NIHRDataInsights/HRCSData huggingface dataset:
Title: A chemical genetic approach to identify pharmacological targets co-operating with melanoma drivers and their validation as combinatorial therapeutic targets
Funder: Cancer Research UK

Abstract: BACKGROUND: Melanoma incidence is still rising, making it the 6th most prevalent cancer in the UK. Metastatic disease is largely incurable. 15% of those diagnosed with melanoma will succumb to their disease, accounting for approximately 2000 deaths every year in the UK and, on average, 20 years of life lost per death. Notwithstanding recent clinical success through targeting mutant BRAF, new therapeutic avenues must still be explored if advanced melanoma is to be cured. The extensive reprogramming of intracellular signalling, metabolism and gene expression in advanced melanoma cells makes target selection a significant challenge. Screening of biologically active compounds in a whole-organism cancer model represents an alternative, efficient and unbiased method of probing the proteome for therapeutic targets. Increasingly, combining drugs is seen as a way of improving efficacy; an added challenge is to identify safe and effective drug combinations. AIMS & OBJECTIVES: The overall aim of our proposal is to identify pharmacological targets that co-operate with melanoma drivers to induce melanoma and to subsequently validate them as combinatorial therapeutic targets. Our specific objectives are: 1. To identify small molecule hits from libraries of biologically active compounds that in combination with PD184352 or NVPBEZ235 selectively antagonize melanoma onset in a RAS-driven zebrafish transgenic melanoma model we have recently developed. 2. To assess the ability of hits to antagonize the proliferation or survival of human melanoma cells in 3D culture models and to inhibit melanoma growth in zebrafish and mouse models. 3. To assess the mode of action of hits through gene knock-down approaches as well as by target identification. METHODS: Libraries of compounds of known biological activity, including licensed drugs, will be screened for Hits that suppress the development of melanoma in V12RAS-expressing zebrafish embryos when combined with either PD184352 (a MEK inihibitor) or NVPBEZ235 (a dual PI3K/MTOR inhibitor). Activity of the combined agents will then be confirmed in 3D culture models of human melanoma cells, as well as in tumours in adult zebrafish and human melanoma xenografts in mouse. The mechanism of action of Hits will be investigated by gene knock-down, but since the targets of Hits may not always be known, we also propose employing Magic tag technology to identify putative targets in these instances. HOW THE RESULTS OF THIS RESEARCH WILL BE USED: Validated therapeutic targets could serve as entry points for future rational drug design projects. Alternatively, the screen may repurpose existing drugs.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Breast tissue composition at young ages and its determinants: a study nested within a British birth cohort
Funder: Cancer Research UK

Abstract: 1) Background Breast tissue composition is a strong and independent biomarker of susceptibility to breast cancer (BC), which accounts for a substantial proportion of cases in developed countries. Typically, breast tissue composition is assessed by the amount of radiodense (fibroglandular) tissue in the gland as measured on a mammogram. The mammary gland is susceptible to carcinogens early in life. However, little is known about the distribution of breast tissue composition at young ages, and of its prenatal and early life determinants, because mammography, which involves exposure to radiation, cannot be performed in young women. 2) Aims & Objectives The main aim of the study is to use magnetic resonance (MR), which is radiation-free, to examine breast tissue composition in young women and its determinants. Specific aims are to investigate variations in breast tissue composition in relation to: (i) markers of foetal, childhood and adolescent growth; (ii) concurrent levels of endogenous sex hormones and growth factors; (iii) genetic markers; and (iv) mammographic density in their mothers. 3) Methods We shall conduct a study nested within the Avon Longitudinal Study of Parents and Children (ALSPAC) - a population-based cohort of children born in 1991-2 in Avon, UK, with detailed questionnaire data and anthropometric measures collected at birth and throughout infancy, childhood and adolescence, as well as genotyping and sequencing data. The study population will comprise 500 women aged ~20 years and their mothers. Young women will undergo a breast MR scan and detailed hormone measurements. A genome-wide association study (GWAS) will be performed to identify common variants associated with breast tissue composition; genome-wide sequencing data will also be analysed. 4) How the results of this research will be used The findings will further our understanding of the biology of breast tissue composition in young women, its determinants, and the links between this biomarker and BC risk. Such findings may lead to the development of novel approaches for BC prevention as, unlike many other risk factors, breast tissue composition is modifiable by hormone interventions. The genetic data will contribute to an international collaborative effort on the genetics of breast tissue composition. Newly-identified variants associated with breast tissue composition will help our understanding of the biological determinants of breast tissue composition and will be ideal candidates for BC association studies, with such studies requiring much less stringent statistical criteria than those used in current hypothesis-free BC GWAS.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Investigating the role of LIMD1 loss in the aetiology of lung cancer stem cells
Funder: Cancer Research UK

