NIHRDataInsights/HRCSData huggingface dataset:
Title: Characterisation of the deubiquitylase USP8 as a regulator of anti-apoptotic signalling pathways
Funder: Wellcome Trust

Abstract: Ubiquitylation is a major post-translational modification that regulates most cellular processes including DNA-repair and cell division. This modification can be reversed by one of 75 deubiquitylases (DUB) encoded in the human genome. DUBs are currently being assessed as potential drug targets for the treatment of many human pathologies including cancer. This project sets out togain detailed information on the role of the deubiquitylase USP8 in regulatingOur key goals are:nalling. 1. To characterise the relationship between the deubiquitylase USP8 and the panti-apoptotic kinase AKT/PKB. 2. To identify and characterise new interaction partners of USP8 in cells, ibiwith particular relevance for AKT-dependent cell survival pathways. 3. To explore a synthetic lethality approach combining USP8 depletion with inhibitors of the PI3K and AKT pathway in a panel of isogenic cell lines carrying different oncogenic mutations (EGFR, PI3K, PTEN-/-), with the long-term aim of assessing USP8 as a candidate drug target for combination therapy in cancer treatment.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS
Title: Molecular and Cellular Biology
Funder: Wellcome Trust

Abstract: AMPK is a known sensor of cellular energy status. Once activated by increases in AMP and/or ADP, AMPK promotes ATP-producing catabolic pathways and switchesoff ATP-consuming anabolic pathways. AMPK activation occurs through two different mechanisms, triggered by increased AMP/ADP or Ca2+ and involving increased phosphorylation of Thr172 within the ? subunits by the two major upstream kinases: the tumor suppressor LKB1 and the Ca2+/calmodulin-dependent protein kinase, CaMKK . Apart from these classical activation pathways, other "non-canonical" pathways have been proposed. During my 3-Year PhD project I will try to determine how AMPK is activated both by oxidative stress and DNA-damaging agents used for cancer treatment. This work aims to elucidate thepossible importance of AMPK in the oxidative stress response, as well as in the mechanism of action of some anti-cancer drugs. The main objectives of thisproject will be: 1) to determine the precise mechanism by which oxidative stress activates AMPK ; 2) to evaluate if DNA-damaging agents activate AMPK through a CaMKK -dependent me3) to verify if DNA-damaging agents activate AMPK also as a result of oxidative s4) to determine the source of the nuclear Ca2+ that activates CaMKK and hence AMPK.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;5.1 PHARMACEUTICALS
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS
Title: PDGF as a cell autonomous regulator of Epithelial-to-Mesenchymal-Transition (EMT) in neural crest cells.
Funder: Wellcome Trust

Abstract: A defining characteristic of neural crest (NC) cells is the epithelial-to?mesenchymal transition (EMT) they undergo to segregate from the neural tube to start migration. EMT is a cellular process converting non-motile epithelial cells to motile mesenchymal cells, showing strikingly common characteristics in metastatic cancer cells and NC cells. Preliminary data suggests that PDGF signalling is required cell-autonomously for NC cell migration in Xenopus laevis embryos whereas PDGF loss-of-function is sufficient to inhibit EMT in in vitro cultures. The proposed project aims to investigate cellular and Molecular mechanisms governed by PDGF during EMT of NC and to extrapolate the gained knowledge onto cancer cell metastasis. We will perform high-resolution time-lapse video analysis of NC EMT comparing gain-of-function and loss-of-function of PDGF in vivo and in vitro. Further study will aim to identify the pathways and downstream targets triggered by PDGF signalling. Finally the gained knowledge will be used to study EMT in cancer cell lines and a transparent zebrafish model allowing the live-imaging


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS
Title: Elucidating BAP1-miRNA regulatory networks
Funder: Wellcome Trust

Abstract: BAP1 is a deubiquitylase enzyme that is essential for normal embryonic development, and is a tumour suppressor that is inactivated in many cancers. In some cancers like mesothelioma BAP1 is commonly mutated, but non-small celllung cancers can lose BAP1 protein expression through unknown mechanisms. BAP1has many cellular roles, predominantly in DNA repair and transcriptional regulation. In this project we will explore for the first time the correlativeand functional relationships between BAP1 and cellular miRNAs. We have established isogenic mesothelial cell lines with clinically relevant mutationsengineered into one or both of the BAP1 alleles, to determine the transcriptional and protein-level consequences. Our preliminary data from these cell lines suggest that reduction in BAP1 leads to altered expression ofseveral cancer-associated miRNAs. Key goals are to: (1) Identify miRNAs that regulate BAP1 and may be altered in cancer, (2) Expand our panel of BAP1 isogenic cells, (3) Determine the extent of the microRNA-ome that is dependenton BAP1 status using PCR screens and nanostring technology in these isogenic cells and other cancer cell lines, (4) Investigate the functional relevance ofBAP1-dependent miRNAs on cellular physiology.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS
Title: Investigating the role of Mitf in the resistance of melanoma to targeted therapies
Funder: Wellcome Trust

Abstract: Approximately 90% of malignant melanomas are driven by constitutive activationof the ERK/MEK/MAP-kinase (MAPK) pathway. Inhibitors targeting the MAPK pathway are potent, but responses are transient due to the development of resistance. Various resistance mechanisms have been identified, amongst them mutations in the MAPK or PI3-kinase (PI3K) pathway, and amplification of the MITF gene. MITF is a bHLH-ZIP transcription factor that regulates genes involved in survival and proliferation, but also the majority of melanoma differentiation genes. Importantly, melanoma-differentiation gene expression correlates with increased immune-cell infiltration, which can improve immunotherapy approaches. On the other hand, we found that MITF, by regulating proliferation and survival genes can contribute to resistance to MAPK pathway inhibitors. Thus, identifying mechanisms that direct MITF to melanoma-differentiation genes but not proliferation and survival genes could help developing strategies to prevent resistance and render melanoma cells susceptible to immunotherapy. This project aims to dissect how MITF is regulated in drug tolerant/resistant melanoma on treatment with MAPK and PI3K inhibitors, and how this impacts on its transcriptional activity towards differentiation, proliferation and survival genes. Findings from protein-biochemical and functional analyses in cell culture systems will be validated in patient short-term cultures and in xenograft studies in vivo.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS
Title: Transcriptional regulation of hematopoietic self-renewal, lineage specification and leukemogenesis
Funder: Medical Research Council

Abstract: The purpose of the proposed Programme is to conduct an integrated research projects addressing how intrinsic regulators (transcription factors) and extrinsic cues (cytokines) interact to control the lineage commitment and self-renewal of hematopoietic cells, specifically through modulation of of their lineage priming and gene expression. We will also investigate the role played by these processes in the formation of leukemic stem cells in CEBPA mutant AML. To achieve this we will use conditional genetics to specifically eliminate intrinsic regulators (GATA-1, FOG-1, C/EBPa) and activate cytokine/growth factor receptors (Flt3, GM-CSFR, EpoR), and generate genetically precise models of human AML. The analysis of the hematopoietic system by flow cytometry will be complemented by characterization of the transcriptional changes induced, as well as studeis of the kinetics by which leukemic stem cells arise, and how this is modulated by extrinsic signals.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS;BLOOD
Title: Biomedical sparse parametric imaging.
Funder: Wellcome Trust

Abstract: Many of us know someone who has had to visit the hospital for a scan . There are several different types of scan, but all involve taking pictures of the inside of the body. These pictures are viewed by a specialist doctor who can identify any disease and recommend treatment. It is also possible to make measurements from the pictures that scans provide. For example, it is possible to measure how much blood a patient s heart can pump around the body (patients whose hearts are failing will be a ble to pump less blood than healthy people). Another measurement that can be made from pictures made by scans is the leakiness of the blood vessels inside a tumour (this is useful for testing new anti-cancer drugs because effective drugs tend to reduce blood vessel leakiness). Unfortunately, it is currently very difficult and expensive to make these kinds of measurements, so they are not available at most hospitals. This project aims to develop an easier way to make these kinds of measurement s, so that they can be made available in most hospitals.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;4.5 RESOURCES AND INFRASTRUCTURE (DETECTION)
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS;CARDIOVASCULAR
Title: The overall objective of the Group is to identify critical features of radiation-induced DNA damage such as clustered DNA damage, including complex DNA double strand breaks, which are
Funder: Medical Research Council

