NIHRDataInsights/HRCSData huggingface dataset:
Title: A multi-functional theranostic nanoparticle against colorectal cancer.
Funder: Medical Research Council

Abstract: Background: Curative surgery for colorectal cancer (CRC) involves radical surgery to remove the primary cancer along with the regional draining lymphatics to minimise the risk of locoregional recurrence. Only 30% of patients have lymph node disease, meaning that 70% of patients undergo unnecessarily radical surgery. There is a clinical need to distinguish patients with and without lymph node disease, but current imaging modalities lack sensitivity, with CT scan having only 50% accuracy. An aging population means that more elderly patients are developing CRC and are less able to tolerate radical surgery. In addition, the National Bowel Cancer Screening Programme (NBCSP) is resulting in a shift to earlier stage disease. A proposed solution is to develop a multifunctional nanoparticle that will allow accurate intraoperative cancer staging and surgery tailored to the individual patient. Aims: To develop a multifunctional silica NP, targeted to CRC and incorporating an MR contrast agent and photosensitiser, for accurate intraoperative staging to facilitate stratified CRC surgery. Methods: We have previously identified carcinoembryonic antigen (CEA) as the preferred biomarker for CRC and conjugated an anti-CEA antibody to a fluorescent silica nanoparticle (Si-NP). Testing of the functionalised Si-NP in vitro and in a small animal model has shown it to be specific and sensitive for CRC. We will build on the Si-NP platform, incorporating a photosensitiser (PS) and MRI contrast agent (Gadolinium, Gd) for added functionality. The anti-CEA antibody will be replaced with an anti-CEA adhiron to enhance sensitivity and specificity and to enable mass production of the targeting element. The multifunctional nanoparticle will be tested in vitro and in a small animal model of CRC for sensitivity, specificity, and phototherapeutic efficacy. Novelty: This will be the first time a theranostic NP, combining a PS with a paramagnetic agent, has been developed against CRC.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: Identifying molecular drivers and early diagnostic biomarkers in breast cancer leptomeningeal metastasis by the interrogation of cerebrospinal fluid
Funder: Medical Research Council

Abstract: Breast cancer leptomeningeal metastasis (BCLM) is a form of central nervous system (CNS) metastasis with a dismal prognosis of around 4 months despite currently available treatment. Despite the increasing incidence of CNS metastasis, there lack of translational research focus in BCLM. In addition, diagnosis using current methods is challenging. Overall the project aims to improve scientific understanding and develop a diagnostic biomarker by using cerebrospinal fluid (CSF). Methods Clinical samples will be obtained from patients with BCLM and will comprise cerebrospinal fluid (CSF), blood and primary tumour tissue; all accessed through currently active studies through the Royal Marsden and South East London Cancer Research Network (SELCRN). 1. Genomic analysis DNA will be extracted from CSF tumour cells and/or from the CSF supernatant. DNA will undergo whole exome sequencing, and will be compared, within the same individual, to germline, primary tumour and other metastatic site DNA, and also to existing breast cancer sequencing datasets to identify recurrent or unique somatic genomic aberrations in BCLM. 2. Functional genomics Genomic aberrations will be investigated for functional consequences through the establishment of an in vivo model. Established human tumour cell lines will be manipulated by transfection via lentiviral expression constructs, and gene knockdown by RNA and CRISPR interference. 3. Biomarker discovery Levels of circulating tumour DNA (ctDNA) in CSF will be determined by digital droplet (ddPCR) in patients being investigated for BCLM, in parallel with standard cytological analysis. Serial CSF samples will be analysed for ctDNA dynamics to correlate this with other parameters of disease status, including the clinical decision to stop ineffective treatments. Through the scientific methods used and findings generated, this research will impact not only breast, but other cancer types, in addition to other neurological conditions.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: Leveraging circulating tumour DNA (ctDNA) to dissect the evolutionary genomic dynamics of drug resistance in prostate cancer.
Funder: Medical Research Council