Abstract: BACKGROUND: Our group is an internationally recognised authority on the role of Lim domains containing protein 1 (LIMD1) in lung cancer. To date, we have shown: (1) LIMD1 is localised to chromosome 3p21.3, a region that commonly undergoes early homozygous deletion, loss of heterozygosity and epigenetic silencing in many carcinomas, including the lung. (2) LIMD1 protein expression is reduced in 80% of lung adeno and squamous cell carcinomas. (3) Stable expression of LIMD1 in lung cancer cell lines significantly reduces their ability to form lung tumours in mice. (4) Limd1-/- knockout mice are predisposed to chemically-induced lung adenocarcinomas and (5) Genetic inactivation of Limd1 in mice heterozygous for oncogenic K-Ras(G12D) show markedly increased tumour initiation, progression, and mortality. To determine how LIMD1 works as a TSG and advance our understanding of the early molecular pathogenesis of lung cancer we have identified LIMD1 as a critical regulator of microRNA (miRNA)-mediated gene silencing. Depletion of endogenous LIMD1 results in loss of miRNA-mediated gene silencing. AIM/OBJECTIVES: The above discovery prompting the following hypothesis: ‘Squamous cell carcinoma (SCC) of the lung is a disease of cancer stem cell formation and LIMD1 loss plays a critical role in mediating this transition through deregulation of miRNA-silencing’. To test our hypothesis we will recapitulate the LIMD1 loss that is observed in SCC, in vitro, using human bronchial epithelial cells (HBEC). We will then scrutinize the phenotype in vitro and in vivo for evidence of transformation. METHODS: We will use Lentiviral-driven vector systems to obtain both stable shRNA-driven LIMD1 knockdown in HBECs. We will then perform in vitro and in vivo tumourigenicity assays. The functional readout of which will then be used to correlate with miRNA/mRNA profiles obtained from Deep Sequencing of the same HBEC lines. i.e. align the transformed phenotype with its respective RNA profile and examine how this is influenced by LIMD1 loss. HOW THE RESULTS OF THIS RESEARCH WILL BE USED: These results will indicate the functional significance of LIMD1 loss in human lung epithelia. Furthermore, we will identify ‘LIMD1-loss’ specific downstream miRNAs and signalling pathways to investigate with respect to lung cancer biology with the aim of using these to develop methods for increasing early detection and novel ‘early disease’ treatments.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Models of melanoma driven by oncogenic Kras
Funder: Cancer Research UK

Abstract: Background Melanoma is a potentially fatal skin cancer that causes ~2,000 deaths in the each UK year. There have been tremendous advances in our understanding of melanoma biology in recent years, with RAS/RAF/MEK/ERK signalling emerging as a particularly important pathway. To understand melanoma biology, we have developed mouse models of melanoma driven by oncogenic Kras (G12DKras). When expressed at endogenous levels, G12DKras induces melanoma with a median latency of >15 months. However, when G12DKras is expressed with kinase-dead Braf (D594ABraf), tumours arise with a median latency of ~6 months and importantly, these tumours metastasise to the spleen. These models offer an exciting opportunity to study Kras-driven melanomagenesis and metastasis in a relevant and tractable genetic model. Relevance to Cancer There are over 10,000 cases of melanoma each year in the UK and melanoma incidence almost doubles every decade. In recent years, BRAF and RAS have emerged as the most important oncogenes in melanoma, and a full understanding of both RAS-driven and BRAF-driven melanomagenesis and metastasis is essential to allow development and implementation of therapeutic strategies for this disease. Specific Aims 1. The long latency required for tumour induction by G12DKras alone suggests that additional genetic events are required for Kras-driven melanomagenesis. Our first aim is to identify these co-operating genes and also to identify the co-operating genes that drive metastasis in the G12DKras/D594ABraf tumours. These studies will provide the improved biological understanding necessary to develop new therapeutic approaches for Ras-driven human melanoma. 2. The only known environmental risk factor for melanoma is UV radiation, which could either induce co-operating gene mutations, or provide a permissive micro-environment to drive tumour progression. We shall use our mouse models to address the role of UV radiation in Ras-driven melanomagenesis. Plan of Research Gene-gene interactions: identifying cooperating genes. We shall use Sleeping Beauty-insertional mutagenesis, array-comparative genomic hybridisation (aCGH), gene expression array analysis, and next generation sequencing (NGS) to identify the genes that cooperate with G12DKras and G12DKras/D594ABraf to drive melanomagenesis, and to identify the genes that drive metastasis in the G12DKras/D594ABraf tumours. These genes will be subjected to functional studies using our established in vitro and in vivo assays. Gene-environment interactions: the role of UV. We shall expose G12DKras expressing mice to UV radiation and examine the effects on tumour formation. Comparing tumours from UV-treated and non-UV-treated mice using the approaches described above will allow us to determine how UV affects melanomagenesis and metastasis.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Evaluation of histone methyltransferase inhibitors for neuroblastoma therapy
Funder: Cancer Research UK

Abstract: BACKGROUND:_x000D_ Neuroblastoma (NB) is one of the commonest solid tumours of childhood, and includes a large clinical subset refractory to currently available therapies. In common with other malignancies, loss of gene function resulting from DNA hypermethylation has been shown in NB. To date however, other mechanisms such as histone methylation, and their gene targets have not been characterised. As several novel small molecule drugs capable of specifically targeting components of the repressive epigenetic machinery are now emerging, it is vital to define the full spectrum of repressive marks in NB cells together with the genes they affect. drug induced removal of such epigenetic blocks may represent a new therapeutic option for cancer._x000D_ _x000D_ AIMS & OBJECTIVES:_x000D_ This study will evaluate epigenetic inhibitors for their therapeutic potential on NB cells. In particular, we will compare drug treatments with highest efficacy against cells representative of poor prognosis NB, in parallel with transcriptomic and epigenetic profiling. We will therefore determine which genes/pathways and epigenetic marks are integral to development and maintenance of neuroblastoma. _x000D_ _x000D_ METHODS:_x000D_ This study assess cell growth, differentiation and apoptosis together with array-based gene expression and epigenetic analyses._x000D_ _x000D_ HOW THE RESULTS OF THIS RESEARCH WILL BE USED:_x000D_ By determining which genes and epigenetic marks are important to NB aetiology, and which epigenetic inhibitors, or combinations thereof, are optimal for reactivating silenced genes, we will evaluate potential novel therapies for NB.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Structure-function studies on CCN family of proteins involved in cancer
Funder: Cancer Research UK

Abstract: Cells communicate and control their actions through proteins. One family of proteins that is essential to this process is the CCN family which are involved in different types of cancer. They act as cellular &'masterminds' talking to dozens of other proteins and manipulating the pathways that control critical biological functions. CCN proteins are modular with each of the four different modules conferring defined functions of the protein, such as interactions to specific ligands and effectors. Based on prediction, it appears that the structure of the CCN proteins should have features found in many extracellular matrix (ECM) proteins constructed from a library of commonly used modules. Although the modules have been classified through recognizable motifs, the exact role of each domain in CCN biology is not fully understood. It is unlikely that their function is a direct result of their individual modules acting independently, but rather represents a cumulative effect between multiple modules and target molecules. Although differences in amino acid sequence can lead to large variations in surface charge and substrate binding, the elucidation of the three-dimensional structure is vital to answer many remaining questions surrounding the CCN family of proteins. Despite the importance of CCN proteins in biological processes and disease, thus far there is no structural data on any member of the CCN family, and little data on how CCN proteins interact with protein ligands and effectors. Thus, we have a very incomplete understanding of the molecular mechanisms of CCN proteins and a limited understanding of their functions of CCN proteins. We aim to address these questions. We would like to determine the three-dimensional structures of CCN family of molecules and their interactions with cognate ligands and effectors using structural biology, biochemical and biophysical tools. The proposed structure-function study will answer some important questions about cellular communications and help us gain an insight into how many biological functions operate through the CCN proteins and their receptors. As the CCN proteins are also implicated in cancers with poor prognosis such as pancreatic cancer or aggressive inflammatory breast cancer. It is hoped that the proposed study on this family of molecules could open new avenues for the design of pharmacologically important molecules for therapy.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: CANCER AND NEOPLASMS
Title: New roles for the RelA(p65) NF-kB subunit in cancer
Funder: Cancer Research UK

Abstract: BACKGROUND:_x000D_ Aberrant regulation of the Nuclear Factor kappa B (NF-kB) transcription factor family, together with their activators, the IkB kinases (IKK), plays a critical role in tumorigenesis and the response of cancer cells to therapy. As a consequence, there is much interest in the development of drugs that target the NF-kB pathway, while many treatments currently in clinical use are thought to exert at least part of their effect though inhibition or modulation of NF-kB/IKK signaling. A comprehensive understanding of the NF-kB/IKK pathway is therefore not only required for the development of accurate models of tumorigenesis but also for future cancer drug discovery._x000D_ _x000D_ Two major objectives of our research have been to investigate the function of NF-kB following different forms of DNA-damage and to understand how NF-kB activity is integrated with tumour suppressors. A theme emerging from these studies has been the importance of context and post-translational modifications for NF-kB activity. We have argued that the activities of parallel signaling pathways have a critical role in determining NF-kB dependent transcriptional output and propose that models in which NF-kB activity is always tumour promoting are too simplistic. Rather, tumour suppressors can act to keep the oncogenic activities of NF-kB in check with their loss during tumour development being required to unleash NF-kB’s anti apoptotic and pro-metastatic activities in malignant cancer cells._x000D_ _x000D_ AIMS & OBJECTIVES:_x000D_ We have recently discovered new pathways through which the RelA(p65) NF-kB subunit can contribute to tumorigenesis and the response to cancer therapies. In the next quinquennium we will use these as the basis for a programme of research to:_x000D_ (1) Investigate NF-kB function after DNA damage and define the mechanisms through which the RelA subunit regulates DNA repair through non-transcriptional mechanisms_x000D_ (2) Dissect the mitochondrial and non-mitochondrial pathways through which NF-kB regulates energy production and metabolism_x000D_ _x000D_ METHODS:_x000D_ We will use molecular and cell biological techniques as well as the creation of new mouse models, to determine the physiological role of RelA in these processes and define their significance during tumorigenesis._x000D_ _x000D_ HOW THE RESULTS OF THIS RESEARCH WILL BE USED:_x000D_ Our proposal will advance our knowledge of the mechanisms by which NF-kB regulates two key events in cancer cell biology, DNA repair and mitochondrial activity. This will open up new directions of clinically relevant research, with the potential to enhance the use of both current and future anti-cancer drugs.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Standardization of DWI MRI for quantitative assessment of ovarian cancer and implementation in clinical trials
Funder: Cancer Research UK

Abstract: In advanced ovarian cancer, assessment of response to chemotherapy is based on serial measurements of serum CA125 combined with size evaluation of lesions on morphological imaging. However, measurable morphologic changes often appear late after initiation of even successful cytotoxic treatment. This is even more relevant with the advent of molecularly targeted therapy and anti-angiogenic strategies, which have a primarily cytostatic effect. Further, the diverse morphology of peritoneal disease hampers accurate measurements; lesions are often too confluent and ill-defined or too small to fulfill response evaluation criteria in solid tumours (RECIST) requisites for "measurability". Also, in a 10% subgroup of biochemically "silent" patients, imaging-derived RECIST measurements are the only means of assessing treatment efficacy. CT imaging, though routinely used, has poor tumour to normal tissue contrast and offers only morphological data. Functional imaging methods, such a diffusion-weighted magnetic resonance imaging (DW-MRI) offers improved tumour-to-normal tissue contrast and has shown promise for quantifying early treatment response in ovarian cancer in single-centre studies. This project therefore seeks to develop DW-MRI as a Quantitative Imaging Biomarker for evaluating ovarian cancer metastases and assess its potential in monitoring treatment response in a multi-centre setting. This will involve standardizing DW-MRI for the abdomen and pelvis across multiple centres and platforms, assessing reproducibility of the measurement in patients due for neoadjuvant chemotherapy (cohort 1) and assessing its utility as an early response biomarker in patients with platinum sensitive relapse due to receive therapy with carboplatin (cohort 2). In cohort 1, tissue will be acquired from patients pre and post chemotherapy and apparent diffusion coefficients (ADCs) will be correlated with tissue changes on histopathology in order to link the biomarker with response mechanisms In cohort 2, ADCs after 1 cycle of chemotherapy will be compared in responders vs. non-responders (as defined by performance status, serum CA125 at 6 months and soft tissue response on CT or conventional T2-W MRI). At the end of the project it should be possible to implement a robust and reproducible methodology across multiple vendor platforms in several additional cancer centres. Used clinically, quantitative DW-MRI data will enable identification of residual disease and enable optimization of the timing of surgery as well as allowing more effective adaptation of chemotherapeutic regimens. It would also aid the future design of clinical trials of novel therapeutic agents.


Research activity codes: 4.2 EVALUATION OF MARKERS AND TECHNOLOGIES;4.4 POPULATION SCREENING
Health categories: CANCER AND NEOPLASMS