NIHRDataInsights/HRCSData huggingface dataset:
Title: Immune-checkpoint therapy in non-small cell lung carcinoma:molecular characterisation of tumour microenvironment to improve anti-PD1/PD-L1 drug class.
Funder: Medical Research Council

Abstract: PLAN OF INVESTIGATION Phase 1 Archived, formalin-fixed, paraffin wax-embedded (FFPE) tissue blocks are available from 651 resected specimens of NSCLC and are consented for research purposes. Of these, 156 have accompanying, involved, regional (intrathoracic) lymph nodes. Standard immunohistochemical analysis will determine the expression levels and heterogeneity of PD-L1 in tumour and immune cells and the nature of the immune cell populations within the tumour. The presence of EGFR gene mutations and ALK gene rearrangement will be determined where not known. Phase 2 There are various options locally available for analysis of extracted genetic material. This field is constantly updating in techniques and panels of genes to be targeted. However the use of cutting-edge technology such as NGS-panels, Nanostring and MassArray has been ascertained as feasible with this tissue by discussing with the respective teams and companies. The specific panels may update to reflect the changing environment, but these can be used to assess TMB, immune profiling, actionable mutations and so on. Validation of techniques, including the minimum amount of genetic material required for sufficient analysis, will be performed and can be combined with approaches for minimal sampling, including laser-capture microscopy (LCM) and needle core biopsy. Phase 3 This phase will mostly concentrate on working with Eli Lilly (see part B3b) and local oncologists for access to tissue samples after immune checkpoint therapy. Patients who fail immune checkpoint therapy are the primary group of interest and both post-therapy and archival tissue can be assessed for inherent and de novo resistance.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Investigating the function of the BCL-3/Beta-catenin complex in promoting intestinal tumorigenesis and acquisition of therapeutic resistance.
Funder: Medical Research Council

Abstract: Colorectal cancers are thought to arise from stem (or stem-like) cells that gain a competitive advantage over their neighbours via deregulation of Wnt signalling, most commonly through inactivating mutations in APC. Important studies have begun to identify the mechanisms underpinning the expansion of the APC mutant stem cells that contribute to the earliest stages of colorectal tumour development. Mechanisms that support tumour progression may also contribute to the refractory nature of advanced colorectal cancer to chemotherapy. This proposal is based on our novel observation that BCL-3 (a key regulator of NF-kappaB signalling) enhances deregulated beta-catenin activity: we propose that increased BCL-3 expression in colorectal epithelial cells, through promoting beta-catenin transcriptional activity, will drive cells towards a more stem cell-like phenotype enhancing tumour progression, de-differentiation and therapeutic resistance. This suggests that targeting BCL-3 could be important for cancer prevention and/or inhibition of tumour progression, as well as improving therapeutic efficacy. This research proposal uses cross-comparison of data from mouse and human tumour models with state-of-the-art epidemiology to: 1. Determine whether targeting BCL-3 inhibits intestinal tumorigenesis. 2. Investigate the mechanism by which BCL-3 promotes the outgrowth of APC mutant cells and identify novel transcriptional targets for the BCL-3/beta-catenin complex. 3. Determine whether the BCL-3/beta-catenin targets are related to colorectal cancer risk and/or response to conventional therapy. This proposal will establish the role of the BCL-3 in promoting the earliest events in colorectal tumorigenesis; identifying the BCL-3/beta-catenin complex as potential marker of and target for prevention in colorectal tumorigenesis. In addition, it will identify novel targets to improve therapeutic efficacy and inhibit disease relapse in colorectal cancer.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Finding new insights into cancer metastasis: Linking cell migration to metabolic energy flux
Funder: Medical Research Council

