NIHRDataInsights/HRCSData huggingface dataset:
Title: Dissecting and exploiting enhancer dysregulation in T-cell acute lymphoblastic leukaemia
Funder: Cancer Research UK

Abstract: Background Approximately 50% of cases of T-ALL are driven through aberrant overexpression of the TAL1 oncogene. This is activated through an 80 kb deletion juxtaposing it to STIL or due to non-coding driver mutations 7.5 kb proximally. The small non-coding mutations create binding sites for MYB that recruits a complex consisting of CBP, TAL1 itself, GATA3, RUNX1 and RNA POLII, creating a neomorphic enhancer that drives TAL1 expression. MYB, TAL1, GATA3 and RUNX1 form a feedforward loop by activating their own enhancers and activate a number of downstream targets, including MCL1, to maintain the oncogenic state. Targeting this oncogenic complex has remained challenging, in part because the constituents and vulnerabilities of the complex are not fully understood. Aim 1: dissecting oncogenic enhancer structure and function at TAL1 and other driver oncogenes in T-ALL Aim 2: characterise the oncogenic MYB protein complex in T-ALL cells Aim 3: developing therapeutic strategies through targeting the MYB-TAL1 core regulatory circuitry (CRC) Methods: In Work Package 1, we plan to uncover novel TAL1 regulators through CRISPR screens in Jurkat cells where GFP has been knocked in-frame with TAL1 on the same allele as the enhancer mutation. Furthermore, we aim to exploit the fact that heterozygous non-coding mutations lead to allele specific expression (ASE), enabling the discovery of novel driver oncogenes that might prove to be new therapeutic targets. We will also explore alternative mechanisms of ASE of oncogenes through analysis of methylation and chromosome conformation. In Work Package 2, we will use proteomic techniques to dissect the native MYB complex in T-ALL cells. Our preliminary ChIP-mass spectrometry experiments have identified a number of novel members of the complex, some of which are targetable with drugs that are in clinical development. In work Package 3, we plan to utilise CDK9 inhibitors as a means of targeting the MYB-TAL1 core regulatory circuitry. CDK9 inhibitors lead to marked downregulation of CRC genes, as well as MCL1, leading to apoptosis at low nanomolar concentrations. We will determine the genetic modifiers of sensitivity and resistance to CDK9 inhibition, that can inform novel synergistic combination therapy and biomarkers of clinical response. These results will provide new mechanistic insight into the oncogenic function of MYB and uncover novel therapeutic strategies that can be taken forward for clinical development.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Newcastle ECMC
Funder: Cancer Research UK

Abstract: The vision of the Newcastle ECMC are: • To develop new treatments for cancer patients. • To include biomarkers early in the drug development pathway. • To ensure that the right patients are treated with the right drugs at the optimal doses. • To minimise toxicities and late adverse effects. Specific aims of the ECMC are to increase access to novel anti-cancer agents for adults and children in the Northern region, to use clinical pharmacology approaches to optimise drug delivery and safety in adults and children, and to develop tissue biomarkers and/or use imaging techniques to improve outcomes with new treatments. In addition we will continue to build a blood and tumour tissue banking resource which supports further target discovery research and future drug development alongside clinical trial sample collection.


Research activity codes: 4.5 RESOURCES AND INFRASTRUCTURE (DETECTION);6.1 PHARMACEUTICALS;4.2 EVALUATION OF MARKERS AND TECHNOLOGIES;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: Targeting Autophagy and Aberrant Metabolism of Leukaemic Stem Cells
Funder: Cancer Research UK

Abstract: Abstract. Background: Therapy resistance and disease persistence remain major challenges for developing curative approaches in cancer. In chronic myeloid leukaemia (CML), both of these features are fuelled by a reservoir of rare, drug resistant leukaemic stem cells (LSCs), which need to be eradicated in order to achieve cure. Cancer cells require metabolic changes to fuel their high-energy demands. Autophagy is a major contributor to cellular metabolism through autophagic secretion of substrates for biosynthesis and energy generation. Therefore, targeting autophagy and metabolic reprogramming offer novel opportunities for cancer treatment. However, robust investigation of metabolism in LSCs is challenging and often restricted by technical limitations. To address this, my team has developed and optimised robust metabolic assays, complemented by measurements of mitochondrial function and autophagy, to study the rare LSC population for the first time. By applying these approaches, we revealed that autophagy inhibition sensitises bone-marrow located CML LSCs to drug-induced death. In parallel, we also demonstrated that CML LSCs are metabolically distinct from normal haematopoietic stem cells and rely on mitochondrial oxidative phosphorylation for survival. These results provide a strong rationale for targeting metabolic vulnerabilities in LSCs. Importantly, this may not be restricted to CML, as similar metabolic dependencies are emerging in other related leukaemia types. Aims: Our aim is to directly address the issue of drug resistance and develop strategies that kill LSCs but spare normal haematopoietic stem cells. By focusing on CML, we will take advantage of our unique expertise and environment, including access to patient-derived LSCs and state-of-the-art pre-clinical models, coupled with the ability to integrate and develop technological advances in the field. This will enables us to make significant discoveries and evaluate our working hypothesis that targeting aberrant metabolic programming disrupts the maintenance and function of CML LSCs. Methods: In this programme, we will integrate and further innovative cutting-edge technological advances, including stable isotope-assisted metabolomics, integration of ‘omic’ data, and intravital microscopy. We will complement these approaches with drug-repurposing screening, and testing of novel autophagy inhibitors in field-leading pre-clinical CML mouse models. How the results of this research will be used: We will reveal for the first time the metabolomic vulnerabilities of drug-treated CML LSCs in hypoxia and morphological/functional changes in the leukaemic niche, thus enabling the development of novel targeted drug therapy. The proposed work will deliver new therapeutic strategies that may have wider impact beyond CML, and be applicable for other stem cell driven tumours.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Understanding the origin and pathogenesis of MLL-AF4-associated infant leukaemia
Funder: Cancer Research UK

Abstract: Background: Infant B cell lymphoblastic leukaemia associated with the MLL-AF4 translocation is characterised by an early onset ( 1 year of age) and a dismal prognosis. Twin studies and retrospective analysis of neonatal blood spots have established that MLL-AF4+ infant leukaemia has a prenatal origin, and, consequently, very little is known about its cellular origins and pathogenesis. Recent sequencing studies were unable to detect any additional recurrent mutations, suggesting that the disease initiates in a cell with a chromatin milieu that permits transformation by the fusion gene alone. Due to the inaccessibility of the pre-leukaemic stages which take place in utero, a faithful in vivo model is required to study the origin and early steps of this disease and to test therapeutic avenues. Aims: Using a newly developed model, we have recently identified a putative cell-of-origin in which MLL-AF4+ infant leukaemia is likely to arise. Furthermore, we have characterised the initial changes in blood development induced by the oncogene during the pre-leukaemic state. The aim of this proposal is to further dissect this early transformation stage on a molecular level and to understand the permissive chromatin context in the cell-of-origin. As there are still discrepancies between the disease arising in our in vivo model and the phenotype in infant patients, we also plan to study these early events in a human context. Finally, a contribution of the foetal stromal microenvironment will also be addressed. Methods: Early transcriptional changes induced by the oncogene in the cell of origin will be determined by RNA-Seq, analysed for enrichment of haematopoietic and oncogenic pathways and compared with expression data from human patients. Chromatin architecture in the cell of origin will be mapped by ATAC-Seq and correlated with transcriptional activity. To study these events in a human context, human foetal cells will be transduced with the oncogene and the effect studied in functional assays and by molecular profiling. By simultaneously inducing oncogene expression in the haematopoietic and stromal compartment, their respective contributions to and interactions during disease pathogenesis will be determined. How the results of this research will be used: The results of this research will provide a better understanding of the early stages of MLL-AF4+ leukaemia and the molecular and cellular components that contribute to its development. They will be used for the generation of a more faithful model in which early detection markers can be identified and potential drug treatments tested.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: HIPK2 as a novel determinant of cancer therapeutic resistance
Funder: Cancer Research UK

Abstract: Background The homeodomain-interacting protein kinase 2 (HIPK2) is a multi-functional transcriptional regulator that works as an integrator of stress signals and is involved in cell growth, apoptosis, proliferation and development. Traditionally HIPK2 has been considered a potential tumour suppressor, but recent studies suggest a novel oncogenic role for HIPK2. While the pathways involved in its tumour suppressor role are relatively well studied, the underlying mechanisms mediating the pro-oncogenic function(s) of HIPK2 remain unclear. We have already uncovered a link connecting HIPK2 with a mayor pathway involved in chemoresistance. Our hypothesis is that HIPK2 is a major factor controlling cancer cell fate, by inducing either cell death or cell survival, and it can promote chemoresistance by activating multiple pathways. Understanding the conditions that drive HIPK2 towards cell survival and the signalling pathways involved, could establish HIPK2 as a potential therapeutic/prognostic factor. Aims Aim 1. To identify and characterise pathways involved in HIPK2-mediated chemoresistance Aim 2. To determine what makes HIPK2 a pro-survival factor Aim 3. To define the potential clinical value of HIPK2 Methods - CRISPR/Cas9 to knock-out, knock-in mutations or tag endogenous genes. - SILAC and RNA-seq to identify pathways regulated by HIPK2. - CRISPR-based library screening to identify HIPK2-regulated pathways involved in chemoresistance. - Automated quantitative multiplex immunofluorescence analysis of HIPK2 in tumours and correlation with survival/response to treatment. How the results of this research will be used It will provide key insights into the mechanisms underlying tumour therapeutic responses, by characterising new pathways involved in chemoresistance that may reveal HIPK2 as a potential prognostic/therapeutic target.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Improving health status and symptom experience for people living with advanced cancer.
Funder: Yorkshire Cancer Research

Abstract: In Yorkshire, over 14,000 people die from advanced cancer each year, a number expected to rise to 17,000 yearly by 2030. In the weeks or months before they die, people with advanced cancer often experience pain, breathlessness or fatigueexhaustion, which significantly reduce quality of remaining life. Our programme will directly improve the health status and symptom experience of Yorkshire patients living with advanced cancer and support their families. We will achieve this by (1) recognising early those who need help, (2) implementing regular assessment and monitoring of symptoms and other concerns, (3) providing better management of the most challenging symptoms.

Lay abstract: In Yorkshire, over 14,000 people die from advanced cancer each year, a number expected to rise to 17,000 yearly by 2030. In the weeks or months before they die, people with advanced cancer often experience pain, breathlessness or fatigueexhaustion, which significantly reduce quality of remaining life. Our programme will directly improve the health status and symptom experience of Yorkshire patients living with advanced cancer and support their families. We will achieve this by (1) recognising early those who need help, (2) implementing regular assessment and monitoring of symptoms and other concerns, (3) providing better management of the most challenging symptoms.

Research activity codes: 7.1 INDIVIDUAL CARE NEEDS;8.1 ORGANISATION AND DELIVERY OF SERVICES
Health categories: CANCER AND NEOPLASMS
Title: The impact of genetic interactions on DNA methylation in breast cancer
Funder: Cancer Research UK

Abstract: Background: Epigenetic dysfunction is a near universal feature of carcinogenesis. DNA methylation alterations affect key breast cancer genes such as BRCA1 suggesting their importance to carcinogenesis and progression. However, the mechanisms underpinning such alterations in DNA methylation are unknown, so their significance remains unclear. My recent work suggests epigenetic marks are strongly programmed by the underlying DNA sequence. This means that sequence variants are likely to be an important and underexplored influence on breast cancer epigenomes. Aims: This project aims to understand the role of the genome in programming the epigenetic mark DNA methylation in breast cancer through two aims. 1. Define the extent to which germ-line and somatic DNA sequence variants modulate local levels of DNA methylation in breast tumours in vivo. 2. Understand how the effects of regulatory variants on DNA methylation and gene expression interact and how such variants impact on clinical phenotypes. Methods: I will elucidate the frequency to which germ-line and somatic sequence variants affect DNA methylation in breast cancer through machine-learning analyses of HER2-driven mouse mammary tumours and clinical high-grade luminal breast tumours. The interaction between variant-modulated alterations in DNA methylation and gene expression will be tested using genome editing technologies and the promoter of BRCA1 as a paradigm. The phenotypic impact of BRCA1 regulatory mutations will be assessed through engineering into mice. These synergistic approaches reinforce one another to uncover the global impact of sequence variation on DNA methylation, the mechanistic details underlying these effects and their clinical relevance. How the results of this research will be used: This project uses state-of-the-art computational and laboratory approaches to leverage genetics towards tackling our lack of understanding regarding the impact of DNA sequence variation on epigenetic alterations in cancer. In doing so, it impacts on our understanding of the regulation of a key breast and ovarian cancer risk gene, BRCA1, and provides new approaches to delineate the contribution of regulatory variants to carcinogenesis and progression.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Oxford ECMC
Funder: Cancer Research UK

Abstract: The major strategic aim of this bid is to integrate more closely with our Biomedical Research Centre and CR UK Major Centre to deliver even more world class Oxford cancer science to our patients and to the wider Network. In the ECMC we will focus on five key scientific themes in the coming quinquennium, to deliver distinctive high quality outputs that draw together scientific and clinical expertise from across the University and the Hospital and integrating them with local commercial and industrial partners. These aims are: 1) Targeting mRNA translation dysregulation 2) Stratification of patients with lymphoid haematological disorders 3) Stratification of patients for immunotherapy 4) Inhibitors of cancer metabolism 5) Establishing combination studies for radiotherapy In addition, Oxford ECMC will continue to participate in National ECMC activities, such as the ECMC Nurses group, CM-PATH, JING and ECMC Steering committee and Combination Alliance activities.


Research activity codes: 4.5 RESOURCES AND INFRASTRUCTURE (DETECTION);6.9 RESOURCES AND INFRASTRUCTURE (TREATMENT EVALUATION)
Health categories: CANCER AND NEOPLASMS
Title: Cellular interplay in oesophageal cancer
Funder: Cancer Research UK

Abstract: Background Oesophageal cancer is a research priority. However, a key knowledge gap hinders the prediction of which patients will benefit from treatment because the contribution of the tumour microenvironment is not considered in new mutational signatures. Cancer-associated fibroblasts (CAFs) are common in solid tumours and their accumulation correlates with poor prognosis across cancer types. CAFs are associated with the regulation of a number of tumour promoting processes. However, these cells are yet to be adequately classified at a molecular level. The in vivo “education” or “reprogramming” of normal fibroblasts by tumour cells is an established mechanism by which cancer cells take advantage of the plastic nature of reactive cell populations to generate a tumour-supportive microenvironment. It remains unclear how tumour cells perform this “education” and what the role of specific cancer cell genomic changes have in this process. To address this question tumour and CAF sub-groups require comprehensive characterisation at a level that cannot be delivered by bulk sequencing technologies. Aims The composition and phenotype of cells in the OAC tumour microenvironment is determined by genomic changes in the tumour cells. We aim to interrogate this relationship using whole tumour single cell sequencing and novel ex-vivo organoid models to identify potential targets for therapy. Methods We will combine single cell sorting of tumour biopsies from different tumour regions with highly parallel genome-wide expression profiling of individual cells using nanoliter droplets (DropSeq) to understand and predict the contribution of different cell types to the genotype/phenotype of each other. This package of work will identify candidate driver genes/pathways in cancer cell populations that determine the phenotype of CAF to be tested as potential tractable targets using complex near-patient organoid models. We will develop and validate patient-specific multi-cellular organoid models, including fibroblasts and possibly immune cells. We will use sub-clones from tumours with autologous NOF/CAF to understand the role of driver mutations on fibroblast phenotype and vice versa. Using established gene-editing technology we will investigate the functional relevance of these genes/pathways to tumour development and progression. We will use a range of inhibitors of CAF differentiation as molecular tools to establish the role and timing of fibroblast activation. Relevance This proposal directly investigates the biology of oesophageal adenocarcinoma, a cancer of unmet need, and a priority for CRUK. The refinement of DropSeq for use in solid cancers and the development and validation of multi-cellular organoid models have direct application to other malignancies


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: Definition and Functional Characterisation of Follicular Lymphoma-propagating cell populations
Funder: Cancer Research UK

Abstract: Background Tumour-propagating cells are believed to contribute to therapy resistance and disease relapse, yet the notion of such populations have been largely unexplored in lymphomas. Evidence generated by ourselves and others suggest the existence of these reservoir populations in follicular lymphoma (FL) and may explain the continued remitting, relapse pattern and incurable nature of this malignancy. I propose that a full characterisation of these elusive populations will play an important role in the future development of novel therapeutic strategies. Aims: 1) Determine the sequence of recurring genetic aberrations and pinpoint where they arise along the haematopoietic hierarchy of B-cell development. 2) Identify the cells with tumour-propagating potential using xenotransplantation systems. 3) Engineer mouse models that mimic the initiating genetic events in FL. Methods To define the sequential mutational events and identify the cell populations from which the oncogenic aberrations arise, I will conduct whole-exome sequencing of the overt FL tumour and subsequently backtrack a selected panel of these somatic mutations in purified haematopoietic cellular fractions derived from primary FL bone marrow biopsies by using a combination of targeted ultra-deep and single cell gene sequencing. I will analyse the transcriptome of these mutated FL-precursor fractions using RNA-seq precursors to determine the biological and signalling pathways altered by the presence of such aberrations. The permissiveness, multi-potency and tumour-propagating capacity of bulk and purified mutated cell fractions will be tested in vivo using sub-lethally irradiated NOD/SCID/IL-2Rgc-null (NSG) mice in serial xenotransplantation assays and limiting dilution studies. Finally, combinatorial genetically-engineered conditional mouse lines will be developed based on the order and stage of development of mutations to evaluate the clonal dynamics, evolutionary trajectory and phenotype of the tumour. How the results will be used This project addresses a problematic area of cancer research in defining precursor and/or reservoir cell populations that promote cancer initiation and relapse. It will enable a better definition of the tempo of FL tumorigenesis and how evolution of the cancer might be governed or constrained by the sequence of oncogenic events. This understanding together with the development of refined clinically informative mouse model systems aims to facilitate and provide a platform in which to guide and test more effective and rationale novel therapeutic approaches in FL with a curative intent. Lastly this work may serve as a tractable model to inform our understanding of other lymphoid malignancies.


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