NIHRDataInsights/HRCSData huggingface dataset:
Title: Derivation and validation of a novel model incorporating PET-CT for predicting malignancy in screen detected lung nodules - The PRECISE Study
Funder: Medical Research Council

Abstract: Problem to be addressed: Pulmonary nodules are a common finding on CT scans and their frequency is increasing due to the implementation of lung cancer screening. In the US there are 1.5million people detected with lung nodules each year. Current nodule management estimates the probability that the nodule is malignant using risk prediction models. However, the existing Herder model (which includes PET) underestimates lung cancer risk and a more accurate model for predicting risk in pulmonary nodules is urgently required. Despite PET-CT being an expensive and limited resource, its role in nodule management has not been fully evaluated. Research questions 1. The sensitivity, specificity, accuracy and cost-effectiveness of PET-CT in screen detected nodules (solid and part solid) using varying cut-offs of SUV threshold 2. The efficacy and cost-effectiveness of PET-CT prior to treatment of screen-detected nodules 3. The clinical utility and cost-effectiveness of a novel nodule risk model including PET-CT compared to current nodule risk predictors 4. The additional clinical utility and cost-effectiveness of PET-CT in patients with multiple pulmonary nodules Methods: An individual patient data (IPD) meta-analysis will be conducted of PET-CT in completed lung screening trials in the US, UK and Europe. This dataset of >8000 patients with nodules will be powered to generate a novel multivariable logistic-regression model to estimate the risk of lung cancer in screen-detected lung nodules, including predictors such as smoking exposure and nodule characteristics. The model derived from the screening trials will then be validated in the SUMMIT trial which aims to recruit 25000 individuals at high risk of lung cancer in London undergoing low dose CT chest by 2021. The cost-effectiveness of using the novel algorithm in a screened population will then be modelled. The model will also be tested in nodules detected in routine practice and in patients with multiple nodules.


Research activity codes: 4.2 EVALUATION OF MARKERS AND TECHNOLOGIES;8.2 HEALTH AND WELFARE ECONOMICS
Health categories: CANCER AND NEOPLASMS
Title: Identifying New Drugs for the Treatment of Castrate Resistant Prostate Cancer: Targeting the Achilles' Heel of the Androgen Receptor.
Funder: Medical Research Council

Abstract: The androgen receptor is a key drug target in advanced and metastatic prostate cancer, a major cause of cancer-related death in men. However, tumour cells become resistant to antiandrogen drugs, while remaining dependent on the receptor for growth and survival. There is, therefore, a need for new drugs to switch-off receptor activity. Our strategy is to develop small molecule inhibitors that bind to a different part of the receptor, the amino-terminal domain (NTD), which is essential for function. Such inhibitors will be effective against receptor splice variants lacking the ligand-binding domain and point mutations that alter the receptor ligand-binding profile, changes that result in the development of castrate resistant prostate cancer. The NTD is intrinsically structurally disordered and therefore not amenable to structure-based drug design. We have screened three libraries of drug-like molecules and have identified novel candidate small molecule inhibitors of receptor function. Two of these hits have been further validated in secondary assays. As these compounds target the NTD they are likely to have novel mechanisms of action from current antiandrogens. We aim to determine and optimise the structure-activity relationships of our two lead chemotypes. We will prioritise one hit series for extensive in vitro/in vivo DMPK studies, and demonstrate efficacy of the most promising candidates against preclinical models of prostate cancers. Our candidate inhibitors will be bench-marked against existing antiandrogens (biclautamide and enzalutamide) and an experimental inhibitor (EPI-001).The outcome will be the optimisation of a 'lead candidate' inhibitor of the androgen receptor-NTD, that can be taken forward for preclinical and clinical studies. The project represents the critical steps towards new drug development, with the potential to improve current treatment modalities for men with advanced prostate cancer.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: IDENTIFYING AND FUNCTIONALLY CHARACTERISING RENAL CANCER DRIVER MUTATIONS
Funder: Medical Research Council

