NIHRDataInsights/HRCSData huggingface dataset:
Title: BALI – A new technology for multiplex spatial molecular analysis
Funder: Cancer Research UK

Abstract: Background: The need to perform spatial molecular measurements on biological tissues, bridging the gap between high-resolution methods such as histology and microscopy and high-throughput ones such as sequencing, is emerging as one of the defining future themes for many areas of biology. This is particularly true for cancer biology, as the evolution of tumours through time and in response to therapy is affected by local interactions between sub-populations of cancer cells and the tumour micro-environment surrounding them, which cannot be captured by studying in vitro or disaggregated samples. In the last few years many methods have been proposed for in-situ transcriptomic analysis. Unfortunately, the application of these new technologies to cancer research has been complicated by many issues, mostly due to the need to perform high-resolution single molecule imaging, repeatedly and reliably, on extremely challenging samples. In addition, these methods require costly equipment and are often limited in either the number of genes they can detect, their speed, or their resolution. Aims: We propose a ground-breaking new technique using light to “write” a distinct spatial barcode on each cell of a biological sample, enabling the use of high-throughput sequencing to resolve spatial information. We call this new method “BALI”. 1. Aim 1: Development of BALI for spatial RNA profiling. 2. Aim 2: Content-aware cell tagging. 3. Aim 3: Simultaneous multi-modal measurements. Methods: Our proposed method is based on using light to guide the assembly of spatial barcodes onto cells of interest in a tissue section. At the end of the protocol, the unique spatial barcodes on each cell can be resolved by sequencing with high speed and accuracy. The spatial barcodes could also easily be applied to other biological molecules, enabling simultaneous measurement of gene expression and other parameters. How the results will be used Success in this grant would provide cancer biology with an extremely, high yield and low-cost method to measure gene and protein expression in situ on large samples. We estimate that our method could initially analyse 1000 genes in every cell of a 2x2cm tumour section in just a few days, and propose a number of potential improvements.


Research activity codes: 2.6 RESOURCES AND INFRASTRUCTURE (AETIOLOGY)
Health categories: CANCER AND NEOPLASMS
Title: TreeC: a novel low-input, ligation-free approach of detecting chromatin interactions
Funder: Cancer Research UK

Abstract: Background Chromosome Conformation Capture methods have revolutionised our understanding of gene regulation by uncovering how the 3D architecture of the cell nucleus creates complex networks of regulatory regions. Accurately identifying such interactions is paramount for understanding the mechanisms behind gene activation and repression both in normal physiology and disease. Enhancer-promoter (EP) interactions occur between gene promoters and distal regions (enhancers) and can determine the expression of multiple genes by forming large transcription factor complexes, sometimes hosted within so-called chromatin loops, which are still poorly understood. Current methods for interrogating these interactions, such as 3C or Hi-C, are based on restriction enzyme digestion followed by re-ligation and pull-down. This limits their resolution and ability to detect long-range interactions. These methods also require a large number of cells as starting material and cannot be applied to tumour or rare tissue samples, especially from the clinic. Moreover, they have low efficiency, requiring hundreds of millions of reads for each sample, high cost, and cannot capture effectively interactions between a locus and multiple others unless information from many cells is averaged. This limits their usefulness in investigating the role of chromatin dynamics in cancer progression. Aims 1. Development of a low input, multiplexed method for chromatin conformation capture 2. Modulating the range of contact detection and identifying different types of chromatin contacts 3. Expanding TreeC and integrating it with spatial and imaging technologies 4. Development of a specific statistical framework to identify interactions at multiple ranges Methods We propose TreeC, a high-resolution, novel technology for the multiplexed detection of interactions between a set of chromatin loci (possibly expandable to genome-wide) and their interactors within a specified range. TreeC is based on Tn5 transposition from a branched detection probe hybridised to the interrogated loci into interacting regions of chromatin, followed by in-vitro transcription and sequencing. Our method can detect hundreds of interactors for each donor locus, can be targeted to specific regions with great precision, and can detect interactions at multiple ranges by modulating the branch length and stiffness. How the results will be used TreeC will allow researchers to detect simultaneous interactions between multiple regions of interest at high resolution, using 100,000 cells or less instead of 5-10 million, at a reduced cost. This enables studying the role of chromatin structure on gene regulation in cancer with greater depth and in samples previously not accessible to this technology, i.e. clinical biopsies.


Research activity codes: 1.5 RESOURCES AND INFRASTRUCTURE (UNDERPINNING)
Health categories: CANCER AND NEOPLASMS
Title: YOUTH RESPONSES TO E-CIGARETTES, E-CIGARETTE RETAILING, AND E-CIGARETTE PACKAGING IN ENGLAND, CANADA, AND THE UNITED STATES
Funder: Cancer Research UK

Abstract: Background: There are concerns that e-cigarette use (vaping) among youth may lead to exposure to nicotine and other constituents, nicotine addiction, and progression to tobacco smoking. Vaping among UK youth is low but there are concerns that this could increase, particularly given rises in youth vaping in Canada and the US. Aims: We aim to examine 1a) youth responses e-cigarettes, among older youth, 16-24 years old, including patterns of use, dependence, products used, and brands used, and exposure and 1b) perceptions and exposure to public health messaging around e-cigarettes in England compared to Canada and the US, 2) levels content of e-cigarettes marketing at the point-of-purchase, and 3) the content, appeal and harm perceptions of e-cigarette packaging, including the possible impact of standardised packaging of e-cigarettes among youth and adults. Methodology: 1) Augmentation of the International Tobacco Control Youth Survey (16-19 years) in England, Canada, and the US, to include 16-24 year olds to examine patterns of use, dependence, and products used among older youth, and measures of exposure to e-cigarette public health messaging. 2) an audit of brick and mortar and online e-cigarette retailers. 3) Analysis of e-cigarette packaging in England, Canada, and the US, and packaging experiments to compare branded v standardised packaging among youth and adults. Results: This study will help inform policy decisions regarding whether further regulatory action around e-cigarettes is needed in order to prevent youth uptake, such as stricter regulations on advertising at the point-of-purchase, and standardised packaging, while at the same time considering the impact that these regulations could have on smokers who may use e-cigarettes for cessation.


Research activity codes: 3.1 PRIMARY PREVENTION INTERVENTIONS TO MODIFY BEHAVIOURS OR PROMOTE WELL-BEING
Health categories: CANCER AND NEOPLASMS
Title: IDENT: Improving Design and analysis of oncology trials Evaluating New targeted Therapies
Funder: Cancer Research UK

Abstract: Clinical trials are used to test the risk and benefit of a new therapy before it can be made widely available. These trials have been designed to test if the ‘average’ patient benefits. However, in trials of new cancer treatments, patients can respond very differently to the same treatment. This is often because tumours have different mutations. Modern ‘targeted treatments’ are developed to target particular genetic make-up of the tumour instead of the location of the cancer in the body. My work will focus on a new trial approach called ‘basket trials’, which can enrol patients of different cancer types, for example, lung cancer and breast cancer that share similar genetic profiles, to receive the same anti-cancer therapy. There are two main advantages of basket trials. Firstly, it is easier, quicker and cheaper to run a basket trial than assess each cancer location separately. Secondly, basket trials allow patient information to be fully used for understanding how the therapy works in different cancer types. Current approaches often 1) analyse each part of a basket trial separately, 2) ask for a maximum number of patients to establish the efficacy, which is inefficient and exposes more patients to an unproven treatment than might be necessary, and 3) do not allow making changes as the trial continues. My statistical expertise will help improve basket trials to find effective cancer treatments. I will develop analysis models to make better use of basket trial data. They will allow sharing of information between similar cancer types. This will mean that we get a better understanding about which treatments work, and for whom. These new statistical approaches will make a difference to the way we design basket trials. I will propose new methods to calculate the required number of patients to recruit in a basket trial. Because information from similar parts can be combined, a considerably smaller number of patients will be needed. More flexible designs will also be developed to allow making changes as the basket trial continues. For example, it would be possible to stop some parts earlier than planned, if evidence shows a meaningful improvement in patients’ outcome. As a result, basket trials can be completed quicker and at a lower cost, allowing new therapies to go from creation to use in practice considerably quicker. In this way, cancer patients can be assured to be treated much quicker and with more effective therapies.


Research activity codes: 6.9 RESOURCES AND INFRASTRUCTURE (TREATMENT EVALUATION)
Health categories: CANCER AND NEOPLASMS
Title: Investigating the Implications of Transcriptomic and Metabolic Heterogeneity for Therapy Resistance in Myeloid Leukemia Stem Cells
Funder: Cancer Research UK

Abstract: Background Molecular therapies in cancer can often induce patient remission without achieving a complete disease eradication. A better understanding of cancer heterogeneity is crucial for the development of effective therapeutic strategies. One level of cancer heterogeneity is the proposed hierarchical structure of tumors, with “cancer stem cells” (CSCs) being able to propagate the tumor and recapitulate its heterogeneous features. Chronic Myeloid Leukemia (CML) is propagated by CSCs (CML-SCs) that are selectively resistant to therapy. My postdoctoral project focused on characterizing CML-SCs heterogeneity using single-cell transcriptomics. This analysis revealed a complex molecular heterogeneity, with cells carrying a distinct transcriptomic signature of “therapy-resistance” being detected already at diagnosis and progressively enriched during treatment. One of the main drivers of such heterogeneity appeared to be the cell metabolic state. Metabolic reprogramming is well recognized as a hallmark of cancer, but whether a metabolic heterogeneity exists within the leukemic stem cell pool at diagnosis and if this may be linked to heterogenous responses to therapy remains to be established. The lesson learnt from therapy-resistant CML-SCs may be translated from CML to other CSCs-based hematological cancers with poorer prognosis, such as Acute Myeloid Leukemia (AML). Aims -AIM1. Can we identify therapy-resistant CML-SCs at diagnosis? -AIM2. Can we manipulate CML-SCs metabolic programs to prevent therapy resistance? -AIM3. Can we exploit CML-SCs “identikit” to predict therapy resistance in other hematological malignancies (AML)? Methods Using a combination of transcriptomic and metabolomic measurements, I will test whether the signature of therapy resistance derived from CML-SCs can be applied to diagnostic samples to identify and characterize therapy-resistance-prone CML-SCs, already present at diagnosis. Next, by perturbing pathways relevant to therapy-resistance in-vitro and in-vivo, I will test whether CML-SCs therapy-resistance and malignant transformation can be prevented. Finally, by performing single-cell transcriptomic on AML diagnostic samples, I will test whether the signature of therapy resistance obtained from CML-SCs can be applied for the early identification of therapy-resistance-prone LSCs in AML. How results will be used This project will provide a new understanding of the impact of LSCs heterogeneity on the development of therapy resistance. We will determine whether, by using the activation of specific transcriptomic and metabolic programs, we can identify CSCs programmed to give rise to therapy-resistance. This approach may result in the development of novel strategies for the early detection and monitoring of therapy-resistance-prone cells in cancer, with important implications for the development of therapeutic strategies to prevent disease progression.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: CRUK/17/013 E-smart: European proof of concept therapeutic stratification trial of molecular anomalies in relapsed or refractory tumours in children
Funder: Cancer Research UK

Abstract: Background Cancer is the leading cause of death in children beyond infancy.There is an urgent need to improve therapeutic options for children and adolescents with poor prognosis and high risk cancers. Stratified precision medicine approaches have started to revolutionize treatment and outcomes in the adult cancer setting and it is crucial that this progress is harnessed for children. The advent of advanced molecular profiling has increased our understanding of actionable alterations in paediatric malignancies which may be targeted by novel agents developed for adults but with a mechanism of action relevant to paediatric tumour biology. Challenges include the relatively small individual patient populations, and diversity and heterogeneity of detected molecular alterations. There is a high unmet need for more efficient drug development strategies to help progress promising drugs quickly and safely into combination approaches, avoiding treating children at sub-optimal doses in multiple unnecessary dose escalation cohorts, and better assessment of efficacy. Aims Primary: Phase I - to dose-validate and establish the safety profile of the selected novel agent/drug combination in paediatric and adolescent patients with recurrent or refractory malignancies using a dosing schedule extrapolated from the adult recommended phase II dose. Phase II - to determine the anti-tumour activity of the novel agent(s)in molecularly enriched patient cohorts by assessing response rates. Secondary: To characterize the toxicity profile and pharmacokinetics of the agent(s). To evaluate progression free survival and incidence of long-term responders. To evaluate whether response rate is higher in enriched compared to non-enriched populations. Exploratory: To explore pharmacodynamic biomarkers of target inhibition and relationships between tumour expression of the target(s), circulating tumour DNA and tumour growth. Methods E-SMART is the first international, multi-arm, open-label, prospective, dose-validation basket study (Phase I), with expansion to an anti-tumour activity assessment in molecularly enriched cohorts (Phase II) for several novel agents alone or in combination, for children and adolescents with relapsed/refractory malignancies. The trial will open with seven arms and recruit 200-285 patients across Europe over 3 years. The adaptive design allows for the introduction of new therapeutic arms as novel targets and agents emerge. How the results will be used If promising activity is seen for one or more of the arms, the aim would be to incorporate the drugs/combinations into more front line treatments via randomized clinical trials. Knowledge obtained regarding predictors of response including specific molecular alterations will be used to inform patient enrollment and stratification for future studies.


Research activity codes: 6.1 PHARMACEUTICALS;4.2 EVALUATION OF MARKERS AND TECHNOLOGIES;5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Targeting MYC through next generation structure-function
Funder: Cancer Research UK

Abstract: Background: It is estimated that dysregulation of MYC occurs in over 70% of all human cancers, making it one of the most enticing targets for cancer drug development. However, no efficacious small molecule inhibitors have reached clinical stage development for this challenging target. Through CRUK Pioneer funding, we have shown that the N-terminus of MYC is absolutely required for tumour maintenance. We performed a site-saturation structure function screen, identifying 19 different N-terminal residues that are crucial to function, many of which involve novel sites. Aims: We plan to validate these mutations for oncogenic function in a variety of in vitro and in vivo tumour models. We hypothesise these mutations disrupt specific protein-protein interactions, and we aim to identify the direct MYC binding partners that are crucial for function. Lastly, we aim to build a 3-dimensional model of the specific protein-protein interface of MYC with its binding partner. Methods: The 19 different mutations will be individually validated for their ability to rescue cell growth in MYC-off T-ALL cell lines, neuroblastoma lines and breast cancer cell lines. We will test the transformation potential of these mutations in an in vivo model of MYC-induced T-cell acute lymphoblastic leukaemia in the zebrafish. Using BioID, we will characterise the protein binding partners of MYC and MYC mutants, enabling us to identify the specific direct interactors of MYC that are crucial for its oncogenic function. Lastly, we will characterise the protein-protein interface using HDX-MS and generate a crystal structure of MYC together with its binding partner. How results will be used: characterising the specific protein-protein interface of MYC with a critical partner protein will provide a framework for rational drug design and enable direct small molecule screens for inhibitors that interrupt formation of the complex.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Infrastructure in FLASH radiotherapy
Funder: Cancer Research UK

Abstract: Background: Ultra-high dose rate radiotherapy (FLASH) (typically > 40 Gy/s) is attracting worldwide interest as it offers the potential of increased normal tissue sparing, compared to conventional radiotherapy, while still supressing tumour growth. However, large gaps exist in the mechanistic understanding of the “FLASH” effect in both normal tissue and tumours. This is why we need an experimental infrastructure that allows researchers access to state of the art technology to deliver FLASH beams and the in vitro and in vivo biological systems to investigate it. Aims: to provide a FLASH infrastructure with world-leading capabilities that will draw on the strengths of the CRUK RadNet partners to provide solutions to the questions that confront FLASH research now and, in the future, and to allow a seamless transition from mechanistic discovery science to early phase clinical evaluation. Methods This RadNet FLASH infrastructure will have access to FLASH proton and electron beams at Manchester and Oxford respectively, it will also have access to a range of in vitro and in vivo biological models (Cambridge) combined with access to the RadNet multidisciplinary expertise across all 7 RadNet centres. The infrastructure will intersect with the RadNet working groups e.g. drug radiation combinations, immune therapy and quality assurance and standardisation. Three FLASH Fellows (PDRA) will be recruited who will be based in Manchester, Oxford and Cambridge and will work together and with the other RadNet centres. The strength of the infrastructure will be demonstrated using exemplar projects which challenge existing ideas and create novel biological datasets to inform the exploitation of the FLASH effect and take molecular biology through to tumour and normal tissue. How this research will be used: The FLASH Fellows will work with RadNet and the wider scientific community on pump-priming and student projects. These projects will provide results for RadNet networking and larger project or programme grants and high impact publications. Funding for infrastructure access from these grants and industry provides a route to the long-term sustainability of this infrastructure, both in terms of funding the FLASH Fellows and running equipment. The infrastructure will report through the RadNet Emerging Radiotherapy Technologies Working Group (ERT) to the RadNet Directors meeting. Applications to access the infrastructure will be presented at ERT where they will be prioritised, each will be supported by a FLASH Fellow. All applications will be dealt with in a fair and transparent manner with evaluators selected to eliminate conflicts of interest.


Research activity codes: 5.9 RESOURCES AND INFRASTRUCTURE (TREATMENT DEVELOPMENT)
Health categories: CANCER AND NEOPLASMS
Title: Using HDGC to build a toolkit to distinguish indolent from consequential early cancer lesions
Funder: Cancer Research UK

Abstract: Understanding the factors that cause normal cells to become cancerous is crucial in developing tools to detect tumours before they become incurable. Our current understanding of how cancers form is that the accumulation of DNA changes triggers a cell to behave like a cancer. Recently, several researchers including ourselves have identified, surprisingly, that a large number of these changes occur within normal cells in healthy people with no cancer history. It therefore remains unclear which changes best identify tissue that is going to become lethal cancer. Hereditary diffuse gastric cancer (HDGC) is the ideal condition to study this. Patients with HDGC develop many small changes in the stomach some of which turn into lethal cancers and some of which don’t. Cambridge has established a unique collection of material donated by patients with this condition. We will study DNA from their normal stomach and stomach pre-cancers. As DNA changes may not be the only factor driving these changes we will also look at the cells surrounding the different stages of the disease to see how these change. We hope to identify those changes that are only seen in high-risk patients and so could be used to predict who will develop lethal cancer and target them for intervention to prevent this e.g. early surgery or enhanced follow-up.


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