Abstract: Pancreatic cancer has less than a 5% 5-year survival rate and this figure hasn't improved in decades. Mutation of the KRas oncogene occurs in almost all pancreatic ductal adenocarcinomas (PDAC) and drives metabolic reprogramming. Our aim in this proposal is to link this metabolic programming with the enhanced migratory and metastatic state of PDAC to find new therapeutic targets. We screened 494 metabolic regulatory genes in a bespoke library of siRNA using high content confocal imaging to identify metabolic regulators of cell shape and migration. Out of 22 hits selected for shape and migration speed alterations with minimal effects on proliferation, 2 classes of hits emerged. This project aims to characterise the top hits from these 2 classes to reveal new targets linking metabolism to cell migration. Class 1: Mitochondrial regulatory genes modulating oxidative phosphorylation driven ATP-production to fuel motility Class 2: Glycolysis regulators which connect trafficking of integrins to nutrient receptors and glycolytic enzymes Our aim in this 2-year project is to use cell biological and biochemical methods to identify 1-2 key pathways linking metabolic control to migration as candidates for anti-metastatic therapy. Future studies will take the top hits in vivo to test their clinical potential.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Developing new paradigms for overcoming drug resistance in cancer using novel humanised mouse models
Funder: Medical Research Council

Abstract: Whereas there is currently an enormous emphasis on cancer genomics, tumour cell heterogeneity, microenvironment, etc, there are essentially no studies on drug pharmacology i.e. how to use the new drugs optimally. Defining the pharmacology of emerging targeted anti-cancer drugs, rather than using dosing regimens based on MTD, has to be a fundamental component of developing new effective cancer treatments, particularly for drug combinations which are being developed to overcome drug resistance. Understanding how best to use targeted agents can make the difference between success and failure of new treatment regimens. Almost all new targeted anti-cancer agents are substrates for the cytochrome P450 system, and the transcription factors (CAR, PXR) which regulate their expression. These enzymes play a major role in circulating & tumour drug concentrations, and the generation of pharmacologically active and/or toxic metabolites. Major species differences in this enzyme system can seriously confound extrapolation of data from animals to man. To circumvent this, we have created a mouse where the major human P450s and CAR & PXR, have replaced their murine counterparts so that Phase I drug metabolism is essentially that seen in man. We will use these models to investigate the pharmacological drivers of drug resistance. We will use melanoma as a model since dramatic patient responses are observed with the current standard of care (dabrafenib and trametinib), and the emergence of drug resistance is a rapid and major problem. We will use the humanised models to understand PK, PD and efficacy relationships and establish the correlation between drug exposure, target inhibition, pathways of cell death and drug efficacy. These data will be used to develop a computational model which allows the relationship between drug exposure and efficacy of drug combinations at different drug exposures to be predicted and therefore facilitate the informed design of combination clinical trials.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;6.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Defining the mechanism and specificity of the 53BP1-Rev7 non-homologous end joining pathway in immunity and oncogenesis
Funder: Medical Research Council

Abstract: This project aims to determine the mechanism and specificity of the 53BP1 pathway in regulating DNA double-strand break (DSB) repair in immunity and cancer. I hypothesise that the three known situations in which 53BP1 mediates NHEJ (class switch recombination (CSR), fusion of uncapped telomeres, and genomic instability in BRCA1-deficient cancers) are connected to a similar DNA intermediate: staggered DSBs comprising secondary-structure forming single-stranded DNA termini. Supported by a body of compelling new experimental evidence, we make the prediction that the 53BP1-dependent repair system integrates a previously unexpected activity to convert staggered DNA ends into DSBs amenable to NHEJ, and that this activity is toxic when such structures form inappropriately, such as at upcapped telomeres or in HR-defective cancers. We will test these predictions using a combination of pre-existing and newly generated transgenic mouse models, with which we will dissect DSB repair mechanisms in the murine immune system and in cellular models of BRCA1-deficiency. In doing so, we will challenge the currently accepted paradigm for the 53BP1 pathway (resection inhibition), and propose an alternative explanation for the molecular events that occur when it fails. If our predictions are correct, this work will underpin a new paradigm to explain the context specificity of 53BP1-dependent NHEJ, with important consequences for understanding vital molecular mechanisms in normal cell physiology and oncogenic transformation.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Fibre-based Photonic Fingerprinting and Theranostic Ablation of Pulmonary Nodules
Funder: Medical Research Council

Abstract: Solitary pulmonary nodules are a huge clinical challenge, which cause considerable diagnostic uncertainty as they may represent early treatable lung cancer. The current guidelines advocate a protracted diagnostic pathway involving radiological surveillance. While endobronchial navigation technologies can access the majority of pulmonary nodules, the diagnostic yield from biopsy is suboptimal - cutting-edge technologies are needed to improve the existing care pathway. I propose to develop a novel optical fibre-based approach to delineate pulmonary nodules and perform in situ therapeutic ablation with dynamic feedback of therapeutic efficacy during intervention. Firstly, I will build a fibre-based sensing and therapeutic platform, using a hollow core optical fibre (capable of delivering excitation light with sensing and therapeutic intent), a multicore imaging bundle, and sensitive detectors. Secondly, systematic ex vivo studies using lung cancer tissue resections will be undertaken to identify key features in the optical fingerprint to discriminate abnormal from normal lung tissue (using optical endomicroscopy, fluorescence lifetime-based spectroscopy and laser-induced breakdown spectroscopy), and to characterise the effectiveness of ultrafast laser-based ablation. Finally, I will evaluate a simple steering mechanism to enable navigation across the nodule - the imaging/spectroscopy, laser ablation and steering capabilities will be evaluated in whole ex vivo human lungs embedded with targets to provide near-human assays with airway and distal lung anatomy analogous to in vivo experiments. This work will leverage state of the art optical fibre technology to allow complete ablation of small nodules or selective removal of the extracellular matrix around larger nodules to potentially augment aligned therapies. This approach may enable a one-stop solution for pulmonary nodules, avoiding the need for radiological follow-up and reducing healthcare costs.


Research activity codes: 5.5 RADIOTHERAPY AND OTHER NON-INVASIVE THERAPIES
Health categories: CANCER AND NEOPLASMS
Title: Novel small molecule inhibitors for the treatment of CCNE1-amplified cancers.
Funder: Medical Research Council

Abstract: CCNE1 encodes for the cell cycle regulator cyclin E which binds to cyclin-dependent kinase-2 (CDK2) to drive cells through a G1/S cell cycle transition. Genetic perturbation of CDK2 indicates that its function is not essential for mitosis to complete in normal tissue development and homeostasis. In contrast, tumour cells in which CCNE1 is amplified are critically-dependent on CDK2 and cyclin E for survival. Such "oncogene-addiction" to CCNE1 occurs in a significant cohort of high-grade serous ovarian cancer (HGSOC) and confers a particularly poor patient outcome to current therapy. Although there have been many attempts to pharmacologically-inhibit CDK2 kinase activity, these have resulted in the development of ATP-competitive inhibitors that do not have sufficient selectivity against other CDKs (involved in essential cellular processes) to exert amplicon-dependent activity. The current application aims to produce novel small molecule inhibitors that are selectively toxic to CCNE1-amplified tumour cells as a stratified medicine for the treatment of HGSOC. The strategy has been approached using crystallographic fragment screening and two series of molecules identified. In this hit-to-lead phase of the project we will utilise structure-based drug design to increase the potency of the hit molecules and aim to demonstrate proof-of-principle through the identification of a cell-penetrant tool compound.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Precision medicine and the mutational landscape of high grade serous ovarian cancer
Funder: Medical Research Council

Abstract: High grade serous ovarian cancer (HGSOC) makes up 75% of new diagnoses of ovarian cancer in Scotland and is almost always diagnosed after the disease has spread. As a result, the 5-year overall survival rate remains low at around 40%. HGSOC is characterised by ubiquitous somatic TP53 mutations and elevated rates of structural variants (SVs) which are thought to drive tumourigenesis. However, HGSOC is poorly understood at the genomic level and the number of available samples is modest. We will analyse high quality whole genome sequencing (WGS) data emerging from a large study of HGSOC (led by Prof. Gourley and co-funded by AstraZeneca) in 200 Scottish patients. Detailed histopathological and clinical data are available for these patients through the Edinburgh Ovarian Cancer Database (Gourley). Using this resource, we will examine the origins and consequences of the somatic mutational landscape of HGSOC. We will calculate mutational spectra in HGSOC WGS samples, as has been done for breast cancer (Nik-Zainal et al, Cell, 2012), and explore their utility in predicting clinical variables, including disease progression and therapeutic responses. We will investigate the role of germline genetic variation in determining mutational spectra and other tumour signatures, such as gene expression signatures, using association testing. The generalisability of our observations will be established by integrating our data with previously published HGSOC WGS data (Patch et al, Nature, 2015) and associated clinical data. We will explore the clinical utility of mutational spectra extracted from the larger cohort (N=450) of FFPE samples. Developing analyses for large collections of FFPE samples may have broader translational impact across oncology globally. We will investigate the utility of newly identified complex SVs in HGSOC in patient stratification as well as investigating the predictive power gained from including these variants in mutational spectra.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: MICA: Targeting the Wnt Receptor Frizzled-7 for the Treatment of Gastric Cancer
Funder: Medical Research Council

Abstract: Frizzled (Fzd) proteins are co-receptors for Wnt ligands, several of which are upregulated in many cancers, including gastric cancer (GC), and thus offer novel therapeutic targets. This project will determine the therapeutic benefit of inhibiting Fzd receptors for the treatment of GC. We have recently identified that Fzd7 is required to transmit Wnt signalling in the stems cells located in the gastric and intestinal epithelium. Cell signalling that regulates stem cell activity is often deregulated in cancer, supporting the hypothesis that Fzd7 could be an attractive target for therapy. We shall establish the requirement for Fzd7 in gastric cancer using gastric specific inducible Cre recombinase technology to genetically delete Fzd7 in several mouse models of GC. To investigate if Fzd7 is also important for human GC cells we shall use inducible shRNA technology to target Fzd7 in human GC cell lines, and using colony forming assays and xenografts. To target Fzd7 pharmacologically we shall employ a monoclonal antibody which is already in clinical trials for breast and lung cancer, which targets the conserved extra cellular domain of Fzd1/2/7, in our mouse models of GC and in xenografts, thus directly informing future clinical trials. Finally we shall perform comprehensive cellular and molecular characterisation of GC cells after Fzd7 inhibition and investigate how GC cells with mutant APC are able to respond to inhibition of Fzd7, thus providing valuable mechanistic insight to help select which patients may respond to this therapeutic approach. This application is based on strong preliminary data showing that genetic inhibition of Fzd7, can block the growth of gastric tumours in mouse models of GC and human GC cells. The data generated in this project will represent a significant advance in the field, as presently the therapeutic benefit of targeting Fzd7, and Wnt receptors in general, for the treatment of GC has not be studied in vivo.


Research activity codes: 5.2 CELLULAR AND GENE THERAPIES
Health categories: CANCER AND NEOPLASMS
Title: Deciphering and targeting cancer metabolism using executable models
Funder: Medical Research Council

Abstract: The progression of cancer is associated with extensive metabolic reprogramming. A key feature of cancer is the Warburg effect, where cells switch from relying on oxidative phosphorylation to anaerobic glycolysis. Similarly, KRAS and BRAF mutations drive widescale reprogramming of metabolism, whilst the mutation of individual metabolic enzymes such as fumarate hydratase can promote cancer progression. Computational models of cancer metabolism could elucidate the links between metabolism and cellular phenotype. Here we propose the construction of an executable model of cancer metabolism, guided by the use of machine learning applied to high throughput expression and metabolomic datasets and the existing literature on cancer metabolism. Executable models do not require the detailed physical parameterisation necessary for continuous models, such as those based on ordinary differential equations. They also allow more complex model behaviours to be described than flux balance analysis, including metabolite accumulation. Finally, they are amenable to analyses based on formal verification, where mathematical proofs are used to offer powerful guarantees of model behaviour by effectively searching all possible states of the model. The models and the new predictions that arise from the model construction will be validated through experiments performed with the Frezza group.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Determining the role of autophagy in mediating resistance to proteasome inhibition in multiple myeloma
Funder: Medical Research Council

Abstract: Multiple myeloma is a common haematological cancer with considerable genetic heterogeneity. This condition remains incurable, and disease resistance to proteasome inhibitors (PI) remains a major barrier to achieving durable remissions for patients. The work in this fellowship will investigate the role of autophagy in mediating resistance to proteasome inhibition therapy (carfilzomib) in multiple myeloma, and define distinct subgroups of patients who will benefit from dual targeting of autophagy and the proteasome. Patient bone marrow samples and myeloma cell lines will be exposed to carfilzomib (second generation PI) and autophagy inhibitors (AI) and cellular cytotoxicity, autophagy protein levels and autophagic function will be assessed. Results will be analysed seeking correlations with genetic translocations and basal autophagic function and reserve. RNASequencing will be used to seek transcriptomic differences underlying divergent cytotoxicity responses in HMCL exposed to PIs +/- AIs. Efficacy of selected combination therapy with PI and AI will be further assessed using ex vivo and in vivo MM models. Patient samples from the NCRN Cardamon study (newly diagnosed MM patients treated with Carfilzomib based regimen) will be examined for relevant autophagic proteins and function identified from previous cell line work, correlating with disease response. Results of this work will contribute to understanding the mechanisms underlying PI resistance, and the therapeutic potential of AI's in combination therapy with PI. Identification of key genes may provide predictive biomarkers for use in phase I combination studies of PI and autophagy modulators. Mechanistic insights will also identify potential novel therapeutic targets to aid future drug development.


Research activity codes: 6.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: MICA: Optimising combination strategies for chimeric antigen receptor therapy in multiple myeloma
Funder: Medical Research Council

Abstract: Myeloma(MM) remains incurable and following the success of chimeric antigen receptors(CARs) in B cell malignancies, CAR T-cells are being tested in MM. However, despite clinical responses, the suppressive immune microenvironment(IME) is well described in MM and likely to explain the high CAR T-cell doses needed in patient studies. The co-administration of immunomodulatory drugs or appropriate T-cell engineering may counter suppressive pathways. However, the suppressive IME in MM following CAR therapy is not clearly understood. This fellowship will focus on the suppressive IME in MM, to provide the evidence base for effective combination strategies to optimise CAR T-cell therapy and improve patient outcome. Specific aims: 1)Characterise the IME effects on CAR T-cells a)The APRIL-CAR, developed during my PhD, is the only MM CAR in clinical trials in the UK. Bone marrow (BM) samples from the APRIL-CAR clinical trial will be analysed by flow and CyTOF and findings clinically correlated with outcome. Solid BM biopsy samples will be studied by chip-cytometry- a novel method allowing multi-parametric analysis of tissues. b)The effects of putative immune suppressive cell types on CAR function will be studied by in vitro culture systems using autologous suppressor cells, and pathways identified evaluated using blocking antibodies or CRISPR editing. c)Developing the first CAR/MM model in immunocompetent mice will allow study of the interaction between CAR T-cells and the IME in vivo. Data by flow, immunohistochemistry and RNAseq of bone marrow, will validate this model against findings in patient samples to assess its clinical applicability 2) Design of rational combination strategies With insight gained, strategies involving a)immunomodulatory agents or b)T-cell engineering will be tested in vitro/in vivo using systems outlined above with the aim of selecting combinations which significantly enhance disease control to take forward for clinical testing.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS