will inform the development and application of PARP inhibitors in cancer therapy.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Viral and host mechanisms in cervical carcinogenesis: towards improved clinical management
Funder: Cancer Research UK

Abstract: Background:_x000D_ _x000D_ Cervical carcinoma is the second most common cause of cancer-related deaths in women. The full impact of vaccination against high-risk human papillomavirus (HRHPV) will not be seen for ~30 years and there will be no benefits for women who are already HRHPV positive._x000D_ We will investigate key events in the development of cervical squamous cell carcinoma (SCC) following HRHPV infection. We will study mechanisms of viral persistence, causes of deregulated viral transcription in proliferating (basal) epithelium and the significance of common host genomic changes induced by over-expressed HRHPV oncogenes._x000D_ Aims/Objectives:_x000D_ (i) Test the value of oncostatin M receptor (OSMR) as a therapeutic target in cervical SCC. OSMR is one of the most frequently over-expressed genes in cervical SCC and predicts adverse overall survival, independent of disease stage. As a cell surface molecule, OSMR is a strong candidate for antibody-mediated inhibition, a strategy that has had a major impact on HER2-positive breast cancers._x000D_ (ii) Discover genes on chromosome 3 that mediate the transition from cervical pre-cancer to malignancy._x000D_ (iii) Identify viral genetic and/or epigenetic changes that determine high levels of HRHPV transcription in basal cervical epithelium._x000D_ (iv) Define the contribution of host genes to cell selection in the early stages of neoplastic progression associated with integrated HRHPV. We will definitively test whether HRHPV deregulates host genes at or near the integration site (i.e. insertional mutagenesis)._x000D_ (v) Test whether the contribution of steroid hormones to cervical carcinogenesis depends on HRHPV physical state (episomal vs. integrated) and/or epigenetic modifications to viral chromatin._x000D_ (vi) Study the significance of down-regulated anti-viral receptors TLR3 and RIG-I in HRHPV persistence. We recently found that both molecules are under-expressed in persistent HPV16 infection, due to an effect of one or more viral gene product(s)._x000D_ _x000D_ Methods:_x000D_ We will use archival clinical specimens, plus the unique W12 system, which accurately models key viral and host events in cervical carcinogenesis. Major resources will be a panel of 24 isogenic W12 clones, each with HPV16 integrated at a different genomic site, plus a long-term W12 culture series in which in vitro carcinogenesis is associated with transcriptional deregulation of viral episomes not integrants. _x000D_ Use of Research: _x000D_ The work will address important clinical needs, including: improved identification of progressive cervical pre-cancers and early-stage SCCs; greater understanding of the effects and risks of anti-HRHPV therapies currently in use or development; and generation of new therapeutic strategies that target viral oncogenes or significant host factors._x000D_


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;5.2 CELLULAR AND GENE THERAPIES
Health categories: CANCER AND NEOPLASMS