NIHRDataInsights/HRCSData huggingface dataset:
Title: Molecular Mechanisms of Cell Death and their role in Cellular Toxicity
Funder: Medical Research Council

Abstract: This programme aims at further understanding the fundamental mechanisms of cell death that regulate cellular resistance/sensitivity to toxic insult. The MRC Toxicology Unit strategy is to employ a systems-based approach to determine the pathways that are initiated following exposure of cells/organisms to a range of toxic insults. However, defined nodes that form the key decision points to regulate the pathways that respond to toxic injury have been identified and these include proteins that control cell death. The objective of this programme is to investigate cell death pathways that are activated in response to a range of agents, namely members of the TNF cytokine family and agents that trigger mitochondrial-dependent cell death. Using unbiased high throughput screening approaches we aim to define key changes in mRNA/miRNA/proteins in cells undergoing distinct modes of cell death (e.g. apoptosis versus programmed necrosis). In addition, we will use targeted pathway analysis and mechanism-based approaches to obtain novel mechanistic insights so that key regulators can be identified and their potential role in cellular toxicity determined. Our Specific Objectives are: 1. Systems-based identification/characterization of novel modulators of cell death pathways 2. Molecular characterization of the DISC and key regulators of death receptor signalling 3. To examine mechanisms of selective potentiation of cell death in primary tumour models 4. Dissecting mechanisms of apoptosis resistance in asbestos-induced malignant mesothelioma


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Transgenerational Epigenetic Inheritance & Evolution
Funder: Medical Research Council

Abstract: Transposons, parasitic DNA segments that can copy themselves independently of the replication of their host genome, are abundant across metazoan organisms. Left unchecked, transposons pose a severe threat to genome integrity, thus organisms have evolved robust mechanisms in order to keep transposons in check. However, transposons are also an important source of genetic diversity, with many examples now documented of how transposon insertions lead to potentially beneficial genetic changes to organisms- indeed up to 40% of primate-specific gene regulatory elements are thought to have originated in this way. Thus the mechanisms that control transposons may themselves be regulated to ensure that they do not completely stifle transposon activity, thereby removing an important source of evolutionary novelty. We are interested in how this delicate balance is maintained, and whether it can be altered in order to facilitate adaptation of organisms to the environment. To address the question of how transposon silencing mechanisms are regulated to control the origin of evolutionary novelty we are using nematodes as a model system. Our main focus is piwi-interacting small RNAs (piRNAs), a transposon silencing pathway that is active in the germline and is conserved across metazoans. Just as in drosophila and mammal, piRNAs in the model nematode C. elegans are able to silence transposons and are important in maintaining the fertility of the animal over many generations. In addition, piRNAs are capable of establishing epigenetic changes that can be inherited for many generations independently of the presence of the initial piRNA trigger. However, we recently discovered that piRNAs are not found universally across the nematode phylum. In fact the entire piRNAs pathway is has been lost several times independently in different nematode lineages. Moreover, even in C. elegans, we showed in collaboration with Shawn Ahmed (University of North Carolina), that the loss of fertility that occurs in animals lacking the piRNA pathway can be completely suppressed by mutations compromising insulin signalling pathways. These two unusual aspects of the nematode piRNA system mean that nematodes offer a unique advantage to study what happens to genome evolution in the absence of the piRNA pathway. By using comparative genomics between different nematode species we are trying to decipher the effects of piRNAs on long-term genome evolution. Moreover, we are using in lab evolution in C. elegans to test in the short term what happens to genome evolution in the absence of the piRNA pathway. Together these two approaches will enable us to answer the fundamental questions of how transposons contribute to evolutionary novelty, and how cellular epigenetic pathways influence this process. Moreover, our work will give insight into the ways in which aberrant transposon silencing, as is known to occur in cancer, may contribute to the development of the disease.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Metabolism and Cell Growth
Funder: Medical Research Council

Abstract: The prevalence of obesity is increasing globally. Accumulating epidemiological evidence implies that obesity—associated with insulin resistance—is a risk factor for several types of cancers. However, a biological basis for the associations between whole-animal metabolism and cancer remain incompletely understood. Using Drosophila, I have developed a model system to study the link between obesity and cancer (Hirabayashi et al. 2013, Cell 154, 664). Feeding Drosophila a high-sucrose diet was previously demonstrated to promote metabolic defects including accumulation of fat, hyperglycemia, increased insulin levels (hyperinsulinemia), insulin resistance, and heart defects, indicating that the simple feeding model recapitulated many of the metabolic features of mammalian obesity. A high-sucrose diet also leads to a striking enhancement of tumour progression in a Ras/Src co-activated Drosophila tumour model. Diet-induced tumour growth has consequences on animal viability, evidenced by the death of most larvae prior to pupariation. This synergistic, diet-plus-cancer dependent mortality is an ideal phenotype for genetic screens designed to identify regulators of obesity-dependent tumourigenesis. I will further utilize this Drosophila diet-enhanced tumour model as useful whole-animal systems to better understand the mechanistic links between diet-induced metabolic defects and tumour progression. Conversely, cancer progression induces metabolic changes including cancer-associated cachexia, a wasting syndrome of progressive muscle and adipose tissue loss. Cancer-induced metabolic changes can profoundly influence treatment efficacy and the quality of life for cancer patients. However, the biological mechanism for the cancer-induced metabolic changes are not well understood. Animals with diet-enhanced Ras/Src-tumours possess less fat body (i.e., Drosophila adipose tissue). This metabolic feature recapitulated cachexia-like adipose tissue wasting of cancer patients and is suitable for addressing a complementary question of how tumours affect whole-animal metabolism. Overall, our research goal is to discover and elucidate the biological mechanisms and therapeutic targets involved in the interactions between metabolism and tumour progression in a whole-animal context.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Clinical Lectureship in Haematology
Funder: Medical Research Council

Abstract: CD8 T-cell heterogeneity and function: defining the fingerprint of a killer for T-cell therapies Infusion of genetically modified T-cells has produced remarkable clinical outcomes in childhood leukaemia. We aim to examine the process of killing by CD8+ T-cells (CTL) at the molecular level to deliver novel cellular therapies for post-transplant viral infections and haematological cancers. We identified TCR-identical HIV specific CD8+ T-cell clones with distinct suppression of viral replication in vitro, antigen sensitivity, transcriptional signatures and cytokine profiles. In depth functional and molecular characterisation identified that the CTL clone with optimal viral suppression was most antigen responsive with higher expression of previously uncharacterized receptors bearing immunoreceptor tyrosine activating or inhibitory motives (ITAMS/ITIMS) and furthermore did not secrete tumour necrosis factor (TNF). Bisulfite sequencing identified heavy CpG methylation in the TNF core promoter indicating epigenetic modification of CTL effector function post antigen encounter. TCR-identical CTL can therefore be heterogeneous in function and small differences in ontogeny may have significant impacts on cytotoxic efficiency. We aim to identify the transcriptional signature of an “optimal” CTL with high killing efficiency, and identify pathways that can be manipulated to produce populations of CTL enriched with this signature for therapeutic use. This will use a two-pronged approach, using RNA sequencing to examine transcriptomes of ex vivo antigen-specific tetramer sorted CTL populations, combined with in vitro high throughput screening of epigenetic modifiers, drugs targeting known CTL signalling pathways and an shRNA screen focusing on the ITAM/ITIM genes identified above. Our aim is to extend our findings to a high-throughput genome wide ShRNA screen using CD8+ T-cell clones specific for EBV latency II antigens as expressed in 40% of Hodgkins and 20% of DLBC lymphomas. The high-throughput screen will utilise a flow cytometry based cytotoxicity assay at a titrated limiting antigen stimulus, to identify factors that modulate the cytotoxic efficacy of latency II EBV protein- specific CTL clones. Successful hits will be followed up by RNA-sequencing to define the molecular fingerprint of an antigen-experienced CD8+ T-cell with optimal killing efficiency and identify pathways and epigenetic networks that contribute to this state with the aim of producing a therapeutic product for infusion to patients with enhanced chance of cure.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Cellular toxicity and translational control in pulmonary epithelial cells
Funder: Medical Research Council

