NIHRDataInsights/HRCSData huggingface dataset:
Title: The Dark side of IFN gamma in Tumour Immunity: Is IFN gamma Receptor on Tumour infiltrating lymphocytes a new checkpoint?
Funder: Cancer Research UK

Abstract: Checkpoint blockade is a form of cancer immunotherapy that stimulates our own immune system to eliminate cancer cells. It had unprecedented success in treating aggressive cancers, but the response rates to these therapies are only 15-30%, and tumours with low-mutational burden, such as oesophageal cancer, are predicted to have a poor response. A current major challenge is to determine whether other immune checkpoints are restricting tumour immunity and whether we can therapeutically exploit them for treating tumours that do not respond to existing checkpoint blockades. Although the efficacy of CD8 T-cells in tumours relies on their production of IFN gamma (IFNg), we discovered that IFNg imposes a negative feedback loop on CD8 T-cells, paradoxically restricting their anti-tumour potential. Blocking this negative feedback loop by deleting the IFNg receptor in CD8 T-cells is sufficient to restore immunity towards non-immunogenic tumours in mice. How IFNg impedes CD8 T-cell activity and whether there is a therapeutic potential is unclear. We propose to unbiasedly uncover the mechanisms leading to IFNg-mediated inhibition of CD8 T-cells and explore the possible applications of these findings. The proposal is orchestrated as such: WP1: Characterising IFNg-downstream pathways in TILs by: - Unbiasedly investigating the IFNg-molecular signature in T-cells - Elucidating the impact of IFNg on T-Cell Receptor Clonality WP2: Deciphering the dynamic relationship between IFNg signalling and T-cells function. T-cells and IFNg deposits are surprisingly segregated, suggesting an intricate relationship between T-cell location and fitness. We will: - Elucidate the distinct micro-environments characterised by T-cell and IFNg location - Investigate the temporal relationship between IFNg production, TIL fitness and localisation - Investigate the Spatio-temporal Consequences of IFNg signalling in TILs WP3: Exploring and Manipulating the IFNg-negative feedback loop in human CD8 T-cells by: - Investigating the IFNg/TIL segregation in human tumours, and its relationship the current tumour immune infiltrate classification - Testing the consequences of IFNg receptor deletion on human T-cell expansion and fitness We will use a combination of genomics, imaging and functional assays to unbiasedly characterise IFNg-negative feedback loop. We will leverage our expertise in CD8 T-cell differentiation and imaging to unravel the potential application of our findings to human anti-tumour responses. Deciphering the mechanisms by which IFNg restricts CD8 T-cell responses might open new venues to treat tumours unresponsive to current checkpoint blockade therapies. In addition, inhibiting the IFNg-negative feedback loop in CD8 T-cells could constitute a novel strategy to improve T-cell transfer therapy.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Defining tumour control by local dendritic cells after checkpoint immunotherapy
Funder: Cancer Research UK

Abstract: Background: Skin cancers outnumber all other cancers, and incidences of melanoma are increasing in the UK. Blockade of inhibitory checkpoints to T-cell activation has opened the door to a new era of cancer treatment. However, release of T-cells from checkpoint inhibition is not sufficient to control disease in the majority of people, and our understanding of the cellular mechanisms leading to tumour regression in patients who do respond remains sparse. Dendritic cells (DC) are antigen presenting cells that are vital for tumour rejection by T-cells, however there is a gap in our understanding of when and where DC are required. Novel findings in our lab have demonstrated a key role for tissue DC in regulating effector T-cell function in the skin, but the functional importance of local DC for tumour rejection by T-cells in malignant tissue at the same site is not known. Here, we will delineate the therapeutic importance of DC:T-cell interactions in tumours, by addressing the following questions: 1. Do T-cells recognise antigen presented by intra-tumoural DC, and how is this altered with aPD-1 treatment? 2. What is the nature and outcome of local DC:T-cell interaction in tumours? 3. When and where are tumour DC required for aPD-1 immunotherapy? Methods: I have expertise in using in vivo models of DC depletion to define the functional outcome of interactions between tissue DC and effector T-cells. This work will combine mechanistic live imaging and flow cytometric analysis using tractable pre-clinical models, and will also benefit from multispectral immunostaining of patient samples. Use: Our lack of understanding about how T-cell immunotherapies lead to durable tumour remission in some melanoma patients is currently a bottleneck in the more effective use of these treatments. This work will fill a gap in our understanding of the biology of local DC:T cell cross-talk for tumour rejection in those patients who are responsive to treatment. This will identify novel pathways that may be targeted for more effective, localised treatment of patients with unresponsive cancers.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Cancer Screening & Statistics
Funder: Cancer Research UK

