NIHRDataInsights/HRCSData huggingface dataset:
Title: Microtubule Cytoskeleton Laboratory
Funder: Cancer Research UK

Abstract: Quantitative Systems Biochemistry of Microtubule Cytoskeleton Architecture: The cytoskeleton is essential for the internal organisation of eukaryotic cells. Microtubules, motor proteins and other microtubule-associated proteins form a mechano-chemical network that determines the dynamic and adaptable nature of intracellular order. Distinct forms of cytoskeletal architectures are required for correct cell division and cell differentiation. How the components of the microtubule cytoskeleton work together as a system is not understood. We address these questions using a combination of physical biochemistry and quantitative cell biology. Advanced fluorescence microscopy (down to the single molecule level), in vitro reconstitutions of dynamic cytoskeleton behaviour, microfabrications, and eukaryotic cell culture are important tools in our research. Our aim is to understand in quantitative terms the molecular mechanisms underlying cytoskeleton function. We focus on the question of how the microtubule cytoskeleton organizes itself within the boundary of the cellular membrane and how the mitotic spindle assembles and functions during cell division. We aim at being able to predict the behaviour of the dynamic cytoskeleton based on quantitative knowledge of the properties of its constituents. In the future, we will address the following questions: * How do single molecules of the microtubule cytoskeleton behave in living cells? * Can an artificial cytoskeleton be constructed from purified components and can it inform us about complex cytoskeleton functionalities? * How do biochemistry and mechanics integrate within the cytoskeleton?


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: CANCER AND NEOPLASMS
Title: Translational Research in Myeloma XI: TRIM XI
Funder: Cancer Research UK

Abstract: Background Myeloma is currently treated as a uniform disease but the research studies performed over recent years have shown that it is, in fact, a group of distinct diseases which all manifest as malignancies of plasma cells. In order to improve clinical outcomes of this disease it is essential to match treatments to specific disease subtypes. In order to achieve this we need to develop a diagnostic test which can define clinically relevant subgroups of disease that can be treated more appropriately. Aims Our aim is to refine the use of treatment in myeloma to improve patient outcomes and reduce side effects. In particular we will do this by defining which molecular subgroup of patients responds best with specific treatments. In order to achieve this we have to effectively split patients into subgroups based on the common genomic abnormalities in myeloma: translocations and copy number abnormalities. Methods We will use massively parallel sequencing to generate data on chromosomal translocations, mutations and copy number abnormalities on patients entered into a large myeloma clinical trial carried out in the UK, Myeloma XI, that will allow us to define groups of patients with specific clinical outcomes. How the results of this research will be used. The results of this work will allow us to understand which groups benefit most from the treatments used in our current treatment strategies. It will identify the known prognostic translocation subgroups and copy number abnormalities and will additionally identify potentially new prognostic mutations related to disease treatments. Sequencing of the targeted abnormalities in myeloma will generate novel data pertaining to mutated oncogenes or tumour suppressor genes which, in this unique trial setting, can be used to not only identify the frequency of mutations in myeloma subgroups but also determine their effect on response and survival. It will also allow us to design specific clinical tests able to rapidly identify the risk group a patient falls into and consequently we will be able to design trials aimed at improving patient outcome.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: RALA/hOC-iNOS: An Alternative Gene Therapy System
Funder: Cancer Research UK