Abstract: Aims/Objectives 1.To use high-coverage targeted next generation (NGS) on sequentially collected plasma DNA to: a. sub-classify and characterise AR-aberrant versus AR-wild-type CRPC. b. define the genomic evolutionary changes that associate with resistance. 2. To use whole genome sequencing (WGS) data from plasma to interrogate the sequence of genomic events following distinct treatment selection pressures 3. To functionally validate AR somatic point mutations and other novel aberrations that associate with resistance in AR wild-type CRPC and develop clinically relevant strategies to target them. Methodology: Aim 1: An expanded high-coverage (>1000x) customised targeted NGS with an optimised panel design will be used. Pre-amplification barcoding of DNA fragments (Agilent Halopex HS) to improve the sensitivity and specificity of established approaches will be explored. Sequential plasma samples will be studied to identify genomic aberrations that temporally associate with resistance.. Aim 2: WGS at 100-150X coverage optimised for plasma will be used to determine clonal diversity of ctDNA and the order of copy number changes. Aim 3: Functional validation of AR mutations and novel targets will be performed in prostate cancer cell lines (LNCaP, VCaP, PC3). Novel targets will be qualified using clinically applicable assays (eg ddPCR) on independent test sets. Scientific and Medical Opportunities Plasma DNA analysis has the potential to improve patient outcomes by: 1. Molecular characterisation of men in real-time and sub-classification of CRPC into AR gain or no AR gain 2. Improving our understanding of the genomic drivers of treatment resistance in prostate cancer 3. Optimising new and existing treatments for prostate cancer by molecularly selecting patients using a minimally invasive blood test.


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: THE IMPACT OF NON-HISTONE PROTEIN METHYLATION BY SET1A IN MAINTAINING GENOME STABILITY AND PREVENTING DISEASE
Funder: Medical Research Council

Abstract: Genome instability underlies cellular transformation, and thus is a frequent hallmark of cancers. One major causative factor is replication stress (RS), which is observed in premalignant cells, where it acts as a significant driver of genome instability. Numerous cellular proteins function to combat RS, acting to maintain genomic integrity. However, the regulation of these factors, particularly the impact of post-translational modifications, is poorly studied. My preliminary data demonstrates that a lysine methyltransferase, SET1A, is crucial for dealing with RS. In its absence, cells are exquisitely sensitive to agents that induce RS, and exhibit catastrophic genome instability. Further analyses demonstrate that SET1A and its binding partner BOD1L regulate the BLM helicase, and suggest that BLM is methylated in a SET1A-dependent fashion. Moreover, initial investigations suggest that deregulation of this Lys methyltransferase complex is involved in haematopoietic malignancies. Taken together, these data suggest that SET1A-mediated methylation of DNA damage response (DDR) proteins regulates the RS response and acts to maintain genome stability and prevent cellular transformation. This proposal therefore has three objectives: to investigate the role of Lys methylation of non-histone DDR proteins in the RS response, to assess the importance of the SET1A-BOD1L interaction in maintaining genome stability, and to analyse the impact of SET1A haploinsufficiency on replication stress and haematopoiesis. The data generated will further our fundamental understanding of the cellular response to RS, which is vital to fully comprehend the basis of cellular transformation. It will provide fundamental insights into the role of Lys methylation in maintaining genome stability, and the impact of unresolved RS on haematopoietic malignancies. Finally, it may lay the groundwork for the future development and use of pharmacological SET1A inhibitors as potential anti-cancer therapies


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: The role of RNA Binding Proteins (RBPs) in breast cancer progression and metastasis
Funder: Medical Research Council

Abstract: My aim is to assess the mechanisms by which invasiveness and metastatic behaviour is regulated via different RNA Binding Proteins (RBPs) in breast cancer cells. While much has been revealed on molecular machineries that control cell motility, little is known about upstream regulators of motility which are deregulated during metastasis. Recent works by me and others have highlighted a crucial role for regulation of local mRNA translation in controlling cell protrusions and adhesions. Accordingly, various RBPs have been reported to localise to such motility related compartments and control cell-migration, invasion, and metastasis. However, it is unclear how different RBPs function to regulate cell motility, and whether their activity could be targeted to tackle cancer dissemination. I will use sub-cellular fractionation coupled with proteomics to reveal RBPs that associate with specific motility related compartments in invasive breast cancer cells. Using RNAi in combination with morphology, migration, and invasion assays, I will reveal key RBPs that regulate breast cancer cell motility in-vitro. RBP roles in-vivo, in regulation of local invasion to lymph nodes and distant metastasis will then be assessed using orthotopic mouse models. Using fractionation coupled with RNAseq and pulse-labelling proteomics, I will investigate how loss of RBPs affects RNA localisation and local translation in motility associated cellular compartments where RBPs are localised. Through analysis of UTR sequence elements, along with methods to assess mRNA-protein binding, I will determine the mechanisms of interaction between RBPs and their local target mRNAs. Finally through mutagenesis, I will abrogate mRNA-RBP bindings and assess the impact on invasiveness and metastasis. Showing that specific RBP-mRNA interactions can impact on invasiveness and metastatic potential may lead to devising new therapeutic strategies to tackle cancer dissemination by disrupting such interactions.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: MICA: Characterisation of a novel bromodomain inhibitor AZD5153 in castrate resistant prostate cancer
Funder: Medical Research Council

Abstract: Prostate cancer (PC) is the most prevalent UK male cancer, accounting for 10,000 deaths per year. The androgen receptor (AR) is a transcription factor that transmits androgenic signals to drive prostate growth and cellular transformation. Inactivation of the AR by anti-androgens is initially effective causing tumour regression. Unfortunately, most patients relapse with a more aggressive form of the disease termed castrate-resistant PC (CRPC) that is unresponsive to treatment, but is AR-dependent. The development of next-generation AR-targeted therapies, including enzalutamide, have shown promise in the treatment of CRPC, but response rates of just 50% and the development of resistance have limited their success in the clinic. Importantly, several aberrations to the AR signalling cascade have been identified in CRPC, including AR mutation and the formation of receptor splice variants, that facilitate AR activity in castrate conditions and contribute to conventional and next-generation anti-androgen treatment failure. A key challenge is to develop novel treatments for CRPC that antagonise all ARs and repress tumour progression. Consistent with a role for Bromodomain and extraterminal motif (BET) proteins enhancing activity of CRPC-relevant forms of the androgen receptor, pre-clinical testing of first-generation BET inhibitors have been shown to compromise PC growth in vitro and in vivo. This study will assess a new and more efficacious BET inhibitor developed by AstraZeneca to attenuate receptor signalling and prevent tumour growth using CRPC cell line models and human PC biopsy samples ex vivo. The ability of this agent to inactivate all AR isoforms has major clinical implications and is the main focus of the project. By determining the efficacy of the BET inhibitor against clinically-relevant AR mutants and splice variants, we will advance our understanding of the receptor in CRPC, and comprehensively validate the compound for patient-tailored treatment.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: The regulation of endocytic sorting and cholesterol transport by PTP1B-mediated ESCRT dephosphorylation at ER-endosome membrane contact sites
Funder: Medical Research Council

Abstract: The EGF receptor (EGFR) activates signaling pathways through reversible phosphorylation of itself and downstream targets, has a well-established role in cancer and is a target for cancer therapies. Endocytic transport regulates EGFR signaling, as ubiquitinated receptor is sorted onto intraluminal vesicles (ILVs) of multivesicular bodies (MVBs), removing its catalytic domain from cytoplasmic targets before lysosomal delivery for degradation. We showed that endocytosed EGFR is dephosphorylated by the ER-localised phosphatase, PTP1B, at membrane contact sites (MCSs) tethered by annexinA1/S100A11 complexes, where the membranes of the ER and MVBs come into close apposition. These MCSs regulate ILV formation, most likely by PTP1B-mediated dephosphorylation of the ESCRT proteins, Hrs and STAM, that sort ubiquitinated cargo onto ILVs, and also by transport of ER-derived cholesterol to MVBs to support ILV formation when endosomal cholesterol is low. Intriguingly, Hrs is also required for cholesterol transport from endosomes to the ER, a process proposed to occur at MCSs. We hypothesise that modulation of Hrs/STAM phosphorylation at MCSs by PTP1B co-ordinates MVB sorting and cholesterol transport functions of Hrs. We will use our established tools to modulate PTP1B activity (PTP1B overexpression/depletion/inhibition), MCS formation (AnnexinA1/S100A11 depletion/overexpression) and cholesterol exchange (culture in delipidated serum/statins) and generate novel gene-edited HeLa cells expressing Hrs/STAM phosphorylation mutants. A combination of electron and super-resolution microscopy and biochemical analysis will be used to determine the role of Hrs/STAM phosphorylation in regulating sorting of EGFR onto ILVs and cholesterol transport at MCSs. These data will help to elucidate the role of PTP1B in EGFR-dependent tumorigenesis, will aid in the design of improved combination cancer therapies and will increase our understanding of the role of MCSs in lysosomal storage diseases.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Defining the role of FOSL2 in molecular adaptation to hypoxia in colorectal cancer
Funder: Medical Research Council

Abstract: Colorectal cancer is the third most common cancer in both men and women and leads to 500,000 deaths a year worldwide. 1 in 3 colorectal tumours contains regions of low oxygen (hypoxia) that are found in most solid tumour types. Hypoxia is caused by high tumour metabolic and proliferative rates and aberrant vascularization. Clinically hypoxia is associated with worse patient survival and chemotherapy and radiotherapy resistance. Hypoxia also induces metastasis, a major cause of cancer death. Identifying novel ways to target hypoxic tumours is a key objective to improve therapeutic response for these patients. We carried out an unbiased induced-essentiality functional shRNA screen to identify novel regulators of hypoxic tumour cell survival in 2D and 3D cell-culture. FOSL2 was the top hit in these analyses where FOSL2 knockdown reduced cell viability in hypoxia. Using published colorectal cancer expression array data we identified that high FOSL2 expression is associated with worse patient survival. We have shown that FOSL2 expression is increased in hypoxia and that knockdown reduces the expression of the key hypoxia regulated gene CA9. FOSL2 binds with Jun proteins to form variants of the transcription factor complex activator protein-1 (AP-1). We hypothesise that FOSL2 promotes hypoxic cell growth and survival via transcriptional regulation of target genes and we will investigate this using 2D, 3D and in vivo xenograft models. We will identify the HIF1a and HIF2a -dependent and -independent gene expression roles of FOSL2. Furthermore a key FOSL2 regulated-transcript will be investigated for its mechanistic role in hypoxic tumour growth and survival. We will examine the associations between FOSL2 and patient survival, and hypoxia using colon cancer TMA. We will investigate FOSL2 as a key regulator of molecular adaptation to the hypoxic tumour microenvironment and as a target for development of inhibitors against the therapy resistant hypoxic tumour microenvironment.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: `Analysis of neo-antigens and immune profiles of Asian breast cancer patients, focusing on common germline deletion of APOBEC3B cytosine deaminase
Funder: Medical Research Council

Abstract: GOALS OF THE PROJECT: The goal of this proposed study is to focus on the impact of common A3B germline alterations on the generation of neo-antigens and an immune signature in Asian breast cancer samples. This will be accomplished through the following methodology: Specific Aim 1: Paired-end whole exome sequencing of 400 fresh frozen tumour and corresponding normal (blood) samples will be performed at 100x and 50x depth coverage respectively using Illumina's TruSeq Rapid Exome on Illumina's HiSeq 4000 platform. For variant analysis, SNVs will be called using CaVEMAN while indels will be called using Pindel whereas mutational signatures will be called using NMF. Risk of developing hypermutator profile will be ascertained. Lastly, bioinformatics tools POLYSOLVER, neoantigen prediction pipeline by Rajasagi et al., and netMHCpan will be used to infer neoepitope load from initial sequencing data. Association between genetic alteration, hypermutation profile, and neoantigen burden will be assessed. Specific Aim 2: Transcriptomic sequencing of mRNA (~30M reads) will be performed on HiSeq 2500 platform. Sequencing reads will be aligned using MapSlice and quantitation will be performed using RSEA. GSEA and DAVID will be used to identify gene sets and pathways significantly enriched in A3B-del group with focus on immune response-related gene sets and pathways. Overall abundance of TILs will be inferred using ESTIMATE while levels of mRNA transcripts corresponding to specific T cell markers and that of corresponding to specific immune checkpoint molecules will be compared across the different genotypes. IHC validation will be performed by staining for CD4, CD8, A3B and PD-1 and CTLA-4 in a representative set of samples. Association between immune signature, specific T cell markers, and immune checkpoint molecules will be assessed.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Translational development of oncolytic Newcastle Disease Virus for treatment of colorectal cancer
Funder: Medical Research Council

Abstract: The purpose of this project is to develop a new target-selective anticancer agent based on a tumour selective variant of the virulent Malaysian NDV AF2240 strain of Newcastle Disease Virus, and to position it ready for clinical trial in treatment of colorectal cancer. AF2240 was shown to have more potent tumour lysis characteristic relative to alternative isolates and vaccine strains currently available. The strain will be rendered inactive in avian cells by mutating the cleavage site of the fusion protein and .replacing the haemagglutination and neuraminidase (HN) gene of the virulent strain with a non-virulent strains. These virus will be assessed for lytic potency on a panel of human colorectal carcinoma cells and selectivity will be assessed by passaging 10 times in 9-to-11-day old SPF chicken embryonated eggs. These constructs will then be modified to express IL-12 and IL-15 in order to stimulate both adaptive and innate immune responses. Functional expression cytokines will be determined by activation of PBMCs in co-culture with NDV infected tumour cells in vivo and in colorectal xenografts in vivo. We will also establish activity in tumour associated stroma cells (such as activated fibroblasts) in 3D organotypic models. Finally, infection selectivity and immune cell stimulation will be characterised in fresh human tumour biopsies maintained in ex vivo culture. These studies will involve surgically removed waste tumour samples, together with normal margin tissue, maintained ex-vivo in the laboratory under local ethical approval. After exposure of tumour explants to NDV, cells will be disaggregated and evaluated by flow cytometry for evidence of virus mediated lysis (staining for viral coat protein, markers of apoptosis) and immune stimulation of resident leukocytes. Together these data should provide sufficient evidence of safety and efficacy for future development towards a clinical trial.


Research activity codes: 5.2 CELLULAR AND GENE THERAPIES;6.2 CELLULAR AND GENE THERAPIES
Health categories: CANCER AND NEOPLASMS
Title: Development of polygenic risk scores for South East Asian populations to identify women at higher-risk of breast cancer
Funder: Medical Research Council

Abstract: Breast cancer is rising rapidly in Asia and is the most common cause of cancer related deaths in Malaysia. Notably, whereas 80% of breast cancer in the UK occurs in post-menopausal women, only 40% occurs in post-menopausal women in Malaysia, and the proportion of risk attributable to genetic factors is likely to be correspondingly higher. In the absence of population-based screening, targeted screening is a viable cost-effective alternative in reducing breast cancer mortality. It has been shown that polygenic risk scores (PRS) constructed using breast cancer-associated single nucleotide polymorphisms (SNP) improve risk stratification in European and East Asian populations. However, there have been no/little studies in South-East Asian, especially Malay and Indian populations - two of the largest ethnic groups in Malaysia and Singapore. In this proposal, using data from Malaysian and Singaporean populations and genome-wide associated SNPs from large Asian cohorts (data generated in the Asian Breast Cancer Consortium and the Breast Cancer Association Consortium), we plan to develop optimal PRS for predicting breast cancer risk in women from all ethnic backgrounds in Malaysia and Singapore. The findings of this research will facilitate the wider use of clinical genetic testing and the development of informed risk-stratified approaches to screening.


Research activity codes: 4.3 INFLUENCES AND IMPACT;4.4 POPULATION SCREENING
Health categories: CANCER AND NEOPLASMS