Abstract: Ionising radiation may be considered as a two-edged sword since it can induce cancer and other adverse responses in normal tissue or alternatively it may lead to cellular inactivation of tumour cells, of considerable importance in radiotherapy. Ionising radiation is also one of the most effective cancer treatments and it is believed that its therapeutic effect in part is attributed to DNA damage and specifically to complex DNA damage where several DNA lesions are induced in close proximity. Therefore the overall objective is to identify critical features of radiation-induced DNA damage such as clustered DNA damage and complex DNA double strand breaks, which are seen as signatures of ionising radiation, and how they may compromise the cell’s ability to maintain genome stability, leading to mutations/tumourogenesis or cellular inactivation involving pathways that may be exploited for cancer therapy. These two outcomes are of relevance to radiation oncology and highlight the dual nature of the effects of radiation. Although information is emerging on the difficulties encountered in repairing clusters of lesions in mammalian cells, very little is known about how they are initially recognised in human cells. Additionally, genomic DNA is tightly packed with histones to form chromatin so that some DNA damage induced by IR may be masked from the surrounding environment. Depending on its location in the chromatin, unwinding or remodelling is required to reveal the damage and accessibility to DNA repair enzymes. To address the objectives we plan to:- • Identify the efficiency of the repair pathways and nucleosome remodelling factors involved in the repair of complex DNA damage when present in a mononucleosome model using biochemical approaches. • i) extend understanding on the orchestrated recruitment of repair/signalling molecules to base damaged sites, particularly those pathways involved in repair of clusters, and ii) identify in real time those proteins recruited during the repair of complex DNA DSB in living mammalian cells. • In collaboration with Boris Vojnovic’s Group, develop a novel application of confocal microscope coupled with the newly developed linear accelerator to explore real time recruitment of proteins to cellular damage induced by a millisecond pulse of ionising radiation. This development will provide an important technique for future real time studies in mammalian cells. • To develop an understanding of radiosensitisation by nitric oxide based from our preliminary findings that radiation induces novel types of DNA damage. The outcome of these studies may contribute to identification of repair pathways for therapeutic exploitation and to the potential health effects to normal tissue


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS;CONGENITAL DISORDERS
Title: DNA double strand breaks and genome stability
Funder: Medical Research Council

Abstract: DNA double strand breaks (DSBs) are highly genotoxic lesions, arising from exposure to ionizing radiation (IR). While normally repaired, such lesions can also promote chromosomal rearrangements and tumourigenesis through oncogene activation and loss of heterozygosity (LOH), resulting in tumour suppressor loss. Despite recent advances, significant gaps remain in our knowledge of DSB repair, and how this relates to genome stability. Our recent studies in fission yeast have identified a number of genes that promote efficient homologous recombination (HR) repair and suppress break-induced chromosomal rearrangements and LOH. A number of these genes are tumour suppressor homologues, including ATR, NBS1, MRE11, BLM, 53BP1 and CHK1 which function directly or indirectly to facilitate efficient HR. Our findings support a general model of break-induced chromosomal rearrangements in which extensive end processing associated with failed or inefficient HR repair promotes chromosomal rearrangements and genome instability. We are currently examining the mechanisms and determinants of efficient DSB repair that maintain genome stability. We are also determining the underlying mechanisms of break-induced chromosomal rearrangements and their genetic requirements. Further, we are developing technology to extend our findings from fission yeast to determine whether these tumour suppressors function analogously to suppress break-induced LOH in mammalian cells. These studies, using both fission yeast and mammalian cells, will contribute to our understanding of the mechanisms that maintain genome stability in response to DSBs in eukaryotic cells. Greater knowledge of these mechanisms will provide important insights into how these events drive tumourigenesis, and will enhance our ability to predict and ultimately modulate the cellular responses to ionising radiation, which will be of significant clinical value.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS;CONGENITAL DISORDERS
Title: Viral silencing and immune evasion pathways
Funder: Wellcome Trust

Abstract: Studying how viruses manipulate their host cell machinery provides insight into both viral function and cellular regulation. Invasion by viral DNA threatens cellular integrity and therefore needs to be detected and suppressed. As the default cellular response is to silence incoming DNA, how do viruses subvert and exploit this hostile environment to their advantage? Our identification of the ‘Human Silencing Hub’ (HUSH) as a novel epigenetic transcriptional repressor complex, responsible for silencing newly integrated retroviruses, has motivated us to further investigate chromatin regulation of viral infection. We wish to: (i) Understand how HUSH silences newly integrated viral DNA. (ii) Determine how lentiviruses antagonize chromatin-mediated repression and identify shared mechanisms by which unrelated, non-integrated viruses counteract silencing. (iii) Understand how and why the lentiviral-Vif accessory protein manipulates the host cell phosphoproteome. To help address these questions we have developed and optimised powerful genetic and proteomic screening technologies. Repurposing CRISPR-Cas9 will enable RNA-guided genome manipulations, including selection of informative point mutants and isolation of DNA sequence-specific regulatory proteins. Together these approaches provide a discovery platform to determine how repressive heterochromatin is established and maintained, how viruses manipulate their chromatin environment and ultimately to develop new therapeutic tools to enable their eradication.

Lay abstract: Invasion of our cells by foreign DNA threatens cellular integrity. Despite all organisms suppressing foreign DNA to protect their genome, DNA and RNA viruses have evolved to enter host cells, and replicate undetected by the immune system. We wish to understand how cells silence DNA, and conversely, how viruses overcome this suppression. Our recent efforts to understand silencing of HIV-like viruses identified ‘HUSH’, a multi-component protein machine which creates a repressive environment that silences retroviruses. Retroviruses uniquely integrate their DNA into host genes, explaining why HIV is so difficult to eradicate. Our aim is to understand how HUSH silences viral DNA and how proteins from these retroviruses manipulate their host cells to both avoid silencing and evade immune detection. Our application of cutting-edge genetic and proteomic technologies puts us in an ideal position to interrogate these host-virus interactions and ultimately to develop new therapeutic tools to manipulate this environment

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS;INFECTION
Title: Innate memory: What is the biological significance of memory NK cells in infection and cancer?
Funder: Wellcome Trust

Abstract: Our goal is to study the newly discovered ?memory? NK cells. The three main aims are: 1. Define their lifespan and effector functions 2. Determine their biological significance in viral infections and cancer 3. Characterize their transcriptome


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS;INFECTION
Title: Oxygen and immune response
Funder: Wellcome Trust

Abstract: Our goals are centered on understanding how hypoxic response affects immunity. The experiments described are in three key areas: The first of these is myeloid immunosuppression by hypoxia, and the mechanisms of immunosuppression that are regulated by the hypoxia inducible transcription factor (HIF). Here, we will characterize and determine the range of factors produced by M1- and M2-polarized macrophages in HIF1a- and HIF2a-dependent manners by macrophages; we will ask how HIF-driven nitric oxide (NO) homeostasis regulates immunosuppression in hypoxia; and we will determine how HIF-driven myelosuppression acts in a model of acute and chronic viral infection. In the second aim, we will focus on cytotoxic T cell activation by hypoxia and HIF. Here, we will address the role of directed HIF expression on T cell function; and the differential metabolism of T cells as regulated by the VHL- and FIH-mediated control of HIF; including immunometabolic analysis of how those two factors affect T cell function. Our third aim concerns the role of the immunometabolite 2-hydroxyglutarate, and here we will carry out work on enantiomer-specific biology of the metabolites; map chromatin and RNA modifications induced by 2-HG; and investigate the potential use of 2-HG to enhance CAR-T therapies.

Lay abstract: Our research considers the role of oxygen sensing in the immune system, and in particular, how changes in the amount of oxygen available in tissues act in immune responses to infections and to cancer. We will address how low tissue oxygen levels (hypoxia) can suppress some aspects of immune response, while at the same time can induce and accentuate other important immune cell functions. The puzzling nature of the dual nature of hypoxia's effects on immunity are both challenging to investigate, and important to understand. An exploration of the immune response to hypoxia may allow us to alleviate unhelpful immune suppression and activate specific immune responses that could increase the efficiency and potency of anti-cancer immune therapies.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS;INFECTION;INFLAMMATORY AND IMMUNE SYSTEM
Title: Decision-making by lymphocytes
Funder: Wellcome Trust

Abstract: It was recognized sixty years ago that a “trigger mechanism” must initiate immune responses. Today, however, not even the broad features of the mechanism are fully agreed, despite its intrinsic scientific interest and the remarkable clinical utility of modulating lymphocyte behaviour. We do know, however, that it encompasses two separate events: receptor triggering per se, and the integration of multiple triggering outputs. Breakthrough developments in fluorescence imaging mean that we can now study molecular behaviour at cell-cell interfaces at single-molecule resolution, in real time. This means that we can directly test whether TCR triggering is explained by a theory relying on the local, physical exclusion of phosphatases from sites of receptor engagement and phosphorylation, called the kinetic-segregation model. We will explore how 'close-contact' formation affects the interplay of local signaling molecules, and test our theory using quantitative models of receptor signaling. We will also study the emergent properties of the types of modular networks known to mediate downstream signaling in T cells and, building on these findings, test a new, simple theory of signal integration. This programme of work will produce a fuller understanding of decision-making by lymphocytes, and a richer framework for thinking about immunotherapy.

Lay abstract: Our immune systems respond to viruses and other harmful threats by triggering the replication of those white blood cells best-suited to neutralizing each specific threat. Remarkably, however, no-one properly understands how each white blood cell decides to respond, despite the importance of the mechanism. For many years, we have studied the behaviour and functions of proteins present on the surfaces of white blood cells, and proposed that changes in their organization are a key part of how immune responses start. Alongside other new types of experiments we will do, exciting developments in microscopy mean that we can now finally see whether the proposed re-organization takes place at the start of immune responses, allowing us to directly test our theory. Having determined how they start, we will be much better placed to boost helpful immune responses against, for example, cancer, and to block harmful ones that cause diseases such as diabetes.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;CANCER AND NEOPLASMS;INFLAMMATORY AND IMMUNE SYSTEM