Abstract: This proposal is designed to offer a treatment strategy for patients with either breast or prostate cancer that has metastasised to the bone. For patients in this position the treatment outcomes are mainly palliative. Thus, there is a desperate unmet need for better treatment options for this group of patients. Gene therapy holds the promise for the treatment of many metastatic cancers but success has been limited because of inadequate delivery vectors. To that end we have designed a novel 30 amino acid peptide delivery sequence (RALA) and our pilot data has shown that RALA can deliver DNA in vitro and systemically in vivo to ZR-75-1 breast cancer tumours. We have also shown that RALA/DNA nanoparticles do not elicit a significant immune response. With respect to the therapeutic payload, we would choose our expertise in nitric oxide biology, by delivery of the cytotoxic and radio-chemo sensitising iNOS transgene under the control of the human osteocalcin promoter (hOC). We have already utilized the human osteocalcin (hOC) promoter to drive iNOS expression with exquisite specificity and therapeutic efficacy in vivo. We now wish to combine these approaches by using the RALA peptide to deliver hOC-iNOS systemically in vivo to any tumour model that has been shown to metastasise to bone. We wish to administer these RALA/hOC-iNOS nanoparticles in tandem with the current chemotherapy regimen of docetaxel. Specific aims include: 1. Providing evidence of the RALA vector overcoming the biological barriers to gene delivery. 2. Determination of the onset and duration of iNOS transgene expression in vivo. 3. Systemic treatment of both local and metastatic breast cancer in vivo using RALA/hOC-iNOS nanoparticles in combination with Docetaxel. 4. Formulation of a dried stable powdered product. 5. Determination of how the nanoparticles are eliminated following systemic administration. The methods employed in this proposal include bio-physical characterisation of the nanoparticles, flow cytometry, confocal microscopy, construction of plasmids that express both iNOS and luciferase under the control of the hOC promoter, in vivo metastatic models via intracardiac injection of tumour cells, in vivo imaging, administration of docetaxel, freeze drying, spray drying, formulation studies, collection of serum, scintillation studies, LCMS, HPLC, rtPCR,ELISA and western blotting. The results will be disseminated to the wider scientific, clinical and industrial communities and it is anticipated that there will be sufficient interest generated to proceed with the clinical development of this novel treatment.


Research activity codes: 5.2 CELLULAR AND GENE THERAPIES
Health categories: CANCER AND NEOPLASMS
Title: Cancer susceptibility genes
Funder: Cancer Research UK

Abstract: Background The overarching theme of the CRUK Gene Function Laboratory research proposal is the identification of new therapeutic strategies based on genetic principles. Over the last few years we have pioneered the laboratory investigation and clinical application of genetic principles such as synthetic lethality, especially where it pertains to breast, ovarian and colorectal cancers. Aims In our future proposals we will expand the application of these concepts to a wider range of cancers and particularly to cancers where there is unmet clinical need, such as oesophageal adenocarcinomas (EAC). In addition, we will continue our work on PARP inhibitors, expanding this to an analysis of other PARP superfamily members including Tankyrase. Finally we aim to identify novel synthetic lethal approaches to the treatment of ARID1A mutant tumours. Methods We will use both standard molecular and cellular biology approaches and combine these with a number if high throughput functional screening strategies. We have a number of platforms available for loss-of-gene function screens and others will be added as appropriate and as new technology becomes available. How the results will be used Regardless of the strategy, the aim is the same: to provide clinically useful information that can inform patient selection for existing trials or the development of new therapeutic strategies.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Preparing the genome for replication: exploring the consequences of origin licensing and exploiting its inhibition
Funder: Cancer Research UK

Abstract: Background: Hexameric Mcm2-7 complexes play a central role in chromosomal DNA replication. In late mitosis and G1 they are loaded onto DNA to license origins for use in the upcoming S phase. As origins initiate during S phase, Mcm2-7 are converted into an active helicase that forms the core of the replication machinery. Re-replication of chromosomal DNA is prevented by ensuring that once S phase has started, no more Mcm2-7 can be loaded onto DNA. Replication licensing proteins are inappropriately expressed at an early stage of tumorigenesis in a wide variety of cancers, and have significant potential as histopathology makers. They also have potential as new targets for anti-cancer treatment. Aims: We will investigate in molecular detail how Mcm2-7 provide a platform for assembling other proteins onto chromatin to promote cell cycle progression and will determine how cells detect and respond to inhibition of replication licensing. We will investigate how Mcm2-7 recruits the ELYS nucleoporin and how this promotes cell cycle progression. We will also examine complexes assembled onto Mcm2-7 in preparation for the initiation of DNA replication and how this is controlled by S phase protein kinases. We will use this information to develop the use of new licensing inhibitors as potential anti-cancer agents. Methods: We will primarily take a biochemical approach to these questions using Xenopus egg extracts, which provides a unique system for studying the cell cycle control of DNA replication in vitro. Results and insight obtained in the Xenopus system will then be used to design further experiments in mammalian tissue culture cells. How the results of this research will be used: The work will advance our understanding of how normal cells regulate the replication of DNA to ensure that the genome is precisely duplicated in each cell cycle. The potential of licensing inhibitors as novel anti-cancer agents will also be assessed and could provide the basis for future anti-cancer drug development. The results may also have implications for interpreting the behaviour of existing cell proliferation biomarkers.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: CANCER AND NEOPLASMS
Title: Human biomonitoring and carcinogen activation
Funder: Cancer Research UK

Abstract: Despite recent emphasis on the discovery of genetic origins of cancer, the facts remain that most cancers result from the combined effect of environmental factors and inherited susceptibilities, and that the environment plays the more dominant role. Environmental carcinogens undergo metabolic activation in mammalian cells to reactive species that bind to cellular macromolecules, including DNA and protein, to form adducts. DNA adducts are the precursors of mutations that initiate the carcinogenic process. The presence of protein and DNA adducts in human tissues serve as biomarkers of exposure and their detection and identification can provide clues to the aetiology of cancer. The proposed programme of research builds on our progress in developing and applying biomarkers of human exposure to carcinogens, in elucidating pathways of activation of environmental carcinogens and in applying toxicogenomic approaches to identifying cellular responses to genotoxic compounds. We will continue with existing successful approaches and also develop new approaches to pursue our interests in molecular epidemiology studies and investigations of mechanisms of environmental carcinogenesis. The main themes of the Programme Grant proposal are: • To develop and apply methods for the detection and identification of DNA and protein adducts in human cells (“adductomics”) for application in molecular epidemiology studies taking a comprehensive approach to defining human exposure and disease causation (the exposome concept). • To apply the techniques of mRNA microarray hybridisation, with associated techniques for phenotypic anchoring, to the gene expression profiling of genotoxicants in human cells in vitro, in order to provide insights into organotropism in carcinogenesis, the effect of cell cycle on carcinogen activation, and the role of p53 carcinogen activation. • To determine the relative roles of cytochrome P450s and other xenobiotic-metabolising enzymes in the activation and detoxication of environmental carcinogens in vivo, and the contributions of hepatic versus non-hepatic enzymes in these biotransformations, in order to provide insights into carcinogen organotropism, and thereby improving interspecies extrapolations. These studies will provide novel insights into environmental factors in cancer causation and inot the molecular mechanisms of carcinogen metabolism and tumour development linked to environmental and nutritional carcinogens. The information gained may ultimately assist in providing a better assessment of the mode of action of these environmental carcinogens and to developing strategies for the prevention of cancer.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Variations in human syndromes with DNA damage response (DDR) defects: implications for new roles of DDR proteins, patient screening and discovery of new cancer syndromes
Funder: Cancer Research UK

Abstract: Background The cellular and clinical responses, following total loss of function of particular tumour suppressor genes involved in maintaining the integrity of the genome, are mostly known, as are the mechanisms involved. However, what is not known is the range of variant or hypomorphic cellular responses and its consequences for cancer predisposition. Aims The aim of this proposal is to examine the cellular and clinical consequences of such variants with respect to particular genes and our study will encompass, ATM, MRE11, and PALB2 genes. It is becoming increasingly clear, that a significant proportion of ataxia telangiectasia (A-T) patients are being diagnosed in mature adulthood but it is also known that the accompanying milder mutations do not protect against later tumour development. An important goal of our study is to identify these ‘hidden’ patients and assess their risk of cancer development, particularly for breast cancer. We will also investigate the function of a novel p.Asp131Asn mutation in MRE11, identified in a patient with clinical features consistent with the cancer predisposing disorder Nijmegen Breakage Syndrome. We intend to dissect the pathological significance of the MRE11 mutation to ascertain which roles of the MRN complex contribute to the development of an NBS- like rather than A-T-like disease. Recently, for the first time, we identified patients with PALB2 mutations and lymphoma and we will investigate whether the PALB2 protein expressed in these patients’ cells has some residual activity explaining the milder clinical appearance. We will also investigate whether PALB mutations occur in other lymphoid tumours. Finally, we recently identified a patient with what we believe are unique spontaneously occurring fragile sites appearing as ‘segmented’ chromosomes. We will endeavour to identify the genetic cause of this phenotype and investigate its consequences. Methods These will be standard cell biology and molecular biology approaches for measuring cellular effects. How results of this research will be used Our hypothesis is that variation of the cellular response to DNA damage can result in a different spectrum of tumours and an altered clinical presentation and disease course. An appreciation of this will increase current understanding of the effects of these genes. In particular it may reveal, potential additional roles of known DNA damage response (DDR) proteins as well as the importance of redundancy between DDR pathways in the clinical response. There is also an undoubted clinical application to the findings which could have potential for impacting on policy and practice.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Identification and functional validation of driver mutations in colorectal cancer
Funder: Cancer Research UK

Abstract: 1). Background to the proposal: Cancer occurs when there is an accumulation of genetic damage that infers a selective advantage on a cell allowing it to evade growth control checkpoints. Uncontrolled expansion of these ‘mutant cells’ ultimately results in tumour formation. While some of the key molecular events involved in tumourigenesis are known, there is still much work to be done to identify potential new diagnostic and therapeutic targets. In this project we will use high-throughput genome-wide insertional mutagenesis and DNA sequencing in combination with the analysis of human tumour collections to identify key drivers of colorectal cancer development, and the mechanisms by which these genes co-operate to promote tumorigenesis. Not only will we identify cancer drivers we will also use an approach that will allow us to validate these genes as potential therapeutic targets. 2). Relevance to cancer: Knowing the collection of genes that drive tumorigenesis of the colon is critical for understanding how cancers form and how they can best be treated. 3). Specific aims of the project: Aim.A. To use transposon-mediated mutagenesis in the mouse intestine to gain a better understanding of tumor heterogeneity, to identify cell autonomous and non-autonomous genetic interactions that promote intestinal tumor evolution, and to identify driver mutations associated with cancer of the intestine and to predict when these genes are operative in the evolution of the cancer. Aim.B. To deploy high-throughput sequencing of the exomes of human and mouse colorectal cancers to identify and validate candidate cancer genes. Aim.C. To use conditional mouse models of cancer to validate the candidate cancer genes identified in Aims A and B, and more specifically to determine if they represent potential therapeutic targets. 4). Outline plan of research: As outlined above we will use mobile genetic elements called transposons to identify genes that drive tumour development in the colon of the mouse. Using high-throughput sequencing we will determine the relevance of these genes to human cancer and then determine if these genes are viable therapeutic targets.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Real-time Electronic Patient Outcome ReporTing of adverse events in UK cancer trials (REPORT UK)
Funder: Cancer Research UK

Abstract: Background Reporting of adverse events (AEs) is essential in clinical trials. The current system for AEs reporting in cancer trials, the Common Toxicity Criteria and Adverse Events (CTCAE) relies on the clinician’s interpretation of patient symptoms The importance and added value of patient self-reports on AEs and other Patient Reported Outcome Measures (PROMs) has been recognised by clinicians, regulatory authorities and health-care commissioners, but robust and cost-effective data collection methods are needed. Aim This application is for a methodological, proof of principle study to develop, introduce, and evaluate feasibility and acceptability of a system for patients to self-report AEs and other PROMs in cancer trials (REPORT-UK). Methods We propose a staged approach addressing the content of the AEs items for patient self-reports, the necessary information technology development, followed by a proof of concept pilot study. Phase 1. Evaluation of CTCAE items for UK cancer patients. Cognitive interviews with 60-70 patients (using purposive sampling) will explore whether NCI PRO-CTCAE items developed in the United States are applicable to UK cancer patients, and adapt them if necessary. Phase 2. Delivering the information technology to support patient self-reports. This includes: 1) implementing the existing web-base questionnaire builder system (Q-Tool) and adapting it to a telephone-based Interactive Voice Response System (IVRS); 2) usability testing (20 patients,2 sites); 3) development of patient education/training to support independent use; 4) robust secure linkage of patient self-reports with the trial Macro database. Phase 3. Proof of concept pilot study will evaluate feasibility/acceptability and patient compliance with the web-based system or IVRS for collecting self-reported AEs and other PROMs (EQ5D, EORTC QLQ-C30 functional scales). We plan a prospective longitudinal study consisting of cross-sectional comparison at first visit and longitudinal patient completion of REPORT-UK for 3 months. 180 patients undergoing chemotherapy, targeted agents, hormonotherapy, radiotherapy or surgery from 2 centres will be asked to complete weekly AEs and monthly PROms Clinicians will record standard CTCAE toxicity. Patient acceptability will be measured by recruitment rates, attrition over time and proportion of missing data. We’ll compare type, grade and timing of patient-reported AEs with clinician-reported toxicity. How the results of this research will be used Successful completion of the project will deliver REPORT-UK system including an item pool of PRO-CTCAE items, a user-friendly electronic data collection system and information on feasibility and patient compliance. REPORT-UK will be implemented in cancer trials alongside traditional approaches aiming to improve data quality and patient safety.


Research activity codes: 7.1 INDIVIDUAL CARE NEEDS;8.1 ORGANISATION AND DELIVERY OF SERVICES
Health categories: CANCER AND NEOPLASMS