Abstract: Renal cell cancer (RCC) is a common cancer and despite recent improvements in its management the outcome remains poor for many patients. The identification of cancer driver genes is central to understanding carcinogenesis and treating cancer. In RCC few common driver genes are established. The full complement of molecular lesions that cause RCC and explain its diversity is unkown because the search for RCC drivers has focused mainly on coding regions of the genome. The recent availability of whole genome sequencing (WGS) data on RCC on a large-scale through initiatives including the 100,000 Genomes Project (100KGP) offers the opportunity to identify different classes of functional mutations for RCC and decipher their biological impact. Our work programme will comprise three phases: (1) cataloguing the mutational landscape of RCC by analysis of 100KGP, in-house and publicly accessible data; (2) identifying recurrently mutated driver loci (coding, non-coding and copy number) by integrating mutation data with tissue-specific gene expression, epigenetic and topographical data; and (3) functional analyses to validate and delineate oncogenic mechanisms. Identifying novel oncogenic pathways will improve patient stratification for personalising therapy using existing agents and facilitate discovery of novel therapeutic and chemoprevention agents.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Irreversibly Silencing Oncogenic Master-regulator cMyc Using Library-derived Electrophilic Helical Peptides
Funder: Medical Research Council

Abstract: cMyc is a master regulator of cancer progression and linked to development of most human cancers. We will use electrophilic peptides derived from Max-based libraries, a known binding partner that forms a cMyc-Max heterodimeric coiled coil, to selectively and irreversibly target and functionally silence cMyc. Since cancer cells depend on cMyc the approach can induce death without killing normal human cells. We will first use intracellular peptide-library screening to identify peptides highly selective for cMyc, thereby providing a platform to inhibit function. Expressing off-target proteins in the assay (e.g. Max/Mad/Mnt/Mga), will enhance selectivity AND free Max to heterodimerise with them, to both silence transcriptional activation AND enhance repression. Intracellular selection will guide affinity/selectivity while removing non-specific, unstable, insoluble, or aggregate prone library members, leaving excellent scaffolds for further therapeutic refinement. We will further modify optimised cMyc-selective peptide sequences by conjugation to an electrophilic 'warhead', itself optimised for reactivity, geometry and location to ensure irreversible, but selective, cMyc binding. Selectivity is driven by a peptide-cMyc coiled coil PPI, while the electrophile acts like a secondary potency-conferring safety pin for irreversible sequestration of cMyc (via a unique cys), that is rendered functionally silent. We have demonstrated that the approach works for other proteins inside cells and now provide preliminary data showing feasibility for cMyc. Peptides and electrophilic peptides with greatest promise will be tested using a range of biophysical, structural, chemical, and cell-based approaches to demonstrate efficacy in entering cancer cells (intrinsically, via mimetic refinement, CPP or lipidic appendage see CfS), ablating cMyc function, resisting metabolism and killing a range of cMyc-expressing cancer cells at concentrations that do not kill normal human cells.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Cell-Cell Communication Analysis of Cancer Organoids Using Multimodal Single-Cell PTM and RNA Profiling
Funder: Medical Research Council

Abstract: Studying how different cell-types communicate is essential for our understanding of metazoan tissues. Recent advances in 3D organoid technology are enabling researchers to accurately model cell-cell interactions. Unfortunately, technologies to measure cell-cell communication in organoids are lacking. We have recently developed a mass-cytometry (MC) technology to measure ~30 post-translational modifications (PTMs) across single epithelial, fibroblast, and macrophage organoid cells (Qin et al., bioRxiv, 2019). While powerful for studying intracellular PTM signalling, MC cannot describe the 1,000s of ligands and receptors responsible for intercellular signalling. As a result, we cannot molecularly 'connect' signals between epithelial, stromal, and immune cells in organoids. To better understand how cells communicate with one another, we need to simultaneously measure which ligands are expressed by each cell, which receptors are found on each cell, and how these drive downstream intracellular PTMs signalling within each cell. This MRC Research Grant will develop a 'multimodal' platform to measure ligand and receptor gene expression and PTM signals within single-cells from colorectal cancer (CRC) tumour microenvironment (TME) organoids. This will be achieved across the following work packages: WP 1 - Integrate 10x Genomics scRNA-Seq and Anti-PTM MC WP 2 - Integrate SPLiT-Seq and Anti-PTM MC WP 3 - Develop a Multimodal SPLiT-Seq with Anti-PTM Oligo-Antibodies WP 4 - Use Multimodal scRNA-PTM to Study Signalling in CRC TME Organoids. MC and scRNA-Seq data will be integrated using Manifold-Aligned Generative Adversarial Networks (MAGANs) in with Prof. Krishnaswamy (Yale University) and ligand-receptor pairs will be established via CellPhoneDB with Dr. Roser Vento-Tormo (Sanger Institute). By measuring single-cell PTM, ligands, and receptors in a single multimodal assay, this project will describe novel cell-cell signalling networks in cancer organoids.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Interactions between hypoxia, HIF, type 2 IP3 receptors and invasion of glioblastoma
Funder: Medical Research Council

Abstract: Glioblastoma multiforme (GBM) is the most common primary brain tumour. Most patients die within months of diagnosis as the tumour diffusely invades surrounding brain tissue, preventing complete surgical removal of the tumour. Understanding the early steps in invasion might identify new targets for more effective treatment. As with most solid tumours, GBM tumours occupy a hypoxic environment that stabilizes hypoxia inducible factor (HIF), a transcription factor that orchestrates adaptive responses to hypoxia. Hence, GBM cell invasion starts in a hypoxic environment, where tumour cells must detach from their neighbours and begin their migration through brain parenchyma. Our analyses of human glioma cells has shown that hypoxia, through HIF, causes down-regulation of a minor subtype of an intracellular Ca2+ channel, the type 2 inositol 1,4,5-trisphosphate receptor (IP3R2). Hypoxia or siRNA-mediated down-regulation of IP3R2 causes loss of adhesions between glioma cells and an increase in invasion. The results are surprising because the effects are specific for IP3R2, which comprises <2% of the IP3Rs expressed in glioma cells. We will use patient-derived glioma neural stem cells with in vitro and ex-vivo assays (cell aggregation and adhesion, spheroid and organoid invasion), fluorescence microscopy (recording events at nascent adhesions), gene-editing of endogenous IP3R2, and biochemical manipulations (HIF, Ca2+ signalling, IP3R2 expression) to explore the relationship between hypoxia, HIF-1, down-regulation of IP3R2, and disruption of the intercellular junctions that prepare GBM cells for invasion. Our hypothesis is that the activity of IP3R2 is required to maintain intercellular junctions between GBM cells, and that hypoxia, through HIF, causes decreased transcription of the IP3R2 gene, leading to disruption of the junctions and increased invasion. We suggest that a better understanding of these early events in cell invasion might identify new targets for GBM treatment


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Characterisation of a novel phage-guided gene delivery vector and investigation of its gene therapy efficacy against metastatic cancer.
Funder: Medical Research Council

Abstract: Successful treatment of metastatic cancer is refractory to strategies employed to treat confined, primary lesions and thus must be addressed by systemic delivery of anti-cancer agents. Conventional systemic chemotherapy is often ineffective and comes with severe dose-limiting toxicities. Improving specificity of action appears to be key goal in the development of novel treatments against metastases. Gene therapy has been attempted against cancer for decades; but has been significantly hindered by lack of tumour-selective vectors through systemic administration and by problems with repeated delivery. We have introduced a unique prokaryotic viral-based approach of intravenous gene delivery to target tumours specifically by using the harmless filamentous M13 bacteriophage (phage), a virus that infects bacteria only. In this vector, named AAV/phage (AAVP), the M13 phage capsid delivers AAV vector genomes and was engineered to display the RGD4C ligand that binds the alpha-V/Beta-3 integrin receptor, overexpressed on tumour cells and supporting vasculature in most cancers, but barely detectable on healthy tissues. To date, we and collaborators have established that these vectors target various preclinical models of human cancer. Additionally, the vector showed efficacy in pet dogs with natural cancers. Repeated administrations proved anti-tumour efficacy in immunocompetent mice despite IgGs against the phage capsid. We have improved the technology and generated a vector with escape ability from the endo-lysosome degradative pathway. Importantly, we have further refined the hybrid vector by eliminating the phage genome, which decreased the vector size and generated a Phage-pseudotyped AAV (Ps-AAV) with large cloning capacity and improved gene delivery. We propose to investigate cellular entry and intracellular trafficking of this new hybrid Ps-AAV. Next we will investigate the vector in repeated systemic gene therapy dosing against metastatic cancer in preclinical models.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Investigation of the processes determining mitochondrial fate in normal and malignant haematopoiesis
Funder: Medical Research Council

Abstract: Acute myeloid leukaemia (AML) is an age-related disease that is highly dependent on the bone marrow (BM) environment. My group has recently shown that AML acquires functional mitochondria from the bone marrow environment through tunneling nanotubules, and that this promotes AML survival and proliferation. Moreover, we have found this increase in functional mitochondria to significantly increase oxidative phosphorylation in AML cells when compared with non-malignant haematopoietic progenitor cells. To further understand how AML maintain a functional pool of mitochondria this project will determine how AML regulates the disposal of mitochondria and also determine the impact of this disposal system on AML survival and proliferation. First, we plan to confirm preliminary findings which show that mitochondria are removed from AML in large extracellular vesicles. Then we will establish what impact AML derived mitochondria have on bone marrow associated macrophages. Finally, we will determine the impact if BM macrophages on AML survival and proliferation. Together, the data generated in this proposal could yield a substantial advancement in the understanding of AML pathobiology. which in future may allow the development of new treatment targets.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Recruitment of BRCA1-A complex to nucleosomes and sites of DNA damage
Funder: Medical Research Council

Abstract: BRCA1 forms three main complexes (A, B and C) in the cell, each having different roles in the DNA repair of double-strand breaks. The composition and recruitment of each complex to sites of DNA damage is well-known, however, it is difficult to delineate the exact function in vivo since there is overlap in sub-cellular localization, but also overlap of some molecular recognition modules that triggers the incorporation of BRCA1-BARD1 into the higher-order A- B- or C- supercomplexes. For example, all three supercomplexes require a phosphorylated pS-P-X-F motif that specifically interacts with the BRCT domains of BRCA1. The BRCA1-A complex is unique as it is selectively recruited after K63-linked ubiquitin chains have accumulated on chromatin. BRCA1-A also contains two sub-complexes with opposing activities: an E3 ligase module formed by BRCA1-BARD1, and a deubiquitylase module consisting of ARISC-RAP80. How these activities are coordinated in the context of the full BRCA1-A supercomplex and the precise function of each module is currently unknown. We have recently developed recombinant systems to produce active forms of each subcomplex as well as chemical biology methods to generate specific substrates for both. We aim to test each subcomplex in vitro for their enzymatic activity, either alone or together to delineate their precise function. We also have preliminary EM maps for both subcomplexes and our objective is to solve the structures of each subcomplex with and without substrates. We also aim to solve the structure of the fully assembled BRCA1-A supercomplex with and without ubiquitylated nuclear core particles after identifying the optimal nucleosomal substrate or nucleosomal binding partners. The molecular details and predictions revealed by our structural studies will be tested using in vitro and cell-based assays to understand the precise function of BRCA1-A in the DNA damage response pathway.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: The Genomic Atlas of Dermatological Tumours (DERMATLAS)
Funder: Medical Research Council

Abstract: Our overarching hypotheses for the studies proposed in this grant are that: 1). Most skin tumour subtypes can be defined by a discrete set of drivers, some of which can be targeted therapeutically; 2). Some skin tumours are caused by germline predisposing alleles, chemical exposures or viruses and these can be revealed by DNA/RNA sequencing and analysis. Collectively these studies can help define new screening and public health approaches. Specifically we will use state-of-the-art DNA sequencing technology to identify somatic and germline variants in 70 skin tumour entities defined by the WHO so that we can generate an atlas of dermatological tumours. We have a proven track record in this area and this grant represents a scaling up of our already successful programme of work.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Molecular mechanisms conferring risk for colorectal cancer
Funder: Medical Research Council

Abstract: In this project we propose to develop a quantitative model of gene expression that explains in molecular detail how genotypic variation of an individual CRC leads to activation of downstream genes that drive uncontrolled cell growth. To do this we have developed several novel methods that allows determination of transcription factor (TF) binding activities from cell extracts (ATI assay; Wei et al., Nature Biotechnology, 2018) and methods to determine high-resolution binding specificities of human and mouse transcription factors (TFs; Jolma et al., Cell 2013; Nitta et al., eLife 2015; Yin et al., Science 2017), and analyzed the role of TF-TF and TF-nucleosome interactions on their binding specificity (Jolma et al., Nature 2015; Zhu et al., Nature 2018). Since specific DNA binding is only one activity of TFs, and alone insufficient to explain how DNA sequence directs gene expression, we will also test biological activities of specific contextual combinations of TF motifs in vivo using a massively parallel enhancer-reporter assay (modified from Starr-seq protocol; Arnold et al., 2013) that we will use to identify active enhancers in target CRC cells. We will use our measurements to determine activities of TFs in a set of human CRC cell lines and intestinal tissues to identify the TFs that display strong activity in CRC, and then use this information to predict the effect of risk variants in gene expression using computational models. The modelling methods will range from easily interpretable regression models (Hughes et al., 2018) using pre-existing transcription factor binding motifs, to methods that learn the features of the sequences de novo, such as convolutional neural networks (Alipanahi et al., 2015; Zou et al., 2019). In the last steps this model will be tested with cell lines altered with CRISPR-Cas, to determine how changes in gene expression translate to an increased risk for tumourigenesis.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Pre-clinical development for IND application of a novel systemically deliverable oncolytic Vaccinia virus for treatment of pancreatic cancer
Funder: Medical Research Council

Abstract: Pancreatic ductal adenocarcinoma (PDAC) is an almost uniformly lethal disease with less than 5% survival at five years. This is largely due to metastatic and locally advanced disease, and new treatment strategies are clearly imperative. Tumour-targeted oncolytic viruses (TOVs) are attractive therapeutics for cancer. TOVs not only kill the tumour cells by direct lysis but also act through multiple other mechanisms of action by targeting molecular pathways involved in carcinogenesis, as well as breaking down the immuno-suppressive tumour microenvironment and inducing a long-lasting tumour-specific immunity. Furthermore, TOVs can specifically deliver therapeutic proteins into tumours at increasing levels following viral replication within the malignant cells. Although clinical trials with various TOVs have produced evidence of response, many have ultimately disappointed, especially for PDAC. Vaccinia virus (VV) has several features that make it a promising therapeutic agent, especially since one such virus (JX594) has recently been shown to effectively target tumours after intravenous infusion, making VV an ideal TOV for treatment of inaccessible tumours such as pancreatic cancer. We recently have developed a novel and powerful oncolytic VV which is systemically deliverable, shows improved intra- and inter-tumoral spread and has a potent ability to activate anti-tumour immune responses, providing a robust therapeutic success in several in vivo models of PDAC. Furthermore, we have demonstrated powerful synergy of the virus with immune checkpoint inhibition, a mode of immune therapy to which pancreatic cancer is characteristically unresponsive. Here we propose to complete a pre-clinical package that further demonstrates efficacy and safety, scale up vector production at GMP standard, deliver a pre-clincial toxicity package and submit an IND application for our therapy, prior to initiation of phase I clinical trials.


Research activity codes: 5.1 PHARMACEUTICALS;5.2 CELLULAR AND GENE THERAPIES
Health categories: CANCER AND NEOPLASMS