Abstract: There is a lack of information to show how exposure to environmental toxins changes gene expression patterns. A greater understanding of these pathways is important for a number diseases that are associated with environmental exposure and the lung is particularly important in this regard. It is planned that cigarette smoke will be used at the toxicant since cigarette smoking is linked to a host of diseases, both malignant and non-malignant, and many constituents of cigarette smoke are known mutagens. However, little is known of the direct effects of smoking upon gene expression, especially at the level of translation, and how these effects may influence disease progression. Elucidation of these mechanisms will shed light on the aetiology of smoking-related disease, and will hopefully lead to novel therapeutic targets as well as prognostic and diagnostic markers for toxic exposure. This project will use mRNA and polysome profiling techniques to identify mRNAs that are up- down-regulated lung epithelial cells in response to cigarette smoke using an already established cell culture model. The assays used will address both total mRNA abundance (by conventional mRNA profiling) and polysomal abundance (ie translational activity, by polysome profiling and/or ribosome footprinting).. Patterns of gene expression re-programming following smoke exposure will be detailed in both transformed and normal-like lung epithelial cell lines. In this way we will identify groups of mRNAs that respond to smoke exposure at the level of translation. We will then seek to relate these changes to several disease phenotypes- e.g. metaplasia, pro-inflammatory and fibrogenic changes. We will also seek to identify pathways the up- or down-regulation of which are related to smoke exposure, either transcriptionally or translationally. These will be validated at the protein level (by Western blot, and also by immunohistochemistry in archival formalin-fixed tissue), and investigated as possible interventional targets in cell culture and ultimately in animal models. In addition to this, we will identify patterns of translational dysregulation, and dysregulated single mRNAs, that occur in tumour vs normal tissues.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: CANCER AND NEOPLASMS
Title: Toxicity and the DNA-damage response.
Funder: Medical Research Council

Abstract: Exposure to high-energy radiation can lead to severe toxic DNA damage in cells (for example by generating double strand DNA breaks). If not promptly repaired DNA damage can result in the accumulation of deleterious alterations to chromosomes and as a consequence produce various toxic outcomes, such as acute cell death. We are developing a Toxicology platform for studying toxic effects of agents that cause DNA damage in cells (MIE – molecular initiating event). Examples of such toxic agents include ionizing radiation (e.g. X-rays) and radiotherapy. Our unique approach uses proteome-wide analysis of DNA repair complexes for identification of crucial mediators governing toxic outcomes to DNA damage. We are primarily interested in identifying proteins regulating cellular radiosensitivity. We believe that a radiosensitive phenotype typically identifies a key mediator of cellular response to DNA damage. Thus measuring a single parameter we are able to pinpoint some key regulatory components in cellular DNA damage response. The final element of our Toxicology platform is the in-depth mechanistic study aimed at understanding in molecular terms the function of proteins identified in our proteomic screens. Currently we focus mostly on defining the function of XLS/PAXX protein and NR4A nuclear orphan receptors in double-strand DNA break repair. We are using a variety of genetic and biochemical approaches based on mammalian cell culture and rodent animal models. Our goal is to provide new insights into the complex process of toxic DNA damage response, such that would increase our understanding of toxic outcomes after radiation exposure.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.2 CELLULAR AND GENE THERAPIES
Health categories: CANCER AND NEOPLASMS
Title: Exploring novel solutions of radiotherapy delivery and using biology, imaging, new fractionations and radiobiological models to improve TCP/NTCP ratio
Funder: Medical Research Council

Abstract: To develop and optimise novel radiotherapy delivery strategies, additionally incorporating novel agents, with the goal of maximising tumour control and minimising toxicity with a specific focus in gastro-intestinal malignancies. The ultimate aim is to personalize radiotherapeutic management using molecular and imaging biomarkers to select a patient /cancer specific radiation treatment with individualised dose, fractionation and choice of radiation sensitizer. The aim of my research has three main themes 1. Strategies of modulating radiotherapy (SMART) with drugs or new modalities of delivering radiation. Radiotherapy dose escalation techniques using ‘Simultaneous Integrated Boost’ permit intensification of radiotherapy dose to predetermined volumes within the tumour, derived from biological imaging such as PET or functional MRI. Tumour control probability and normal tissue control probability models can then be used to refine the dose escalation within the tumour further and spare normal tissue exposure. Continue to understand this concepts wich are now tested in phase III trials in oesophageal and anal cancer. In parallel we are testing DNA damage response modifiers ( e.g. ATR-i) in combination with radiation to optimise the therapeutic window. 2. Advanced radiotherapy as a bridge to radical surgery. The use of stereotactic ablative radiotherapy to areas at risk of not being completely cleared with surgery; with the aim of achieving complete tumour resection. Continue to test this concept in the preoperative setting for tumours such as pancreatic cancers that are difficult to clear due to proximity to critical organs. 3. Refining normal tissue toxicity modelling in gastro-intestinal malignancies receiving radiotherapy. We have identified that substructures of heart receiving a specific radiation dose could adversely affect radiation outcomes. The aim is to study mechanisms of damage and how to minimise radiation to certain substructures. This would allow selection of the best radiotherapy dose delivery technique in patients receiving combined chemoradiation and surgery.


Research activity codes: 5.5 RADIOTHERAPY AND OTHER NON-INVASIVE THERAPIES;6.5 RADIOTHERAPY AND OTHER NON-INVASIVE THERAPIES
Health categories: CANCER AND NEOPLASMS
Title: Biochemistry and Regulation of Mammalian DNA Repair
Funder: Medical Research Council

Abstract: DNA base excision repair (BER) is the principal DNA repair system in cancer cells, which counteracts the killing effect of major cancer treatments e.g., chemotherapy (alkylating agents) and ionizing radiation (about 80 % of DNA damage induced by ionizing radiation are SSBs and base lesions which, as a result of BER, can be converted to DSBs during DNA replication). Changes in BER capacity most probably are responsible for the efficiency of cancer treatment, as many cancers have an altered expression of BER proteins. Although BER enzymes have been studied in detail, the mechanisms involved in BER coordination, their regulation and consequences of their malfunction are unclear. This gap in knowledge is impeding the discovery of new cancer therapy targets and the development of novel treatment strategies. The objective of the Biochemistry Group is to identify new mechanisms and proteins that are responsible for the coordination and regulation of the BER pathway in human cells and to understand their role in processing endogenous and radiation induced DNA lesions, with a final goal to improve the efficiency of cancer therapy. Our recent studies have allowed us to formulate the basic principles behind the regulation of steady state levels of BER proteins and coordination of the BER process with cell cycle progression. Consequently, the major goal of future studies would be to build a comprehensive model for regulation and coordination of the BER response to ionizing radiation in order to identify new targets for improvement of cancer radiotherapy. To achieve our goal we will: 1. Investigate the mechanisms regulating the transcription of BER genes and their regulation under DNA damage stress. 2. Study the role of ATM in regulation of BER gene expression. 3. Address the effect of BER deficiency on cellular gene expression and its role in tumorigenesis. 4. Search for new genes involved in DNA damage response which are synthetically lethal with BER genes.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Molecular Determinants of Radiosensitivity
Funder: Medical Research Council

Abstract: The maximum radiation dose that can safely be delivered to patients is limited by the side effects caused by damage to the healthy tissues that surround the tumour. The aim of our research is to improve radiotherapy treatment by making the tumour cells more sensitive to ionising radiation without altering the sensitivity of normal tissues. Tumour radiosensitivity is determined by intrinsic sensitivity, the inherent sensitivity of the tumour cells, and extrinsic sensitivity, resistance to killing that is imparted through the tumour environment. Our work has identified several targets that allow manipulation of both of these parameters in order to improve the radiation response. To identify novel intrinsic radiosensitisation targets, we developed a high throughput colony formation assay that closely reflected the clinical use of radiation. Using this assay to screen large siRNA libraries, we identified several genes not previously identified with radiation sensitivity. These included SRP72 (signal recognition particle 72), which is part of the signal recognition particle complex responsible for transporting secretory proteins, and thiamine pyrophosphokinase-1 (TPK1). The discovery that thiamine metabolism is associated with tumour radiosensitivity may represent a new clinical strategy for augmenting radiotherapy. So far the most promising target we identified in our high throughput screens is POLQ, a DNA polymerase involved in microhomology-mediated end-joining repair of double-strand DNA breaks. We demonstrated that POLQ mediated tumour radioresistance, and that its overexpression is a highly significant prognostic factor in breast cancer. The subsequent demonstration that it is synthetically lethal in cells lacking functional BRCA1 has greatly increased the interest of these studies. One key factor determining extrinsic radiosensitivity is tumour hypoxia. Solid tumour often have large hypoxic regions, which can be up to three times more radioresistant. A possible strategy to reduce tumour hypoxia is to decrease the oxygen consumption rate in the normoxic tumour cells thereby increasing the availability of oxygen to the hypoxic areas. We developed a high throughput screen to measure oxygen consumption in cancer cells and screened library of 1,697 FDA-approved compounds. This screen identified the anti-malarial drug atovaquone as a potent reducer of oxygen consumption. Atovaquone was subsequently demonstrated to reduce hypoxia in spheroids and xenograft tumours. Most importantly, atovaquone was shown to cause significant tumour growth delay in combination with radiation in these models. We are now conducting clinical trials to assess whether atovaquone reduces tumour hypoxia in patients.


Research activity codes: 5.1 PHARMACEUTICALS;5.5 RADIOTHERAPY AND OTHER NON-INVASIVE THERAPIES;6.5 RADIOTHERAPY AND OTHER NON-INVASIVE THERAPIES
Health categories: CANCER AND NEOPLASMS
Title: Gene-drug interactions in the melanocyte lineage and melanoma
Funder: Medical Research Council

Abstract: My research goal is to develop new therapeutic approaches to treat melanoma. Our strategy is to interrogate the melanocyte lineage in zebrafish as a novel source of therapeutic targets and drug-leads that can target the diverse, heterogeneous subpopulations in melanoma. As supported by an ERC Consolidator Award and a BBSRC funded screening facility, we perform phenotype-based small molecule screens on the zebrafish melanocyte lineage to identify new drugs that can target lineage specific vulnerabilities in melanoma. Within the context of my core MRC Programme research, I now propose to translate one of the hit classes from our screen, the 5-NFNs, to target ALDHHigh subpopulations in cancer. In parallel, we will use zebrafish genetic technologies to discover and dissect the melanoma lineages that underpin the cancer cell subpopulations that drive disease progression and treatment failure. These efforts are further supported by a Melanoma Research Alliance-L’Oreal Team Award for Women in Science to identify and target dormant melanoma subpopulations. The two main experimental aims of my MRC programme are: Aim 1: To develop the potential of the 5-NFNs to target melanoma subpopulations and to reveal new 5-NFN synthetic lethal interactions. Aim 2: To discover new melanocyte lineage and melanoma subpopulations in zebrafish and to test their role in melanoma progression and therapy. We will use single cell sequencing, transcriptomics, and fluorescent reporter lines to identify and label heterogeneous cell populations in melanocyte development and in our melanoma models. Select chemical compounds from our screens will be tested in the context of targeting melanoma cell populations, and developed in pre-clinical models for drug-development.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS