NIHRDataInsights/HRCSData huggingface dataset:
Title: Investigating heterocellular signalling in the micro-metastatic stage of colorectal cancer recurrence in the liver
Funder: Cancer Research UK

Abstract: Background: Despite adjuvant chemotherapy, over 30% of Stage III (node-positive) colorectal cancer (CRC) patients suffer post-operative recurrence, which is most frequently seen in the liver. In these cases, micro-metastatic disease has not been effectively cleared, leading to persistence and establishment of colorectal liver metastases. Certain molecular variants (CMS-4) have worse prognosis and these will be our initial focus. Aims: The aims of this project are to: (i) model the micro-metastatic stage of post-surgical CRC recurrence in the liver; (ii) map the signalling cross-talk between CRC cells, hepatocytes and hepatic stellate cells (HStCs); (iii) predict targeted inhibitors which disrupt growth and survival signals conferred on CRC cells by the liver microenvironment; (iv) determine the signalling effects of selected inhibitors compared to standard adjuvant therapy, in co-culture systems, using patient-derived organoids (PDOs). Methods: Micro-metastatic CRC recurrence in the liver will be modelled using 2D and 3D co-cultures of CRC cells/ PDOs, hepatocytes and HStCs. Initially, the effect of resident liver cells on CRC growth and morphology will be assessed by microscopy. Next, reciprocal changes in cell state and signalling will be identified by subjecting co-cultures to mass cytometry (CyTOF). These data will guide the selection and testing of signalling inhibitors (small molecule inhibitors/ blocking antibodies), which abrogate growth and survival benefits conferred upon CRC by the liver microenvironment. Finally, co-cultures comprising PDOs from Stage III CRC will be used to assess signal-directed interventions (e.g. EGFR/ MEK/ PI3K inhibitors) in comparison to and combined with standard of care (e.g. capecitabine/ FOLFOX). How the results of this research will be used: The study will generate a network of signalling between CRC cells and the liver microenvironment, which can be utilised in biomarker development studies and clinical trials for post-surgical Stage III CRC. Signalling nodes and pathways which are activated in co-culture assays will be put forward as predictive biomarkers for selection of targeted adjuvant treatments. Furthermore, clinically approved inhibitors already exist for the majority of signalling nodes being assessed, allowing for potentially rapid translation to clinical trials, or co-clinical trials using PDOs.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Quantifying the impact of novel cancer treatments on Lung Cancer Control and Normal Tissue Complication Probability
Funder: Cancer Research UK

Abstract: Background: Lung Cancer (LC) has has seen little improvement in survival in the past several decades. While Stereotactic ablative radiotherapy (SABR), proton radiotherapy and immunotherapy have individually shown promise, their relative impact on toxicity free patient survival is not yet well understood or quantified. Ultimately, to probe the inner mechanisms of treatment impacts on tumour control probability (TCP) and normal tissue complication probability (NTCP), validated models must be built and analyzed in order to determine which treatment features can maximize clinical outcomes for patients. Aims: We aim to generate validated TCP/ NTCP models via machine learning (ML). We subsequently aim to analyze predictive ML models to determine the relationship between treatment features (e.g. dose distribution, immunotherapy interval, radiotherapy particle) and TCP/NTCP to gain insight into which features are most predictive of toxicity free tumour control. This project also aims to quantify the relative degree to which these features (and their interactions) have an impact on patient outcomes. Methods: We have arranged to acquire a dataset of 1607 LC patients treated with curative intent. This dataset contains information on patient demographics (age, gender, etc.), diagnosis (tumour type, location, stage, etc.), treatment (radiotherapy dose distribution and particle, immunotherapy, concurrent chemotherapy, etc.). The dataset also contains patient follow-ups on incidence of various self-reported toxicities and follow-up CT scans. We seek to fund clinician time to sift through these patients and determine progression free survival (PFS) to use as a definition for tumour control. From this data we aim to identify and collate key patient dosimetric and non-dosimetric features for input into ML based TCP/NTCP models. Lastly, we seek to determine which treatment features (and interaction effects between features) have the largest relative impacts on patient TCP. How the results will be used: Our results could provide insight into which treatment characteristics most affect TCP/NTCP. Some key questions that we wish to answer are 1) which treatment parameters in this large dataset are most predictive of TCP/NTCP? 2) Are there any important interactions between treatment features that have not noticed in previous studies? 3) Can we answer lingering questions that can help clinicians gain insight on how best to plan LC treatments (e.g. in cases where patients receive sequential immunotherapy following radiotherapy (RT), there is an open question about the the time interval between these two therapies as it affects progression free survival). Therefore the results should help clinicians best optimize LC patient outcomes.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: Exploring loco-regional heterogeneity in head and neck squamous cell carcinoma within the ART DECO trial
Funder: Cancer Research UK

Abstract: Background Head and neck squamous cell carcinoma (HNSCC) can be cured by radical radiotherapy, often in combination with chemotherapy. Approximately half of people treated in this way are cured, but there is currently no way to predict who will be cured and who will not. Patients with disease that has spread to the local lymph nodes are less likely to be cured. Those patients who relapse have limited treatment options and very poor clinical outcomes, reflecting a significant unmet clinical need. HNSCC remains a less well-studied cancer, with the biology underpinning radiotherapy resistance and lymph node metastasis in HNSCC largely unknown. Large genomics studies have revealed the importance of tumour heterogeneity in other cancer types but there are few data available for HNSCC. An early study of HNSCC in TCGA data suggested patients with a greater index of heterogeneity have a worse outcome (Mroz et al 2015 PLoS Med), inviting the hypothesis that greater subclonal diversity could be a factor in poorer outcome despite radical radiotherapy. Aims We hypothesise that clonal evolution drives loco-regional progression in HNSCC, leading to regional lymph node metastases and sub clonal diversity that increases resistance to radical radiotherapy. We aim to characterise the genomic differences between primary HNSCC and local lymph node metastases collected in ART DECO, a large phase III trial of radiotherapy in HNSCC, generating preliminary data for a larger translational study that will include clinical outcomes. Methods First, we will assess tumour evolution in matched primary tumour and lymph node metastases by exome sequencing tumour tissue collected in the ART DECO trial, a negative study of radiotherapy dose escalation in locally advanced HNSCC. This will allow comparison of copy number and mutation profiles between matched pairs to look at genomic changes that could precipitate loco-regional spread. Secondly, we will infer the sub clonal architecture in the matched pairs. This will allow assessment of the mutational signatures at a clonal and subclonal level, enabling comparison to see if genomic drivers of diversity differ between primary and regional metastases, and between different subclones. Lastly, we plan to conduct an exploratory analysis of neoantigens and neoantigen binding in the context of the observed immune cell infiltrate. How the results of this research will be used This will potentially break new ground in the understanding of HNSCC lymph node metastases and provide proof of principle for a larger translational analysis of the ART DECO trial.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Patient derived co-cultures for studying immunotherapy resistance in bladder cancer
Funder: Cancer Research UK

Abstract: Background: Immune checkpoint inhibition (CPI) in metastatic bladder cancer (mBC) shows promising response rates but many patients fail to respond or develop resistance. Tumour infiltrating lymphocytes (TILs) are thought to play a key role in the activity of CPI. Patient derived bladder cancer organoids and co-cultures of other tumour organoids with peripheral blood mononuclear cells (PBMCs) or TILs have been developed. However, their utility to interrogate tumour reactive T cells is limited due to the sparse population in PBMCs and the technical difficulties and lack of patient acceptance of repeated invasive biopsies required for TILs. We have previously demonstrated that urine derived lymphocytes (UDLs) may be a surrogate for TILs and hypothesise that UDLs would be highly accessible source of tumour reactive lymphocytes to develop a clinically relevant co-culture bladder cancer organoid model. Such a model could be used to interrogate immunotherapy treatment resistance over time and to generate adoptive cellular therapies. Aims: The aim of this study is to develop a bladder cancer organoid model and to co-culture UDLs. The main objectives are: 1. To establish a human bladder cancer organoid model, 2. To co-culture UDLs and organoids to enrich tumour-reactive T cells, 3. To use this model to assess mechanisms of immune mediated resistance and response to treatment. Methods: We will perform a non-interventional study in patients with mBC undergoing treatment with CPI. Urine and bloods samples will be collected for UDLs and PBMCs. We will collect matched tumour tissue derived from needle biopsies or surgical specimens. We will generate organoids from bladder cancer tissue and non-tumour autologous tissue as controls. PBMCs and UDLs will be co-cultured with these organoids to create organoid-lymphocyte co-cultures. Flow cytometry will be used to confirm tumour recognition by T cells by staining for markers for population, activation, differentiation, proliferation and cell viability. Cell death of organoids following exposure to T cells will be evaluated. How the results of this research will be used: Establishing bladder cancer organoid co-cultures will allow us to study the interactions between T cells and tumour cells and help to support T cell-based therapies. The model allows us to study mechanisms of immune resistance and make predictions about rational combination approaches with immunotherapy. This model will help us expand tumour-reactive T cells by co-culture of UDLs with the organoids. This may allow for the generation of large amounts of patient-specific T cells for use in adoptive cell therapy.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: The genomic and phenotypic characterisation of inflammation, injury and repair in the oesophagus
Funder: Cancer Research UK

Abstract: Background Recent advances in whole genome sequencing have shown that somatic mutagenesis is not unique to cancer. Non-cancerous diseases of the oesophagus are rising in incidence with a significant effect on life expectancy and quality of life. Repeated cycles of inflammation, injury and repair are thought to contribute to their pathogenesis and associated cancer risk, yet the process of how cells in the oesophagus respond to injury and renew remain poorly understood. Unravelling this will advance our understanding of how tissue regenerates appropriately and how this process goes astray and contributes to the earliest steps of carcinogenesis. Aims We aim to determine the effect on the human genome and transcriptome in the oesophagus, in the context of inflammation, injury and repair. This will be in the context of diseased non-cancerous conditions and epithelial loss and regeneration in patients with oesophageal perforation. We aim to delineate the somatic mutagenesis and associated effects on the transcriptome in injured and regenerated tissue, and compare this to normal epithelium and cancer development. Methods This pilot study will be divided in two groups. Cohort 1: Diseased non-cancerous conditions (n=5) including esophagitis and achalasia; Cohort 2: Epithelial loss undergoing regenerative therapy (n=5) in cases of oesophageal perforation. Samples will be collected using endoscopy and at surgery for Cohort 1 and a combination of endoscopy and vacuum sponge therapy for Cohort 2. The latter involves an endoluminal vacuum sponge inserted into a hole in the cavity, connected to negative pressure and changed every three days until the cavity regenerates (median time of 21 days). Live cell suspensions (from the enoluminal vacuum sponge), and snap frozen samples will be collected at several time-points and undergo whole genome sequencing using high resolution techniques developed at the WTSI (including Laser Capture Microscopy) and single cell RNA sequencing. Data analysis will include mutational signatures, somatic variant and copy number calling (DNA) and gene expression analysis (RNA). How the results of the research will be used We anticipate that this experiment will provide preliminary results for use in a larger study, for which further funding will be applied. The changes that characterize the genome and transcriptome in the injured and regenerated oesophagus will advance our knowledge of this process, and its association with the earliest steps of carcinogenesis. In the longer term, understanding how the oesophagus regenerates will also provide valuable information for clinical tissue engineering applications associated with cancer therapies.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: CANCER AND NEOPLASMS
Title: A07 - Generating personalised preclinical models for advanced paediatric thyroid cancer
Funder: Cancer Research UK

Abstract: Background Thyroid cancer is increasing in incidence, but children are also more likely to present with advanced (i.e. Stages 3 or 4) or multi-focal disease and are more likely to relapse than adults. Patient-derived xenograft models (PDXMs), where tumour tissue is implanted and expanded subcutaneously in immune-compromised mice, have emerged as an important preclinical system for faithfully recreating tumour behaviour in vivo. Although the value of PDXMs for addressing clinically relevant questions about treatment response has been repeatedly demonstrated in many other paediatric and adult cancers, the technology has yet to be applied in the paediatric thyroid cancer setting. Aims 1. Establishment of a PDXM pipeline and associated cryopreserved bioresources for the study of advanced paediatric thyroid cancer (APTC); 2. Validation of the novel APTC PDXMs’ genetic stability and the closeness of their relationship to the original tumour; and 3. Demonstration as proof-of-principle that the APTC PDXM system can be used for personalised prognostication of disease relapse and treatment response. Methods PDXMs will be derived and characterised from distinct tumour regions (n=4-6/patient) within surgical resected APTC specimens across the histological spectrum (n=10 patients). At every stage, samples of tissue and DNA will be cryopreserved for later analyses. PDXMs will be created by subcutaneous injection of tumour material into immune-compromised NOD-SCID-gamma (NSG) mice followed by four passages to establish lines, according to our group’s established protocols for lung cancer PDX generation. Validation of PDXM genetic stability and behaviour will be performed by comparing matched immunohistochemistry and whole exome sequencing for successful APTC PDXMs and original tumour regions from an individual patient. PDXM data will be correlated with anonymised clinical multidisciplinary follow-up for each recruited child. In the event of any previous donor suffering clinical relapse, recurrent tumour material will also be retrieved at the time of confirmatory biopsy and cryopreserved. How the results of this research will be used The data generated from this project will be used for follow-on funding applications to establish a wider paediatric thyroid cancer research programme including clinical trials using personalised PDXMs to identify patient-specific treatment targets. This will include validating the model’s stability for all recruited patients, recruiting further patients to enable subgroup analysis by histological tumour type. replicate and scale up these findings, and, in any recruited patients who develop recurrence, re-initiating cryopreserved patient specific PDXM lines to model adjuvant therapy administration and response to treatment.


Research activity codes: 4.5 RESOURCES AND INFRASTRUCTURE (DETECTION)
Health categories: CANCER AND NEOPLASMS
Title: ELTD1 (ADGRL4) in glioblastoma: structure and therapeutic targeting
Funder: Cancer Research UK

Abstract: Background: Glioblastoma is the most common and aggressive malignant brain tumour and is generally incurable. Improving outcomes is a serious unmet clinical need. ELTD1 (also known as ADGRL4), is a promising new therapeutic target in glioblastoma and other tumour types (breast, head & neck, renal, colorectal, liver and ovarian cancers). ELTD1, an adhesion GPCR (AGPCR) is upregulated within glioblastoma tumour cells and tumour-associated endothelial cells and plays a role in tumour proliferation, migration and invasion. Aims: My project seeks to use cryo-electron microscopy (cryo-EM) to determine ELTD1’s structure in both active and inactive states at high resolution, to be followed by in silico small molecule screening and in vitro candidate testing. This grant application is specifically to cover the initial structuring work leading to cryo-EM over 24-months. To date, only 1 AGPCR has been partially structured. Method: Various engineered ELTD1 constructs will be designed and synthesised (incorporating various mutations/ truncations to improve expression, stability, or to trigger self-activation). Structuring will be approached through three different approaches: 1) Inactive state receptor, stabilised using the KOR-ICL3-nanobody6 graft approach. 2) Active state receptor, stabilised with its specific mini-G protein. This will be preceded by signalling experiments with all known G proteins done in collaboration with Dr Jayesh Patel (Sosei Heptares, Cambridge) using a proximity-based split nano-luciferase approach (SmBiT/LgBiT). 3) Activate state receptor, stabilised by interacting partner. This will be done in collaboration with Prof Lynn Butler (Karolinska Institute, Sweden) using tagged BioID2 to identify protein-protein interactions assessed using mass-spectrometry). All ELTD1 constructs will be overexpressed in insect lines, followed by purification and cryo-EM recording and data processing (the final milestone of this grant). How the results of this research will be used: Results from this work (the high-resolution resolved active/inactive ELTD1 structures) will be submitted for publication in reputable high-impact journals and used for the next phase of this project: in silico small molecule screening and in vitro candidate testing. Results will also be used to apply for further funding. This research project is expected to generate a large amount of cryo-EM data which will be of significant interest to adhesion GPCR community and to the wider GPCR and structural biology communities. After publication, all cryo-EM data will be deposited at the "The Electron Microscopy Public Image Archive" (EMPIAR) at the EMBL-EBI whilst the high resolution protein structure will be deposited at the “RCSB Protein Data Bank” (PDB).


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Investigation of urinary extracellular vesicle cargo as an early detection method in renal cell carcinoma predisposition conditions.
Funder: The Urology Foundation

Abstract: This project aims to assess the potential of urinary extracellular vesicle RNA cargo as an indicator of renal cell carcinoma for the purposes of early detection in individuals with genetic predisposition to that cancer type.

Lay abstract: In recent years, an increasing amount of research has focused on using body fluid sampling to early stage cancers, termed “liquid biopsy.” This has particular relevance for individuals at higher risk of cancer and has the potential to improve detection and/or patient experience by reducing scan frequency. We are proposing to investigate the measurement of the contents of extracellular vesicles (EVs) in urine samples for the detection of kidney cancer in VHL.

Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: Seeing the unseeable - imaging of drug pharmacokinetics in the CNS
Funder: Brain Research UK

Abstract: Brain cancer is the most common cancer-killer in children and, with regard to drug therapy, the brain is black box; we cannot measure the location, concentration, or activity of drugs we use to treat this disease. This project will test new drugs that can both be seen on MRI and treat brain cancer. In the short term, this will help us see what we are doing, optimise chemotherapy, improve effectiveness and reduce side-effects for patients with brain cancers and other neurological conditions.

Lay abstract: Brain cancer is the most common cancer-killer in children and, with regard to drug therapy, the brain is black box; we cannot measure the location, concentration, or activity of drugs we use to treat this disease. This project will test new drugs that can both be seen on MRI and treat brain cancer. In the short term, this will help us see what we are doing, optimise chemotherapy, improve effectiveness and reduce side-effects for patients with brain cancers and other neurological conditions.

Research activity codes: 5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS