NIHRDataInsights/HRCSData huggingface dataset:
Title: Histones in cancer pathogenesis: defining the role of H3.3 mutations in bone and cartilage tumours
Funder: Medical Research Council

Abstract: Epigenetics are emerging as an important contributor to cancer development. Epigenetic reprogramming caused by IDH1 and IDH2 mutations have been implicated previously in brain and cartilaginous tumours. Recently, driver mutations in the histone 3.3 (H3.3) variant have been identified in over 50% of paediatric glioblastoma multiforme cases and we have also found that these mutations are found in ~60% of conventional central and dedifferentiated chondrosarcomas: the mutations in both these brain and bone tumours lead to modifications of the epigenetic landscape. The identification of direct alterations of the basic building blocks of chromatin represents a paradigm shift in our understanding of cancer epigenetics. Very recently, we have also reported that H3.3 variants are mutated in primary central bone (H3F3A in 92% of giant cell tumours and H3F3B in 95% of chondroblastoma), thus suggesting that direct alterations of histones are more common than previously thought. Several questions remain unanswered: are histone mutations transforming? In which cell type(s) and at which developmental/differentiation stage(s) do the mutations exert their transforming potential? What are the molecular changes caused by deposition of mutant histones? Do H3.3 mutations work in part through a non-cell autonomous mechanism? This proposal will address these questions. In particular, we aim to determine the biological and molecular consequences of bone/cartilage tumour-associated H3.3 mutations. Furthermore, we have set out how we will correlate the epigenetic and transcriptome changes imposed by H3.3 mutations across the different tumour types (bone and brain). Overall, this study will contribute to explaining the mechanisms by which the H3.3 mutations bring about the disease phenotypes. Our finding will provide opportunities for developing targeted therapies, which may be valuable for treating more than one tumour type.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Identification of oncogenic drivers in aggressive B cell Lymphoma by ribosome profiling and a novel primary human lymphocyte transformation assay
Funder: Medical Research Council

Abstract: Deregulated gene expression is fundamental to the development of malignant disease. Much of our current understanding of lymphoma biology comes from transcriptional profiling and the study of mutations in transcription factors and components of the signalling pathways that regulate transcription. Recent work suggests that translational regulation may be of equivalent magnitude to transcriptional regulation and that translational deregulation is a prominent feature of malignant disease including lymphoma. This study proposes to use the ribosome footprinting technique to profile translation across three major classes of aggressive B cell lymphoma; ABC DLBCL, GCB DLBCL and Burkitt lymphoma using both cell lines, primary tumour biopsy tissue and non-malignant, "normal" human germinal centre B cells. Modifications of this assay will also identify non-canonical translational start sites that either inhibit translation of the true ORF or generate altered protein isoforms or translated "micropeptides". Mechanisms of translational deregulation will be investigated by bioinformatics screening of deregulated transcripts for enriched motifs. Biotinylated bait RNA pull-down combined with mass spectrometry will identify potential RNA binding proteins that acts as "translation factors". The functional significance of transcripts deregulated at the level of translation, non-canonical translation initiation sites, putative translation factors and micropeptides will be tested using a transformation assay that uses semi-immortalized human germinal centre B cells cultured in vitro. I will also use this system to investigate the significance of potential translation factors (such as ZFP36L1) known to be mutated in DLBCL from existing RNA-seq data. Finally, I will use a combination of shRNA knockdown, over-expression and pharmacological agents to test the interplay between known lymphoma signalling pathways (eg BCR and TLR signalling) and translational regulation.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: The role of PRMT1-mediated arginine methylation during breast cancer development.
Funder: Medical Research Council

Abstract: We hypothesise that PRMT1-mediated methylation of specific proteins contributes to breast cancer initiation and/or progression. Furthermore, we hypothesise that genetic disruption of the prmt1 loci will reduce oncogenic Her2 penetrance and tumour burden. The first objective is to quantitatively identify and characterise breast cancer specific PRMT1 substrates through SILAC coupled to an affinity purification process that we have already validated. We will then build on preliminary data to further understand the role of PRMT1-mediated methylation of USP7 and USP11 through a combination of methyl-site mapping, mutational analysis and the generation of cell lines ectopically expressing proteins proficient or deficient in methylation. These tools will then be used to study the effects of USP7/11 methylation on DUB activity and the ability of USP7/11 to engage the DNA damage response. We will also establish if USP7/11 mediated stabilisation of PRMT1 is a mechanism of methyltransferase regulation through the use of in vitro methylation assays. In order to explore the transforming potential of PRMT1 we will utilise the 3D acinar formation in matrigel assay that we have already established. To understand the in vivo significance of PRMT1 in the transformed mammary gland, I will use my expertise in utilising genetically modified mice in the study of tumourigenesis. We will cross the conditional prmt1 floxed (prmt1f/f) mouse with a well-established Her2 mouse model of human breast cancer (MMTV-Her2-IRES-Cre) and monitor tumour initiation and burden by generating the MMTV-Her2-IRES-Cre;PRMT1 F/F strain. The breeding and experimental scheme we have devised clearly shows that we are committed to ensuring reduction and refinement of all our animal procedures through design of appropriate experiments. A statistical significance of 5% will be used for data obtained and a power of 80%.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: A novel regulator of DNA double strand break repair fate with roles in immunity and oncogenesis
Funder: Medical Research Council

Abstract: DNA double-strand breaks (DSBs) are highly toxic and must be accurately repaired to counteract the threat of oncogenic mutations. However, in some tissues mutagenic DSB repair is actually favoured by the cell, providing a molecular mechanism by which genetic material can be transferred between genetic loci to create genetic diversity. To cope with this intrinsic discrepancy in desired DNA repair outcome between different cellular contexts, cells have evolved a complex regulatory system to maintain the right equilibrium between repair pathways, ensuring DSBs are appropriately resolved. Recently, we have found misregulation of this system to link normal immune-function to the genomic instability that characterises cancer. Specifically, a chromatin component of the non-homologous end joining pathway that normally mediates antibody gene rearrangements in lymphocytes, is also responsible for the genomic instability that accompanies loss of the tumour suppressor BRCA1. We now identify a new protein whose depletion in BRCA1-deficient cells can rescue the HR defect that normally afflicts them, in turn rendering them resistant to clinically important anti-cancer drugs. Notably, we report that this protein's DSB repair activities are also crucial for normal immune function, protecting the integrity of DSB ends in antibody genes to promote their efficient repair. We propose several integrated approaches to elucidate the molecular basis of this protein's unanticipated function in DSB repair. The benefit of this work will be two-fold: Firstly, it will provide new insight into normal immune function, aiding the understanding of human primary immunodeficiency disorders; Secondly, it will reveal the molecular basis of genomic instability in common human cancers, also yielding insight into the potential mechanisms of drug resistance that face modern personalised medicine approaches. These findings may pave way to improved approaches to diagnose, treat and better manage cancer.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: beta-catenin Ser45 in development and disease
Funder: Medical Research Council

Abstract: It is assumed that oncogenic mutations found in beta-catenin result in activation of the pathway. We have a strong interest in the early steps in the development of Wilms' tumours, in particular the subset that is caused by loss of WT1 and activation of beta-catenin. Interestingly, almost all cases of Wilms' tumour with mutant beta-catenin carry a mutation affecting the Ser45 residue. To study the reason for this selection we have previously generated several mouse models that express different beta-catenin mutations from the Rosa26 locus. We found that the Ser45 mutant does not have an increased signalling capacity, despite being stabilized at the protein level as expected. Still, the Ser45 mutation has a biological effect on Wt1-deficient kidney mesenchyme cells which were driven a step closer towards Wilms' tumours. This finding suggests a complete new dimension to the role of beta-catenin mutations in cancer. However, the fact that our models express their mutant beta-catenin from Rosa26 means we cannot directly translate these finding to patients. In this project we will therefore generate a Cre-inducible Ser45 mutation in the endogenous mouse beta-catenin gene. We will test its capability to increase target gene transcription in ES cells as we did for the Rosa26 models. In vivo we will activate the expression of the mutant allele through a Cre deleter strain and analyse the phenotype in development and/or postnatal. To study the role of this mutation in Wilms' tumour development we will cross the mice with our kidney mesenchyme-specific Wt1 knockout. We will use genome-wide expression analysis to identify molecular changes that could explain the selection for this mutation in WT1-mutant Wilms' tumours. The mice will be followed for Wilms' tumour development and other phenotypes. Finally, we will specifically analyse any phenotypes in the neuronal system caused by the Ser45 mutation.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Characterising and targeting aberrant enhancer function in acute myeloid leukaemia (AML)
Funder: Medical Research Council

Abstract: Acute Myeloid Leukaemia (AML) is an aggressive and often incurable haematological malignancy. Gene expression and mutational studies highlight the importance of abnormal transcription in the induction and maintenance of the leukaemia phenotype. Recent studies of normal transcription have documented the importance of specific enhancers, cis-regulatory elements often at long distances from the genes they regulate, in the induction and maintenance of tissue specific gene expression patterns. Growing evidence links aberrant enhancer function with malignancies such as AML and we propose to document alterations in the enhancer landscape that accompany the evolution of AML. We will use an allelic series of sophisticated mouse strains that model the development of AML at the cellular level. Using pertinent haematopoietic stem and progenitor cell populations from each of these models, we will document alterations in gene expression, enhancer usage and function and enhancer-promoter interactions using state-of-the-art global genomics techniques such as RNA-Seq, ChIP-Seq and Capture Hi-C (CHI-C). We will then correlate the changes in our murine models with the enhancer landscape of human AML with a similar genotype. Finally, we will aim to identify transcription factors and chromatin rmodifiers that are critical for AML enhancer function and will test the therapeutic potential of perturbing these critical regulators with experimental and pharmacological intervention.


Research activity codes: 5.2 CELLULAR AND GENE THERAPIES
Health categories: CANCER AND NEOPLASMS
Title: Characterisation of the signalling pathways involved in cell invasion downstream of extra centrosomes
Funder: Medical Research Council

Abstract: Centrosome abnormalities, and in particular centrosome amplification, are common features of human tumours. However, to date the contribution of extra centrosomes to tumour progression is still unclear. We recently found that centrosome amplification can induce invasion in non-transformed human cells, similarly to the overexpression of known oncogenes, such as ERBB2. This is in part due to RAC1 activation as a result of increased microtubule nucleation downstream of extra centrosomes. However, our preliminary data suggests that RAC1 activation alone is not sufficient to induce a robust invasive phenotype and that other signalling pathways play a role in this process. In this study, we aim to characterise the signalling alterations that are induced by centrosome amplification. To do so we will preform phosphoproteomics to identify altered phospho-sites in cells with extra centrosomes. Next, using 3D cell culture models, we will determine the signalling alterations that are important for the invasive phenotype, which will further clarify the mechanisms behind these striking morphological changes. Finally, we will test whether our findings can be recapitulated in human breast tumours using breast cancer tissue samples. This strategy has the potential for the development of biomarkers to identify tumours with extra centrosomes that would be sensitive to drugs that specifically target these cells (e.g. HSET inhibitors). We anticipate that the experiments proposed here will contribute to our understanding of how centrosome amplification impacts tumour progression. Importantly, these studies will open new areas of investigation in my laboratory regarding not only the role of centrosome amplification in cancer but also how the centrosome regulate intracellular signalling in normal cells.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: Ubiquitin-mediated events in cell fate decisions
Funder: Medical Research Council

Abstract: Recent work in the field has demonstrated that cell fate choices are not restricted to G1 phase, since cells exit mitosis already committed to enter a subsequent round of cell division. Our own recent work has identified cellular components that are specifically ubiquitinated during the wave of proteolysis that accompanies exit from mitosis. Many of these components are predicted to be involved in rebuilding the interphase cell, and we hypothesize that ubiquitination of these components contributes to organization of the interphase cell in a way that depends on cell fate. We propose here to identify components that are specifically targeted in cells of differing fate, and to understand 1) how they are targeted 2) how their ubiquitination contributes to interphase 3) how their ubiquitination marks and influences cell fate choices.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Mechanisms of Radiation-Induced Bladder Toxicity in Prostate Cancer Treatment: Correlation of Urinary Biomarkers with Bladder Pathophysiology
Funder: Medical Research Council

Abstract: Radiation therapy for prostate cancer (PCa) patients is potentially life-saving but is associated with adverse effects. Close proximity of the prostate to the bladder means that unavoidable collateral damage to the bladder commonly leads to bladder dysfunction. Acute effects of radiation induced bladder toxicity (RIBT) during the radiation therapy period often diminish in severity within 3-6 months. However, intolerable bladder dysfunction can develop months or even years after the post-treatment. We cannot currently predict which patients are at risk of late RIBT; furthermore we do not understand the underlying mechanisms. The proposed project will define the mechanisms underpinning RIBT using integrated multi-disciplinary approaches. We are currently recruiting PCa patients to a research clinical trial. Biomarkers of bladder dysfunction (ATP and neurotrophins) in urine samples will be measured before, during and at follow-up appointments, up to 24 months post-treatment. Urinary biomarker concentrations will be correlated with IPSS/RTOG derived information on bladder toxicity and health-related quality of life. The applicants have complementary expertise in bladder physiology, radiation biology and clinical treatment of PCa. Development of an animal model of clinically relevant, PCa radiation therapy will allow us to assess the manifestation of RIBT during and after radiation at specific time points post-treatment by characterising changes in micturition patterns. The underpinning molecular mechanisms driving cellular remodelling and aberrant contraction will be evaluated employing a panel of cell physiology, cell biology and cell imaging. The research will enable development of strategies to limit radiation damage to the bladder, allowing delivery of larger, effective radiation doses. The biomarker work will enable us to predict which patients are at risk of irreversible late bladder dysfunction and stratify these patients towards radio-protectant therapy.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: Literature-based discovery for cancer biology
Funder: Medical Research Council

Abstract: We will improve automated LBD so that it can better support biomedical research. Our idea is to replace current, fairly shallow LBD methodology (e.g. dictionary matching) by methodology capable of deeper, wider and more dynamic knowledge discovery. We will base this methodology on advanced Text Mining (TM) and Data Mining (DM). Application of TM to LBD is challenged by the fact that real-life knowledge discovery integrates knowledge from different areas of biomedicine, while most current TM is optimised to perform well in a clearly defined area. Extending recent advances in Natural Language Processing (NLP) and TM, we will develop adaptive, minimally supervised techniques for identification of concepts, events and relations in diverse biomedical texts. We will formulate our models as probabilistic graphical models and will optimise their performance via use of joint learning and inference of closely related tasks and via guiding learning across tasks and domains with easily obtainable expert (e.g. shared task, domain) knowledge. We will also introduce novel, improved methodology for knowledge discovery which uses link prediction for high quality LBD in the complex network of concepts resulting from TM. Link prediction can optimally exploit the rich information generated by TM, improve the accuracy of LBD and yield more useful output. We will initially target this methodology to the literature-intensive, interdisciplinary area of cancer biology. We will develop an LBD tool in close collaboration with cancer researchers and will evaluate the tool by using it to conduct case studies in cancer biology. Findings will be validated via laboratory experiments. All the outputs from this project will be made freely available and access to them will be maximised by following the best international practices on data standards, management, collection and sharing (e.g. as defined by Open Annotation Data Model, ELIXIR).


Research activity codes: 2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: CANCER AND NEOPLASMS
Title: Non-stationary statistical modeling of circadian oscillations for research in cancer chronotherapy
Funder: Medical Research Council

Abstract: There is now large evidence both in experimental models and in patients that the Circadian Timing System (CTS) of the patients is affecting treatment tolerability and efficacy of anticancer drugs while, on the other hand, the development of the disease and the treatment may have a disruptive effect on the CTS. For example, Costa et al. (2013) found a significant shift in period length during anticancer treatment suggesting that the patient's daily rhythm is altered while receiving anticancer drugs. Hence a personalized chronotherapy needs to take into account the potential effect of the treatment as well as the disease on the CTS of the patient. The aim of this project is develop a statistical methodology that is able to detect and quantify (in real time) such temporal variation in the circadian oscillation and that can be used to study how these are associated with changes in covariates (tumour growth, treatment with drugs and timing of their administration, external factors such as light, temperature, food and other potential Zeitgebers). We address this through non-stationary statistical modeling with the aim of developing a system for online prediction of a patient's CTS. Using spectrum and state-space approaches we will develop non-stationary statistical methods using data from all available biomarkers to construct a robust online prediction of the current state of a patient's CTS that can be used to individualize the timing of chronotherapy. Secondly, we will enhance a mechanistic mathematical modeling approach to gene expression and provide a statistical algorithm of fitting such a model to circadian gene expression data with the aim of gaining a better understanding of how the underlying gene regulatory processes might be affected by the disease and other covariates.


Research activity codes: 2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: CANCER AND NEOPLASMS