Abstract: BACKGROUND: Screening is a fundamental part of cancer control. We have had a major role in developing policy, evaluating efficacy and developing new approaches to cancer screening. AIMS: *Quantify the benefits and harms (including over-diagnosis and excessive treatment) of cervix, breast, bowel and prostate screening and identify best practice. *Evaluate the implementation of primary HPV testing. *Study new technologies to: •Improve access to cervical screening (e.g. self-sampling); •Provide a non-invasive approach (Cytosponge+TFF3 staining) to early detection of Barrett’s oesophagus with a view to preventing oesophageal adenocarcinoma; •Improve the options for anal cancer screening (DNA methylation); •Personalise cancer screening based on an individual’s screening test results and other (genetic and environmental) risk factors. *Estimate years of life lost to cancer attributable to lifestyle and environmental factors and the potential for screening to reduce these. METHODS Our approach to evaluating existing screening programmes is to link routinely recorded screening and cancer registration data to establish nested case-control studies within cohorts offered screening. We use data from trials and other sources to estimate and adjust for various sources of bias. Screening-unit-level data will be analysed to assess the importance of screening parameters. Health economics will be studied via micro-simulation models. Data on 1.5 million women in the HPV primary screening pilot will be linked to health outcomes and analysed. Methods employed to study new technologies will vary depending on the technology and the phase of the research. For cancers with identifiable precursors (cervical, anal and oesophageal), we will compare normal tissue, early abnormalities, high-grade lesions and cancers to identify and validate suitable biomarkers. We will carry out both early phase research (including focus groups and biomarker discovery) and model data from large clinical trials being undertaken outside of the programme. We will develop new methodologies for presenting data for prioritising cancer control strategies and evaluate them with stakeholders. These will be applied to incidence and mortality data and risk factor surveys in different countries. HOW THE RESULTS OF THIS RESEARCH WILL BE USED Results will be used to inform and modify national (and international) policy on cancer screening, including target populations, frequency, screening technology, and management of screen-detected abnormalities. Results from the study of new screening technologies will be used to design personalised screening regimens and, where relevant, to plan large trials of these technologies. The attributable fraction will guide the relative importance of different preventive interventions.


Research activity codes: 2.4 SURVEILLANCE AND DISTRIBUTION;4.5 RESOURCES AND INFRASTRUCTURE (DETECTION)
Health categories: CANCER AND NEOPLASMS
Title: B03 - Evaluating integrated and multi-biomarker driven risk stratification in paediatric acute lymphoblastic leukaemia
Funder: Cancer Research UK

Abstract: Acute lymphoblastic leukaemia (ALL) in children, teenagers and young adults (CTYA) is a treatable disease with high cure rates. The successful treatment of the disease relies on assigning patients to the appropriate risk group for treatment. Typically, stratification involves the sequential application of individual biomarkers including age, white cell count, genetics and treatment response. Our previous research identified more sophisticated and precise methods for risk stratification. We designed a novel multi-biomarker stratification algorithm for a new international clinical trial, ALLTogether 01 (A2G-RSA). In addition, we developed and validated an integrated multivariable prognostic index that outputs patient-specific risk scores providing a precise and flexible system for defining risk groups (UKALL-PI). The aims of this study are (1) to evaluate the novel multi-biomarker stratification tool using data from UK patients treated on ALLTogether 01 and (2) to develop further the UKALL-PI by expanding its genetic functionality. We will evaluate the A2G-RSA in two phases. Firstly, we will retrospectively analyse the outcome of patients treated on the UKALL2011 trial to assess two key concepts underpinning the A2G-RSA; the use of genotype-specific minimal residual disease (MRD) thresholds and the prognostic impact of a novel UKALL copy number alteration profile. The second phase involves the prospective collection of data from UK patients (~350/year) treated on ALLTogether 01 from the trial database and NHS genetic laboratories to study the demographic, clinical and genetic characteristics of patients assigned to each of the five risk-based treatment groups; revealing the distribution of risk factors not included in the A2G-RSA. The development of UKALL-PI requires analysis of large well-annotated datasets. We will use existing and new datasets, including UKALL2011, and those held by the EU-funded Big Data HARMONY Alliance. Currently UKALL-PI calculates genetic risk using two variables encompassing good and poor risk abnormalities assigning risk at the group level rather than individual abnormality level. The new structure will incorporate one variable representing the primary abnormality and a second for secondary abnormalities. This reconfiguration will weight each primary abnormality individually and, if significant, allow the integration of secondary abnormalities. The new model will be more flexible and amendable to the incorporation of new abnormalities. Evaluation of the novel A2G-RSA will determine whether any adjustments are required during 7-year trial and will feed into the development of UKALL-PI. The ultimate aim of the development of UKALL-PI is to make it clinic-ready in time for the next trial, ALLTogether 02 trial.


Research activity codes: 4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: Regulation of DNA replication in Mitosis
Funder: Cancer Research UK

Abstract: DNA must be rapidly and accurately duplicated before each cell division. Failures during replication lead to genomic instability which is a major source of many diseases including cancer. Importantly, the duplication of certain ‘difficult-to-replicate’ loci such as common fragile sites (CFS) is often not completed until mitosis, and this delay can have detrimental consequences. In fact, CFSs are among the most commonly rearranged genomic loci in cancer genomes, highlighting a causal connection between cancer and late DNA replication. It remains unclear how cells mitigate damage associated with late replication in mitosis. By using an unbiased proteomics approach as well as candidate screening, Dr. Can aims to discover new factors that are required for the regulation of DNA replication in mitosis. The newly identified factors will be analyzed biochemically to reveal their roles in genomic rearrangement at CFSs. Understanding the regulation of DNA replication in mitosis may uncover new targets for anticancer therapies.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Don't sugarcoat it: understanding and targeting glycosylation changes in pancreatic and liver cancers
Funder: Wellcome Trust

Abstract: Pancreatic ductal adenocarcinoma (PDAC) and hepatocellular carcinoma (HCC) are leading causes of cancer-related deaths. Despite knowing these cancers’ driver mutations, there are no effective therapies. A universal yet understudied feature of both PDAC and HCC is their aberrant glycosylation. Glycosylated serum proteins act as clinical biomarkers, but it is unknown how altered glycosylation – driven by gene expression changes and mutations of glycosyltransferases/glycosidases – contributes to disease progression. First, I propose to establish a new HCC mouse model combining genetic alterations with chronic alcohol consumption, a major risk factor. Second, I will systematically uncover the glycosylation changes in primary cells of this new HCC model and established PDAC models using unbiased mass spectrometry-based glycomics and lectin microarrays. By applying glycobiological techniques to this setting, I will bring together two hitherto disparate research fields. Third, based on these data, I will manipulate the glycosyltransferases/glycosidases most likely responsible for the glycosylation changes and examine disease progression, yielding new targetable oncogenes. In parallel, based on preliminary data, I will investigate the tumour suppressive mechanism of the fucosidase FUCA1 in mouse models of PDAC and HCC, using glycomics as a starting point. Finally, I will validate my findings in human PDAC and HCC samples.

Lay abstract: Pancreatic ductal adenocarcinoma (PDAC) and hepatocellular carcinoma (HCC), the most common forms of pancreatic and liver cancer, are among the deadliest cancer types. Although we know which mutations cause PDAC/HCC, we have no effective therapies. In addition to mutations, cancer cells exhibit changes in their protein modifications. Glycosylation, the addition of sugars, is one such modification. Doctors measure glycosylated proteins in PDAC/HCC patients, but we do not understand how these glycosylation changes contribute to the aggressiveness of PDAC/HCC. First, I will build new models of PDAC/HCC in mice. Second, working with glycobiology experts, I will use mass spectrometry-based glycomics and lectin microarrays to document glycosylation changes in PDAC/HCC cells compared to healthy cells. Third, by removing them in mice or human cells, I will investigate how proteins responsible for glycosylation changes contribute to PDAC/HCC. This project will provide detailed knowledge of glycosylation changes and possibly new therapeutic targets in PDAC/HCC.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Intravital imaging as a platform for screening checkpoint and focal adhesion kinase inhibitors as potential treatment for cancer metastasis
Funder: Wellcome Trust

Abstract: Despite new developments in treatment, cancer remains the second leading cause of death worldwide. Breast cancer is the most common cancer within the UK, with death generally caused by the formation of metastasis. I intend to investigate the hypothesis that immune responses at the metastatic site determine the long-term outcome of therapy. I will compare immune responses at the primary and metastatic sites upon administration of checkpoint inhibitors that have different clinical success rates. Flow cytometry and t-SNE analysis will provide insight into the affected cell populations and timings. I will then utilise newly developed intravital imaging technologies to visualise immune responses in vivo at multiple cancer sites. I will measure cytotoxic cell activity and tumour cell death as indicators for anti-cancer response. Further, I will examine the ability of a combination of checkpoint inhibitor and focal adhesion kinase inhibitor to fully eradicate tumour cells. An inhibitor will be fluorescently tagged to study its access to tissue and interaction with immune cells dependent on combination therapy. The proposed research will help to elucidate the role of immunotherapy on the metastatic foci and will provide the first insights into the benefit and limitations of combination therapy on secondary site immune responses.

Lay abstract: One in six lives are cut short by cancer, with approximately 90% of mortality caused by spreading of the tumour, also called metastasis. I propose to investigate whether cells from our immune system found in secondary tumours contribute to the efficacy of drugs used in breast cancer patients. I will utilise newly developed techniques to visualise how immune cells function in living animal models of breast cancer, and will compare the efficacy of drugs in primary and secondary tumours. I will measure the anti-tumour activity of immune cells as well as how well they bind to tumour cells. Further, I will investigate how therapies that use more than one drug simultaneously act to eradicate metastatic tumours, studying how clinical treatments enter the metastatic site and fulfil their role. My studies will provide insight into the limitations of current therapies to support the design of new, more effective therapies.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Deciphering the mechanisms of epigenetic evolution driving leukaemia
Funder: Wellcome Trust

Abstract: Epigenetic lesions occur at the early stages of cancer development, and have important roles in tumour initiation and progression. However, our understanding of how cancer cells acquire, propagate and select such aberrant epigenetic states remains very limited. Therefore, I propose to define the mechanisms by which initiating epigenetic defects drive tumour evolution in Acute Myeloid Leukemia (AML), a deadly bone marrow cancer with no effective treatment. I hypothesize that initiating genetic defects in the DNA methylation machinery (TET2 mutations) catalyse epigenetic diversity. The resulting epiclones might acquire properties that increase cellular fitness, predisposing cells to undergo transformation and generating a substrate for selection. Using state-of-the-art single cell DNA methylation and transcriptomic technologies coupled with lineage tracing, I will quantify stably propagated epigenetic diversity in TET2 deficient cells (Aim1), and identify selective advantage of high-fitness epiclones upon cell-extrinsic pressures (Aim2). I will then characterize putative driver epimutations in longitudinal AML patient samples and demonstrate their functional role promoting leukaemic transformation using locus-specific epigenomic editing tools (dCas9-DNMT3A; Aim3). This research will shed light into the fundamental molecular mechanisms driving epigenetic diversification and selection of cancer cells, with the potential to bring an entirely new dimension to cancer treatment by intercepting tumour evolution.

Lay abstract: My research seeks to understand how epigenetic lesions and epigenetic diversity contribute to tumour initiation and progression, and more specifically, how these epigenetic errors can lead to leukaemia. Cells in an individual tumour can vary markedly in their epigenetic states and transcriptional outputs, enhancing its ability to adapt under various conditions and proliferate faster. I will use state-of-the-art single-cell sequencing technologies to analyse individual cancer cells, characterizing their epigenetic errors (epimutations) and the genes that are activated (transcriptome) during its evolution. I will then introduce epimutations in normal blood cells to mimic cancer cell properties. This will enable me to identify which of those errors drive leukaemia progression. This integrated and innovative approach will contribute to our fundamental understanding on how cells acquire epigenetic aberrations and evolve to give rise to leukaemia, and will inform new therapeutic strategies to target epigenetic lesions in cancer patients.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Aptamer-based therapeutic targeting of mutant SRSF2 in myeloid malignancy
Funder: Cancer Research UK

Abstract: Background: The splicing regulator SRSF2 is recurrently mutated across myeloid malignancies, and is common in elderly patients with few treatment options and dismal prognosis. These founder mutations exclusively involve the proline 95 “hotspot” and alter SRSF2’s RNA binding properties, inducing pathogenic impacts on splicing and expression of key haematopoietic genes. Mutant SRSF2 is not druggable by small molecules. We instead propose an aptamer-based approach, exploiting SRSF2’s native function as an RNA-binding protein. Aptamers are synthetic single-stranded nucleotides that form diverse secondary structures, have enormous conformational plasticity and bind target proteins with high affinity. Several properties make them attractive candidate therapeutics. We have demonstrated feasibility to enrich DNA aptamers that selectively bind mutant versus wild type SRSF2 protein. Aims: To design, optimise and validate a useable therapeutic product displaying biological efficacy and suitable physicochemical properties for definitive preclinical testing. Work packages will deliver understanding of binding mechanisms and key properties of lead aptamers whilst addressing potential obstacles to clinical translation including stability and intracellular delivery. Preliminary in vitro and in vivo preclinical evaluation of lead structures will be performed. Methods: Aptamers will be selected by Systematic Evolution of Ligands by Exponential Enrichment (SELEX), using recombinant mutant/wild type SRSF2 protein and a large starting library of random modified RNA aptamers. Through iterative selection cycles applying pre-defined competitive pressures, aptamers with desired binding characteristics will be enriched. Their key properties will be established, including binding affinity by Biolayer Interferometry, stability in biological media, trafficking to/within cells, and in vitro effects on splicing. Repeat SELEX will be performed to (1) identify a nuclease-resistant RNA aptamer displaying optimised mutant SRSF2 binding affinity and specificity; and (2) identify an escort aptamer against cell surface CXCR4, for disease cell-targeted aptamer delivery and internalisation. Optimised components will be assembled and further conjugated if required to evade renal filtration. Lead structures will undergo in vitro validation of binding, pharmacokinetic and biological properties in appropriate cell models, before a proof-of-concept murine in vivo study using a primary human xenotransplantation model. Use of results: Data generated will directly inform subsequent work packages, to optimize design and guide requisite modifications. Preliminary in vitro and in vivo data on lead structures will support further investment and partnerships (e.g. with industry) for more extensive preclinical evaluation and, ultimately, early phase human trials to address this area of unmet clinical need.


Research activity codes: 5.1 PHARMACEUTICALS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS