NIHRDataInsights/HRCSData huggingface dataset:
Title: Defining T Cell Immunity to Merkel Cell Polyomavirus
Funder: Medical Research Council

Abstract: Aim: Defining T cell response to Merkel Cell Virus (MCV) Objectives: 1. Identify, quantify and characterise MCV-specific T-cell responses to the potentially oncogenic LTA and STA proteins in healthy people, patients with Merkel cell cancer (MCC) and control group with basal cell cancer (BCC). 2. Investigate the immunogenicity of MCC malignant cells and of MCV antigens as targets for T-cell immunity. First we will map LTA and STA specific epitopes capable of provoking CD4 and CD8 T-cell responses in healthy volunteer donors by using functional assays with synthetic overlapping and then truncated peptides. This is possible in part by establishment of single cell clones from reactive T-cell populations by limited dilution cloning. We will then use T-cells from both MCC and BCC patients to assess response to these same identified epitopes in both populations. Next, we will construct epitope specific MHC Class I tetramers to label cells and examine total specific CD8 T-cell frequency of both functional and anergic cells. We will then examine if incubation with co-stimulatory molecules can improve T cell response. The next stage involves targeting identified epitopes when they are presented on a cell. Firstly, this is done using model cell lines into which we transfect individual peptide that is processed and presented. We will then use epitope specific T-cell clones in functional assays to assess recognition. This will then be expanded to see if clones respond to HLA-matched MCC cell lines (eg.MKL-1) and matched freshly resected tumour cells. We will also investigate the ability of MCC cells to act as antigen presenting cells by using western blots to examine presence of important proteins associated with this such as MHC class I, MHC class II, TAP1 and TAP2. The major importance of this work is in demonstrating the capability of MCV antigens to act as targets for cytotoxic T-cell responses. This may be the initial step in developing an immunotherapy for MCC.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: Investigating the role of the E5 viroporin of human papillomavirus (HPV) in transformation and the virus life cycle
Funder: Medical Research Council

Abstract: Human papillomavirus (HPV) is a major human pathogen and the major cause of cervical cancer and a growing number of orogenital malignancies in both sexes. Despite the recent development of the vaccines, the long incubation period of the virus and the ineffective nature of the vaccine in HPV-exposed individuals will hinder reductions in HPV-associated cancers. This is a significant health burden, given that HPV screening and treatment costs the USA alone $3 billion per annum. Development of effective treatments to compliment the vaccine strategy is clearly warranted. To develop directly acting antivirals, a detailed understanding of HPV biology is required. The E5, oncoprotein has remained poorly studied. E5 expression causes tumours in the skin/cervix of mice and this is thought to occur by a mechanism that required deacidification of endosomes to deregulate EGFR signalling in cells. how this is brought about is the subject of considerable controversy. We demonstrated that E5 is a member of the viroporin family of channel forming proteins. Furthermore, using in silico molecular modelling techniques we generated small molecule inhibitors of the E5 channel. These reduced EGFR hyperactivation in cell culture, providing the first evidence of a viroporin with transforming abilities. We will test the hypothesis that the E5 viroporin directly alkalinises EGFR containing endosomes to deregulate EGFR trafficking. We will combine our liposome technologies with in silico molecular modelling to understand channel function and inform cell based assays to study EGFR signalling. We will perform a comprehensive analysis of the role of the E5 viroporin in the HPV life cycle studies, we using organotypic raft cultures. These are the gold standard system to study the HPV life cycle. This proposal seeks to significantly increase our understanding of this poorly characterised oncoprotein, with the long-term aim of validating E5 as a possible target for antiviral intervention.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: Elucidating the regulation and function of the cell-cycle regulator RGC-32 in Epstein-Barr virus transformed cells
Funder: Medical Research Council

Abstract: We will investigate: 1. How RGC-32 is transcriptionally controlled by EBV-encoded factors in EBV-infected cells. Using chromatin immunoprecipitation-coupled-to-next-generation-sequencing we have uncovered novel binding sites for key EBV transcription factors at the RGC-32 gene and the gene encoding the RGC-32 transcriptional activator, RUNX1. The role of these enhancer elements in controlling RGC-32 transcription will be investigated using transient and stable reporter assays, ChIP-QPCR for cellular factors that target EBV proteins to these sites and co-immunoprecipitation and re-ChIP assays. 2. How RGC-32 translation is differentially regulated by i) miRNAs and ii) 3' untranslated region (UTR) binding proteins in EBV-infected cells. We have also uncovered translational mechanisms that regulate RGC-32 protein expression in certain EBV-infected cells. We have identified miRNAs that target the RGC-32 3'UTR and binding sites for 3'UTR binding proteins that may regulate RGC-32 translation. (i) We will investigate the role of miRNAs in the control of RGC-32 translation using polysome gradient analysis, 3'UTR reporter assays, site-directed mutagenesis of target sites and endogenous assays of miRNA overexpression and inhibition. (ii) We will investigate binding of potential 3'UTR binding proteins using RNA immunoprecipitation (RIP) experiments and gel shift assays. Further studies will determine whether knock-down of these factors increases RGC-32 expression. In addition to focusing on candidate regulators we will also use an unbiased proteomics approach to identify RGC-32 3'UTR binding proteins. 3. The role of RGC-32 in cell-cycle control. We have shown that overexpression of RGC-32 disrupts the G2/M checkpoint in B-cells implicating RGC-32 overexpression in EBV-mediated growth transformation. Using lentivirus-based RNAi and targeted gene knock-out approaches, we will determine how growth and checkpoint function in infected cells is affected by the loss of RGC-32.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: Functional analysis of the Epstein Barr virus nuclear antigen leader protein (EBNA-LP) in a viral context.
Funder: Medical Research Council

Abstract: Epstein-Barr virus (EBV) is a ubiquitous human pathogen that is involved in 1% of cancer incidence worldwide. In vitro EBV transforms resting B cells into lymphocyte cell lines. EBNA-LP is one of the EBV nuclear antigens (EBNAs) important for this process. Exploration of its role in EBV biology has been neglected because of its complex repetitive nature and the technical challenge of making mutants of EBNA-LP in EBV. I propose to take a genetic approach to clarify the role of EBNA-LP in B cell transformation and identify the mechanisms central to its key biological properties. In vitro EBNA-LP is able to enhance the ability of EBNA2 to activate gene transcription. Sp100, NCoR and HDAC4 have variously been implicated as mediators of this effect. Using an EBNA-LP-knockout EBV (LPKO) and its revertant, we will identify the functions of EBNA-LP in B cell transformation. We will analyse the phenotype of LPKO-infected B cells, and undertake a microarray analysis of LPKO-infected BL31 cells to allow us to identify genes that are co-regulated with EBNA2 and with the EBNA3s, as well as those altered independently by EBNA-LP. In parallel we will map the interaction domains of 10 known EBNA-LP-binding partners. Having identified EBNA-LP mutants that lack defined interactions, we will complement LPKO EBV to establish which mutants restore which phenotypes. This will identify candidate mediators of those phenotypes, which can be tested by knockdown or overexpression. We will establish whether enhancement of EBNA2 function plays a significant role in gene regulation, by altering expression of Sp100, NCoR and HDAC4, and by analysing a recombinant EBV encoding S36 mutants of EBNA-LP. Finally we will use chromatin immunoprecipitation to reveal mechanisms of gene regulation by EBNA-LP and the proteins that mediate its effects. This program will integrate existing knowledge of EBNA-LP interactions with its biological role, providing mechanistic insights for future application.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: Investigating the clinical use of 13-valent pneumococcal conjugate vaccine in childhood Acute Lymphoblastic Leukaemia
Funder: Department of Health (England)

Abstract: Background Acute Lymphoblastic Leukaemia (ALL) is the commonest malignancy of childhood and now has a long-term survival of over 80%. These high cure rates are achieved with treatment protocols entailing 2-3 years of chemotherapy during which children are significantly immunosuppressed and at risk of life-threatening infection. In particular, the risk of invasive pneumococcal disease is reported to be between 10 to 50 fold that of healthy children. Conventional polysaccharide pneumococcal vaccines are poorly immunogenic in immunosuppressed children. New pneumococcal conjugate vaccines (PCV) are more immunogenic, and have been shown to be safe and effective in some groups of immunosuppressed children. However, data on their use in children receiving chemotherapy is still lacking. Aims The primary aim of this project is to investigate whether a 13-valent PCV (Prevenar 13, 13vPCV) can be used to achieve protective levels of anti-pneumococcal antibodies in children who are receiving, or have recently completed, treatment for ALL. Secondary aims of the project are to characterise in detail the immune responses generated in response to the vaccine and to correlate this with immune status prior to vaccination. In addition the impact of vaccination on the nasal carriage of pneumococcal serotypes will be investigated. Plan of Investigation This study will be a non-randomised, open-label study in 3 paediatric oncology centres (Southampton, Royal Marsden and Great Ormond Street). There will be 3 study groups: children receiving maintenance chemotherapy for ALL, children who have recently completed treatment, and children who have completed treatment 6 months earlier. We plan to recruit 120 children (40 per group) over a period of 2 years. Children will receive a single dose of 13vPCV. The primary endpoint will be serum concentrations of antibody to the 13 pneumococcal serotypes (pre-vaccination and at 1, 2 , 6 and 12 months). Planned secondary assays include lymphocyte subsets and immunoglobulin subclasses, functional antibody assays and serial monitoring of nasal carriage of pneumococcal serotypes. Potential Impact This study has the potential to significantly reduce the incidence of severe, potentially life-threatening, infections in children with ALL and will provide evidence on which to base a PCV vaccination guidelines for this population. It is hoped that this study will provide evidence that PCV can be used to generate protective pneumococcal immunity in children with ALL. If this is the case, PCV vaccination will be offered to all children receiving treatment for ALL. In addition, the information gained regarding response to vaccination in these children will inform vaccination against other infectious diseases in children receiving chemotherapy


Research activity codes: 3.4 VACCINES
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: Final development and field testing of scripted consultations for human papillomavirus (HPV) tested women in the National Cervical Screening Programme
Funder: Tenovus Cancer Care

Abstract: Cervical cancer is a rare consequence of specific types of the commonest sexually-transmitted infection (STI) called human papillomavirus (HPV). UK Cervical Screening Programmes are changing to include a test for these HPV types in women who have a borderline or mildly abnormal test result. Instead of having frequent repeat tests, women who have HPV will be referred for treatment straight-away (colposcopy); women who have mildly abnormal cervical screening test results and don’t have HPV won’t need treatment or follow-up and will have their next routine screening test 3-5 years later. Although minor abnormalities of the cervix can be easily treated, women are often very upset by an HPV diagnosis. Few women know about HPV and many don’t read the information sent, much of which doesn’t pass a plain English test. They worry about having an STI, blame themselves, doubt their partner’s fidelity, fear effects on fertility, and find it difficult to confide in anyone. Women who test negative may be concerned about their lack of follow-up. Because scientific explanations about HPV are complex, it’s difficult for doctors and nurses to share information in a short appointment. Our team has developed a full set of educational messages, backed up by science. We want to check, through focus group discussions with women, which messages are most helpful and how best to phrase them in brief and readable scripts for doctors and nurses to use. We will then test them with a small group of women who have experienced an abnormal cervical screening test result and HPV testing. Although minor abnormalities of the cervix can be easily treated, women are often very upset by an HPV diagnosis. Few women know about HPV and many don’t read the information sent, much of which doesn’t pass a plain English test. They worry about having an STI, blame themselves, doubt their partner’s fidelity, fear effects on fertility, and find it difficult to confide in anyone. Women who test negative may be concerned about their lack of follow-up.


Research activity codes: 4.3 INFLUENCES AND IMPACT;7.1 INDIVIDUAL CARE NEEDS
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: Characterisation of the interactions between the KSHV ORF57 protein and the human TREX complex
Funder: Wellcome Trust

Abstract: Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncovirus responsible for the formation of Kaposi's sarcoma (KS). Tumour formation is closely associated with immune suppression1 and shows an epidemic-like morbidity and high mortality in patients with AIDS. Concurrent with the HIV epidemic approximately 17% of the population in Sub-Saharan Africa develop KS. Presently, KS is the most common type of cancer in Africa. The KSHV ORF57 encodes a multifunctional protein essential for virus replication. It recruits the human transcription/export (hTREX) complex to form an export competent viral ribonucleoprotein particle (vRNP), in order to facilitate nuclear export of viral intronless mRNAs. We have recently shown for the first time that CIP29, a newly identified member of the hTREX complex, is also part of the ORF57-mediated vRNP. To date, the role of CIP29 within the hTREX complex remains to be elucidated, although speculations suggest that CIP29 functions as an accessory factor to the DEAD-box helicase UAP56. Understanding the role of CIP29 in both the hTREX complex and the vRNP may have important implications for viral pathogenesis and will aid the development of new treatments. Therefore, this project has the following objectives: 1) Characterisation of the functional significance of the ORF57/CIP29 interaction. 2) Determination if inhibition of ATP-dependent RNA helicase UAP56 using ring expanded nucleosides affects KSHV mRNA export and replication. 3) Elucidation of the role of other putative members in the hTREX complex and their role in ORF57-mediated nuclear export of viral intronless mRNAs.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: Study of hypoxia-inducible mrRNAs and their role in the pathogenesis of KSHV -induced tumors
Funder: Wellcome Trust

Abstract: Kaposi sarcoma-associated herpesvirus (KSHV) is one of seven human cancer viruses. This virus causes Kaposi's sarcoma, a cancer commonly occuring in AIDS patients, as well as primary effusion lymphoma and Castleman's disease. Oxygen deprivation (hypoxia) induces lytic replication of KSHV and production of angiogenic factors. There is evidence that hypoxia may affect KSHV and its tumor induction in other ways as well. In general hypoxia plays a significant role in cancer progression and is known to cause a change in the expression of a number of mRNAs and microRNAs associated with cancer. The function of hypoxically induced microRNAs in KSHV induced tumors will be investigated by identifying their tumor specific expression profile and their target mRNAs.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: PTTG, PBF AND p53 IN HEAD AND NECK CANCER
Funder: Wellcome Trust

Abstract: There has been a steady increase in the incidence of human papilloma virus (HPV) related oropharyngeal cancer in many Western countries, with a doubling of incidence over the last 10 years. HPV-oropharyngeal cancer occurs in younger patients than HPV negative disease, and is less commonly related to smoking. Unlike HPV-negative disease, the biology of HPV-positive oropharyngeal cancer is characterised by p53 degradation, retinoblastoma RB pathway inactivation, and p16 upregulation. Multiple studies have now reportedthat the proto-oncogene PTTG is over-expressed in head and neck cancer, with PTTG over-expression generally predicting higher pathological stage, more extensive lymph node metastasis and reduced survival. Together with its binding partner PBF, PTTG interacts with p53 and alters its functionality. We hypothesise therefore that the interacting proteins PTTG and PBF, which are over-expressed in head and neck cancer and bind p53, are critical to the aetiology of HNC. Our key goals therefore will be to determine the relationship between PBF, PTTG and p53 expression in human oropharyngeal tumours; to assess how p53 might regulate PBF in vitro; to dissect the contributions of PBF and PTTG to p53 ubiquitination and half-life; to examine the down-stream functional implications of altered PBF and PTTG expression in terms of apoptosis and genetic instability; and to challenge key observations of the project in primary cells from PBF and PTTG knock-out mice.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: DNA patents beyond clinical genetics: HPV testing and cervical cancer screening in China, the UK and USA. A comparative investigation of the bioethics of biomarker IP and its implications for public policy.
Funder: Wellcome Trust

Abstract: Should we be able to patent genes? Critics say that gene patents hinder scientific research and make it more difficult for patients to get access to high-quality genetic testing, and they argue that our genetic make-up is the common inheritance of humanity not something to be owned by private corporations. Supporters of gene patents say they are vital protection for private investment in research and that without them many valuable new genetic tests would never be developed. The debate has raged for over a decade but we have little evidence to help us work out how best to respond. This project would look at a widely used test for the detection of cervical cancer, to understand how DNA patents have affected the way in which the test was developed, the quality of the tests which are available and the ease with which women can access the tests. We hope to get a broad understanding of this question by looking not just at the role of DNA patents but at the many different factors which affec t test development and test use and we will compare the situation in different countries to understand whether the interplay of these factors varies across countries.


Research activity codes: 4.4 POPULATION SCREENING
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: Characterisation of anti-inflammatory virulence determinants; their role in Helicobacter pylori persistence and gastric cancer
Funder: Wellcome Trust

Abstract: Stomach cancer is the second leading cause of cancer-related deaths worldwide. The most significant risk factor is infection with the bacterium, Helicobacter pylori, which is present in over 50% of individuals worldwide. Clinical manifestations of infection by H. pylori can vary from inflammation of the stomach lining to stomach ulcers and stomach cancer. What causes the transition of H. pylori from a relatively harmless bacterium to a cancer-causing agent is still not well understood. My pre liminary research suggests that certain proteins, present in a wide range of bacteria including H. pylori, are able to suppress host immunity leading to anti-inflammatory responses. My research proposal will characterise the molecular basis for these interactions and investigate how these interactions aid survival of H. pylori within the stomach. This research will further our understanding of H. pylori infection identifying novel avenues for the prevention and treatment of severe gastric diseas e.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFECTION
Title: The NKG2D pathway in hepatitis B associated hepatocellular carcinoma in a highly endemic setting
Funder: Wellcome Trust

Abstract: Hepatitis B is a life-long viral infection of the liver common throughout the developing world including sub-saharan Africa. It is an important cause of liver failure as well as 50% of the world's liver cancer. Treatments do not cure the disease or prevent the development of liver cancer. NK cells are partof the immune system which are abundant in the liver and can kills virus infected cells and cancer. They do this by detecting the presence of particular proteins on liver cells, using a number of receptors. One of the most important receptors is NKG2D. In hepatitis B infection NK cells fail to kill infected liver cells and do not prevent cancer. Preliminary work has suggested that NK cells cannot kill liver cancer cells because the cancer cells shed proteins that are able to bind NKG2D, deactivating it. Using blood and liver samples from a group of newly-diagnosed hepatitis B patients in the Gambia I propose to demonstrate this effect on NK cells. Using cancer cells inthe laboratory I will replicate the effect seen in people and examine ways to overcome it using drugs, removing the shed proteins and modifying NK cells.


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