NIHRDataInsights/HRCSData huggingface dataset:
Title: Towards new therapeutic strategies: Zika-driven oncolysis of brain tumor cells
Funder: Medical Research Council

Abstract: Recent work has shown that Zika virus (ZIKV) is capable of specifically infecting and destroying stem-like cancer cells from aggressive CNS embryonal tumors. Tumor cells closely resembling neural stem cells at the molecular level, with activated Wnt signaling, were more susceptible to the oncolytic effects of ZIKV and activated Wnt signaling increased ZIKV-induced tumor cell death. How Wnt signaling promotes susceptibility of CNS tumour cells to ZIKV-induced oncolysis is unknown as are the ZIKV-host cell protein-protein interactions that mediate infection. This project will use unique ATRT and medulloblastoma cell-lines that are susceptible to oncolysis by ZIKV and analyse them using a multi-omics approach. Interaction and expression proteomic techniques as well as RNA-Seq will be used to identify ZIKV-host cell protein-protein interactions and to identify protein networks implicated in ZIKV susceptibility, and possible mechanisms by which activated Wnt signaling enhances this process. This pump priming project will focus on identifying protein-protein interactions for two of the non-structural ZIKV proteins (the NS-3 helicase and NS-5 polymerase) and will also provide proof of principle towards a future larger and comprehensive study of the ZIKV protein interactome. The function of selected protein-protein interactions will be analyzed using siRNA and co-immunolocalization to identify host proteins and mechanisms required for oncolysis. This study will provide key information that will advance the goal of using ZIKV as oncolytic therapy. First, a detailed molecular profile of ZIKV infected CNS tumor cells will identify pathways and processes that promote ZIKV infection, providing a means to assess which types of CNS tumour cells could be targeted using ZIKV. Second, the identification of specific protein-protein interactions may identify molecular mechanisms that could be targeted in therapeutic development.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: Molecular Genetics of Lobular Breast Cancer in a South African cohort and effect of HIV infection.
Funder: Medical Research Council

Abstract: Objectives 1 & 2: Characterize clinco-pathological features and molecular genetics of ILC in African women Somatic copy number aberrations will be assessed using the Illumina HumanCytoSNP-12 BeadChip Kit (300,000 SNPs). Raw SNP array data will be processed with the GenomeStudio 2.0 software (Illumina). Segmentation will be done using SNP Rank segmentation algorithm on the Nexus 8.0 software (BioDiscovery) and absolute copy number determined using the Tumour Aberration Prediction Suite 2.0. Targeted sequencing will be performed using the SureSelect XT low input Target Enrichment System (Agilent). Captured libraries will be run on the HiSeq2500 and analysed using our standard pipeline. Objective 3: Does anti retroviral therapy interferes with the efficacy of tamoxifen therapy? Tamoxifen and its metabolite concentrations will be analyzed on a triple quadruple mass spectrometer using a reverse phase column and an isocratic mobile phase system composed of acetonitrile and formic acid solution. Population pharmacokinetic simulation tools in NONMEM will be used to estimate the AUC (a measure of total drug exposure) and Cmax (maximum drug exposure). Multiplex genotyping will be performed on the open-array QuantStudio 12K Flex Real-Time PCR System. The microarray panel will simultaneously detect genetic variants of CYP2C9, 2C19, 2D6, 3A4, 3A5. Objective 4: Assess whether ctDNA can be used to detect metastatic ILC Blood samples will be collected in Cell Preserver tubes (Nonacus.com), centrifuged and plasma transferred into sterile microfuge tubes and stored at -200C before shipping on dry ice to KCL. ctDNA will be extracted using the Cell Xtract protocol (Nonacus) and quantified by Qubit analysis. The protocol for set up of fluorescent assays for wildtype and mutant alleles, droplet generation and PCR is as previously described (Gao F et al, J Thorac Oncol 2015;10: 212-217). Results are read using the QX100 optical reader and processed using QuantaSoft (BioRad) software


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;6.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: Developing a multiplex serology panel to detect and quantify Epstein-Barr virus infection
Funder: Medical Research Council

Abstract: Epstein-Barr virus (EBV) accounts for >200,000 cancer cases each year and 1.8% cancer deaths are due to EBV-attributable malignancies, some with an exceptionally high incidence in low-middle-income countries (LMICs), e.g. NPC in Southeast Asia and North Africa. The mechanisms of cancer causation by EBV remain an area of active investigation and controversy. Since EBV-related cancers are often diagnosed at advanced stages with poor survival rates, identification of biomarkers present in subsets of EBV-positive individuals to aid early detection of disease is particularly important. Twelve EBV antigens best predicting NPC risk have recently been identified by protein microarray technology, but the output from that technology cannot directly translate to an exact amount of circulating antibody. Using the identified 12 EBV biomarkers, the proposed study will develop/validate a Luminex-based EBV-Monoplex panel capable of measuring/quantifying the amounts of serum EBV biomarkers. Due to the high-throughput, low-cost and low volume of samples required of the technology, this EBV-Monoplex panel may be suitable for large epidemiology studies for investigation of disease mechanisms and as a potential early detection/screening tool among high-risk individuals. The 12-EBV-Monoplex panel will then be used in a pilot case-cohort study including 200 each of NPC, gastric cancer cases and subcohort in the China Kadoorie Biobank (CKB) prospective study. It will provide preliminary data on the aetiological role of EBV biomarkers in EBV-related diseases. Using this Luminex technology, we will develop a 46-Multiplex panel (closely followed the panel designed for the UK Biobank with only four EBV antigens included) for assessing multiple infectious pathogens in risk of gastrointestinal cancer. The proposed study will compare the EBV antibody levels measured by both panels to identify potential EBV biomarkers for an improved CKB Multiplex panel design that is more suitable for Chinese.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: Generating Biologics to Modulate IFITM1 in Cancer and Infection
Funder: Medical Research Scotland

Abstract: A major difficulty in treating cancers is the ability of tumour cells to mount a defense against the patients own immune system. Our research has identified a receptor (a protein that detects signals) implicated in resistance to both conventional drugs and immunotherapies (aiming to activate the patients immune system). The receptor has segments that are exposed on the outside of the cell and can therefore be targeted using ‘Biologic’ drugs based on naturally occuring substances (in this case moncolonal antibodies; MAb). Biologics can specifically home-in on a target to activate cancer cell killing and our industrial partner is a world-leader in the development of synthetic MAb’s (produced in microorganisms rather than animals). The student will develop and validate antibodies that target the cancer causing receptor. The receptor is also involved in preventing some viral infections so the Biologics will also be screened for anti-viral activity. We expect to generate MAb’s that can regulate cancer cell growth and/or viral infection. As well we will provide cutting-edge training at the boundry of biology and industrial science. Opportunites for the generation of intellecutal property are high; and impact on patients that have treatment resistant cancers or chronic-viral infections could result from the research.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: Retrovirus–host interactions
Funder: The Francis Crick Institute

Abstract: Genetic analysis of ERV distribution makes it clear that retroviruses and their vertebrate hosts have co-existed for more than a hundred million years. Given the harmful mutagenic or tumorigenic effects potentially associated with provirus formation, it is not surprising that host defence mechanisms to limit retrovirus replication have evolved. Our work has the goal of achieving a better understanding of such natural mechanisms for controlling retrovirus infections as well as the means by which retroviruses overcome such host defences. In the period since our initial cloning of the murine Fv1 gene twenty years ago, the study of mechanisms of intrinsic immunity has become a major focus of retrovirus research. The major topic of research in my lab concerns the restriction factors Fv1, TRIM5 and TRIM5CypA that bind to the assembled capsid (CA) protein present within newly-infecting, incoming retroviruses, thereby inhibiting reverse transcription and/or nuclear import. Our previous work has allowed us to suggest that Fv1, TRIM5 and TRIMCyp, although very different in sequence, share a design characterized by multiple low affinity interactions that allows the recognition of multiple viral targets with minimal genetic change and suggest a major role for these genes in the survival of mammalian species during evolution. We are currently testing these ideas in more detail. Progress has also been made in overcoming difficulties associated with the expression of Fv1 bacterial systems, opening the way for more detailed in vitro studies of the interaction between Fv1 and viral CA. In turn, information from these studies is expected to facilitate the examination of interaction between Fv1 and CA in newly infected cells. We are also carrying out a detailed study of Fv1 evolution in Rodentia. Preliminary results indicate (a) that Fv1 is much older than previously thought and (b) shows considerable variation in target specificity suggesting the presence of constantly changing selective forces. One strategy employed by retroviruses to combat host defences to infection is the deployment of viral accessory proteins. Such viral countermeasures typically act by subversion of a cellular protein degradation pathway. Funded by an Investigator award from the Wellcome Trust we study two related accessory proteins, Vpx and Vpr. We have previously identified the triphosphohydrolase activity of cellular SAMHD1, which represents the primary target of Vpx, leading to the understanding that SAMHD1 inhibits retrovirus replication by depleting cellular dNTP pools and uncovering the structural basis for Vpx mediated SAMHD1 degradation. We are now examining the mode of action of Vpr and its so far unidentified cellular target. It appears that Vpx and Vpr share a common mechanism for degrading host defence proteins that may represent a new target for drug development, one that cannot easily be overcome by viral mutation.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: Understanding the Epithelial Site-Specific Origin of HPV Neoplasia and its Control
Funder: Medical Research Council

Abstract: Human Papillomaviruses cause around 6% of all human cancers, as well as a wide diversity of problematic skin lesions. Although the basic functions of many papillomavirus proteins have been elucidated, the effect of viral gene expression on epithelial homeostasis has not been examined, with the mechanics of lesion-formation and lesion-persistence being only poorly understood at the molecular and cellular levels. The particular focus of the study will be on the organisation and patterns of viral gene expression at of one of the most important epithelial sites where the high risk HPV types cause cancer - the cervical transformation zone, and will compare expression at other vulnerable sites within the body, including oropharyngeal and anal sites. These variations in gene expression have dramatic consequences on clinical pathogenesis and disease outcome, with deregulated viral gene expression driving neoplastic progression and eventually cancer. We will also examine the interaction between viral gene expression and cellular microenvironment following initial infection, as well as during lesion regression and subclinical persistence. These studies will support development of disease stratification approaches that employ biomarker combinations to provide a clearer rationale for markers that are currently in use (e.g. methylation, E4 (4) etc), and will define potential biomarkers to target cell type, microenvironment and viral gene expression, which are urgently required as a complement to HPV DNA testing. As epithelial site-specific regulation patterns become clearer, we also anticipate opportunities to evaluate new antiviral therapies.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: Host cell reprogramming by oncogenic human papillomavirus
Funder: Medical Research Council

Abstract: Persistent oncogenic human papillomavirus (HPV) infection causes cancers within the anogenital and oropharyngeal tracts. The fundamental link between HPV and cancer is established, but the molecular changes that drive disease progression are poorly defined. Importantly, the natural history of HPV infection is different between body sites; disease progression in the uterine cervix follows defined premalignant phases that have not been identified in the oropharynx. In addition, oncogenic HPV types behave differently at specific anatomical sites. While HPV16 causes the majority of disease at both sites, HPV18 is the second most common type in cervical cancers but only rarely found in oropharyngeal tumours. The reasons for these differences are unknown. We hypothesise that HPV16 and 18 differentially induce transcriptional reprogramming of host cells at different anatomical sites, defining niche-specific persistence and disease progression. To test this, we have developed physiological models of the HPV life cycle. Primary keratinocyte cultures from the tonsil and anogenitals are transfected with HPV16 or 18 genomes and persistent episome replication established. We show that HPV18 induces targeted transcriptional reprogramming of host cells by redistribution of an important cellular transcriptional regulator, CCCTC binding factor (CTCF) resulting in altered epigenetic chromatin status. We will use our models of oncogenic HPV infection and innovative methods including RNA-Seq, ChIP-Seq, ATAC-Seq and 4C to unravel HPV type- and anatomical site-specific nuances in host cell manipulation, HPV biology and disease progression. Key pathways will be analysed in our HPV life cycle models and tumour sections to determine their role in HPV persistence and disease progression. Consolidation of our findings will identify virus-specific events important in HPV-driven disease, which are likely to be clinically useful, and answer important questions about HPV biology.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: ISARIC Clinical Characterisation Protocol UK (CCP-UK) - a companion study for patients with Cancer and COVID-19 (CCP-CANCER-UK)
Funder: Medical Research Council

Abstract: Many people with treatable cancers have had treatment delayed or stopped by COVID-19 with potentially life-threatening consequences. Crucial information to guide decision making whether to continue or stop treatment is lacking. As of 27th June 2020 5,395 of 66,574 patients i n CCP-UK have a history of cancer, recorded as Yes/No, on the CRF. No other cancer specific data were collected. We will enrich the CCP-UK data set by collecting detailed cancer data including tumour type, stage, time from diagnosis, and treatment given. These data will answer the following questions: (1) Outcomes: What i s the survival rate in cancer patients with COVID-19, how does this vary by cancer type, and with timing and potency of immunosuppressive treatment? (2) How do outcomes compare with non-cancer patients after controlling for key confounders? (3) Host: Does COVID-19 present differently in immunosuppressed cancer patients, or in different cancer types? Can clinical severity prediction be used to improve clinical management? (4) Disease: What is the impact of the type and stage of cancer on COVID-19 outcomes? (5) Cancer Therapy: What is the impact of chemotherapy, immunotherapy and other types of cancer treatment on risk of infection, severity and outcome? Cancer patients may be more vulnerable to severe COVID-19 making development of a robust evidence base vital. Using the largest prospectively collected COVID-19 dataset of cancer patients will provide a rapid and efficient way to gain clinical evidence that is impactful, relevant and can directly inform practice for the benefit of cancer patients.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: Defining the roles of PP2A B56 isoforms in HTLV-1 infection.
Funder: Medical Research Council

Abstract: Human immunodeficiency virus type 1 (HIV-1) and human T-cell lymphotropic virus type 1 (HTLV-1) are the most notorious retroviruses since they are the cause of severe, disabling and sometimes fatal diseases. The most severe HTLV-1 induced diseases are adult T-cell leukaemia (ATL) and the neurological disorder HTLV-1-induced myelopathy/tropical spastic paraparesis (HAM/TSP). So far, there are no therapies for either illnesses. Patients diagnosed with ATL, typically die within two years of presentation. A critical step in the lifecycle of retroviruses, like HTLV-1, is the integration of a DNA copy of the viral RNA genome into the host DNA. This reaction is catalysed by the viral enzyme integrase (IN). Integration is not random, and we know that integration in certain areas of the genome likely predispose the patients to disease. Our aim is to understand the mechanism of how the integration machinery choses where it will insert its viral DNA. We identified an important host enzyme, protein phosphatase 2A (PP2A), that specifically binds to HTLV-1 IN and strongly stimulates integrase activity. We showed that viruses expressing mutant INs unable to bind to PP2A are non-infectious. PP2A is composed of three subunits; the core is made up of a scaffold and catalytic subunit which can bind to any one type of four different regulatory subunits. HTLV-1 IN specifically associates with PP2A that has a B56 type of regulatory subunit of which there are five somewhat redundant isoforms in the cell. Although IN can bind to all five B56s, we don't know whether all play a role in establishing HTLV-1 infection. We generated a conditional KO cell line that in combination with back-complementation of specific PP2A-B56 holoenzymes will reveal which B56 isoforms are critical to establish HTLV-1 infection. Our findings will guide the design and development of drugs that can specifically prevent the interaction between IN and its host.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: Regulation of T cell differentiation by stimulation strength
Funder: Medical Research Council

Abstract: Through the process of differentiation, a single naïve T cell can contribute to a wide variety of effector and memory responses, providing protection against both current and future pathogenic threats. Understanding the mechanisms by which differentiation fate decisions are made is important for rational design of therapeutics that aim to elicit specific types of T cell responses, such as vaccination and cancer immunotherapy. The affinity with which a naïve T cell binds an antigenic ligand controls the strength of stimulation the T cell experiences and can skew the distribution of resulting differentiated cells among effector and memory subsets. This proposal seeks to uncover the mechanisms underlying the effects of stimulation strength on CD8+ T cell differentiation and determine its impact on the protective functions of differentiated T cells. I will use cutting-edge single-cell genomic and multi-omic techniques coupled with in vivo influenza infection models to interrogate the impacts of altering stimulation strength on CD8+ T cell effector and memory responses. Specifically, this proposal will investigate 1) the transcriptomic and epigenetic underpinnings of altered differentiation outcomes, 2) the relative contributions of stimulation strength and localisation within the lymph node in determining differentiation fate, and 3) the functional capacities of cells that have achieved the same differentiation fate via initial stimuli of different strengths. Together these data will shed light on the mechanisms by which CD8+ T cells, armed with a single set of intracellular machinery, can tune their differentiation according to stimulation context. This will be valuable information for understanding the host response to viral infection, which remains one of the major threats to human health.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: Understanding and targeting the suppressive function of the ARHGEF1 pathway to unleash T cell immunity against cancer
Funder: Medical Research Council

Abstract: Cancer is a major cause of illness and death worldwide. There is an urgent need for improved treatments for cancer. The immune system can recognise and kill cancer cells but its function is powerfully suppressed within tumours. Releasing T cells from immune suppression by targeting immune checkpoints such as CTLA-4 and PD-L1 has revolutionised the way we treat cancer patients. However, only a minority of patients with a subset of cancers robustly and durably respond to existing immunotherapies, termed immunotherapy resistance. There is a need to identify and therapeutically target distinct mechanisms of cancer immunosuppression if we are to build upon early successes in the field of cancer immunotherapy for the benefit of the majority of patients who presently do not respond. We have discovered a new T cell-intrinsic suppressive pathway, dependent upon the activity of the guanine nucleotide exchange factor, ARHGEF1, which restricts T cell-mediated anti-tumour immunity and responses to immune checkpoint blockade therapy. This research will: 1. Determine the T cell-intrinsic function of ARHGEF1 in suppressing anti-tumour immunity and immunotherapy responses, examining whether the ARHGEF1/RhoA pathway can be targeted to synergise with existing checkpoint inhibitors and improve adoptive immunotherapy 2. Determine molecular mechanisms by which ARHGEF1 suppresses T cell signalling and effector functions, and characterise the function of ARHGEF1 in human T cells 3. Define the extracellular ligands and receptors that drive the suppressive function of ARHGEF1 in mouse and human T cells, identifying new immunotherapy targets These studies will define a new suppressive pathway operating within T cells to limit anti-tumour immunity and immunotherapy responses. We will define targets for development of new immunotherapies that act alone or in conjunction with existing immune checkpoint inhibitors to improve therapeutic outcomes for cancer patients.


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