NIHRDataInsights/HRCSData huggingface dataset:
Title: Exploring stromal-epithelial interactions in oesophageal cancer
Funder: Medical Research Council

Abstract: Objectives: This proposal describes an innovative programme of work to establish the importance of stromal-epithelial interactions in human oesophageal cancer. Background: Carcinoma of the oesophagus is the 6th leading cause of cancer death with a 5-year survival of less than 15%. It is the most rapidly increasing cancer in the UK and in December 2008 the Chief Medical Officer for England called for increased research into its causes. Adenocarcinoma of the oesophagus is associated with the finding of a pre-malignant columnar metaplasia in the distal oesophagus - Barrett‘s oesophagus (BE). Recent evidence demonstrates that gene changes in the oesophageal stroma can be independent of changes in the epithelium, and are important in Barrett‘s carcinogenesis. Methods: This project makes use of a novel organotypic model of the oesophagus that allows molecular genetic manipulation of both the epithelial and stromal cellular components in a physiological ex-vivo setting. We will use human tissue from endoscopic biopsies and oesophageal resections, taking both a candidate gene and genome wide approach with three research aims: 1. To build on our preliminary data to establish the role of periostin in oesophageal carcinoma invasion. 2. To define the contribution of other stromal signals to the maintenance and progression of oesophageal carcinoma. 3. To analyse the molecular events required for fibroblast activation in the oesophagus. Outcomes: This project will lead to the discovery of novel diagnostic and prognostic biomarkers, and the potential for the rational development of new interventions and therapies.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Biological Effectiveness Of Ion Beams for Cancer Therapy
Funder: Medical Research Council

Abstract: Cancer radiotherapy employing charged particles (i.e. protons and carbon ions) is currently the fastest growing cancer treatment approach with over 30 centres worldwide and an extra 30 (including 3 in the UK) planned to be operational in the next 3-5 years. Despite the impressive results so far reported, there are still uncertainties on the biological effects caused by ion beams especially related to non-lethal and late effects in healthy tissues which prevent further optimization of cancer particle therapy. The main issue is related to the change of biological effectiveness as the ions penetrate into the tissue and a higher probability of inducing late effects when compared to X-rays. Ultimately, it is normal tissue effects, including risks of secondary cancers, which will determine the treatment outcome. Current lack of experimental data is forcing treatment plans to adopt broadly averaged parameters for estimating tumour cell killing and neglect late effects. More accurate investigations are therefore essential to develop a rigorous theory of ion radiation action at cellular and molecular level to further improve tumour hadrontherapy. Experimental studies investigating the biological response of charged particles have focused mainly on the cell killing effect of tumour cells or tissues at the Bragg peak. Damage caused at the beam entrance channel, beyond the Bragg peak and indeed in the immediate proximity of the ion path is unavoidable and needs to be addressed. Our central hypothesis is that damage and cellular response will vary greatly along and around the ion path as a function of both physics and biological parameters (i.e. depth, physical dose, cell line, ion characteristics). Using a variety of approaches, the present proposal aims to investigate in parallel DNA damage, acute and sub-lethal cellular response caused by therapeutically relevant ion beams (mainly protons but also carbon ions) on a range of normal and cancerous cell lines along the ion path and in its proximity. Data collected will help evaluating more accurate RBE values to be included in new and existing models to design optimal cancer treatment strategies. Determination of biological Bragg curves for radiation risks including late effects will provide critical information for the development and improvement of biological models aimed to improve the therapeutic use of ion beams Additionally, we anticipate DNA damage caused by secondary electrons and cell signalling between exposed and un-exposed samples to play a non-negligible role whose contribution to cancer treatment plans has still to be fully investigated.


Research activity codes: 5.5 RADIOTHERAPY AND OTHER NON-INVASIVE THERAPIES
Health categories: CANCER AND NEOPLASMS
Title: Tumor suppression by chromatin regulators.
Funder: Medical Research Council

Abstract: Oncogene-induced cellular senescence (OIS) is a permanent cell growth arrest caused by an activated oncogene in a primary untransformed cell. OIS is a potent tumor suppression mechanism. Senescence depends on profound changes in chromatin structure. Two chromatin regulatory complexes implicated in control of senescence are the HIRA/UBN1/CABIN1/ASF1a (HUCA) histone chaperone complex and the Brg1/Snf5 chromatin-remodeling complex. HUCA is a histone chaperone that deposits the histone variant, histone H3.3, at transcription start sites and other gene regulatory sites. Since histone H3.3-containing nucleosomes are unstable, this promotes transcription activation. The Brg1/Snf5 complex reshapes chromatin in an ATP-dependent manner, and this also frequently results in transcription activation. Consistent with a role in senescence, the Brg1/Snf5 complex has potent tumor suppressor activity in humans and mouse models. However, the relationship between HUCA and Brg1/Snf5 as regulators of gene transcription and senescence is unknown. Recently, through unbiased, whole-genome ChIP coupled to massively parallel sequencing (ChIP-seq) we discovered a striking overlap between HUCA and Brg1/Snf5 across the human genome. Accordingly, we hypothesize that Brg1/Snf5 and HUCA are intimately associated as regulators of chromatin structure and function. In particular, we hypothesize that HUCA and Brg1/Snf5 collaborate to regulate the onset of cell senescence. We will test this hypothesis as follows: Aim 1. Compare physical and functional overlap of HUCA and Brg1/Snf5 complexes in proliferating and senescent cells. Aim 2. Investigate physical and mechanistic interactions between HUCA and Brg1/Snf5 in vitro. Aim 3. Investigate functional and mechanistic interactions between HUCA and Brg1/Snf5 in vivo.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Chromatin re-establishment after DNA repair
Funder: Medical Research Council

Abstract: Histone proteins are characterized by many different post-translational modifications (PTMs) at many different sites: different patterns are associated with active and inactive genes; different PTMs have been shown to interact, e.g. H3S10 phosphorylation and H3K9 methylation. This diversity and cross-talk has led to the suggestion that histone modifications constitute a ‘code‘. The repair of DNA damage (RDD) occurs in the background of chromatin. A number of histone PTMs and variants are known to be involved in RDD. RDD initially entails histone H4 acetylation and opening up of chromatin structure. Kinases are recruited, resulting in extensive H2A.X phosphorylation. DNA is resected and nucleosomes removed around the site of repair. Subsequent to repair, histone deacetylases are recruited, H2A.X is dephosphorylated and nucleosomes are reincorporated. New H3.1 is incorporated in a CAF-dependent manner. It is unknown, however, whether the original pattern of histone modifications and histone variants is restored after repair. I aim to use MS techniques to characterize in detail the histone PTMs and variants associated with RDD. I will identify which repair-associated modifications are transient, and which are longer lasting. After DNA damage, I will employ four experimental approaches, studying either PTMs from global histones or specific sub-regions: A) global analysis of histone PTMs; B) epitope-tagged H2A.X immunoprecipitation; C) isolation of a targeted double-strand break (DSB) on an S. pombe plasmid; D) isolation of a targeted DSB on a human episome. Mass spectrometric techniques for PTM analysis allow a global analysis of histone modifications, and reveal the stoichiometry of different modified forms, in contrast to antibody approaches. MS is also well-suited to the analysis of histone variants, including those indistinguishable by antibody approaches. The targeted approaches I propose (B-D) will allow me to obtain chromatin enriched for RDD-associated histone modifications, and to characterize in detail the chromatin pattern before and after repair. Using stable isotope labeling I will distinguish new histones from old, enabling me to determine whether the histones are recycled back after repair, or whether new histones are inserted. This has a bearing on the re-establishment of chromatin patterns, as old histones will retain their modifications. The plasmid-based approach will allow the analysis of chromatin re-establishment after RDD from different starting points: an actively transcribed gene, a repressed gene or heterochromatin. Once the basic outline of RDD is mapped out, I will extend the analysis to cancer cell lines and disease-states, where the DNA damage response is impaired.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: CANCER AND NEOPLASMS
Title: Therapeutic Targeting of ALK in Neuroblastoma
Funder: Medical Research Council

Abstract: Neuroblastoma (NB) is the most common non-CNS paediatric cancer. Fifty-percent of children with high-risk disease succumb to relapse. Alteration in MYCN and ALK genes correlates with aggressive tumour biology, increased tumour vascularisation and relapse. Concurrent ALK point mutations and MYCN gene amplification occur in patients with therapy-resistant tumours and poor clinical survival (15% at 5 years), implying a functional interaction between these two genes that induces an aggressive tumour phenotype. We characterised the first MYCN-driven transgenic model of NB and used it to show that PI3-kinase pathway inhibitors destabilise Mycn protein by altering n-terminal phosphorylation. We have now developed the first ALK-driven NB transgenic model in which tumours arise exclusively in mice doubly-transgenic for MYCN and ALK. Compared to MYCN-driven tumours, MYCN/ALK-driven tumours have increased Mycn protein, reduced neovascularisation and an aggressive phenotype mirroring that of human MYCN/ALK tumours. Since ALK is known to stimulate PI3K-patwhay activity, we hypothesise that ALK potentiates MYCN-driven oncogenesis, in part, through PI3K-driven Mycn protein stabilisation. The three aims of this project are to examine: 1) whether ALK potentiates MYCN-driven NB, by stabilising Mycn protein, 2) whether ALK inhibits MYCN-driven tumour neovascularisation, and 3) whether ALK- and/or Mycn-targeted therapeutics are effective against these tumours. Established human and murine NB cell lines with varying expression of MYCN and phospho-mutated (stabilised) Mycn proteins will be transfected with ALK mutants to assess whether stabilisation of Mycn protein occurs through PI3K-pathway induction and Mycn phosphorylation. I will examine in parallel whether MYCN-driven angiogenesis is inhibited using in vitro angiogenesis assays with which I have extensive prior experience. In vivo tissue from MYCN and MYCN/ALK transgenic tumours will be examined for stabilisation of Mycn through assessment of PI3K pathway expression and ratio of Mycn to pMycn protein. Vessels will be analysed by pathology and expression of major angiogenic signalling proteins will be characterised. MRI will be used to quantitate tumour blood flow and size, response in preclinical studies of Mycn and ALK-targeted therapeutics (BEZ235 and PF2341066). Specifically the ability of PF-2341066 alone or in combination with BEZ235 to regress tumours and destabilise Mycn will be assessed. This project presents a unique combination of reagents and validated approaches that will allow mechanistic dissection of the interaction between MYCN and ALK in NB, and will guide the development of targeted-therapeutics for ultra high-risk NB patients.


Research activity codes: 5.1 PHARMACEUTICALS;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: The regulation of microRNA (miRNA) biogenesis and the role of miRNA binding proteins in breast cancer.
Funder: Medical Research Council

Abstract: Aims: The aims of the proposed project are to establish how miRNAs are regulated by the estrogen receptor- (ER ) in breast cancer and to identify the estrogen (E2)-inducible miRNA binding proteins involved. Objectives: 1. To investigate the clinical relevance of the mir-17-92 and mir-106a-363 family of miRNAs in breast cancer. 2. To determine the mechanism(s) by which transcription of the mir-17-92 and mir-106a-363 clusters is regulated. 3. To analyse the mechanism(s) of miRNA biogenesis in breast cancer and establish the identity of the E2-inducible factor(s) involved. Design: Objective 1- We will use quantitative real-time PCR to measure the expression of the primary miRNA transcripts, pre-miRNAs and mature molecules belonging to the mir-17-92 and mir-106a-363 families of miRNAs, in well characterised sets of breast cancer specimens. We will study their clinical relevance by investigating whether these ER -regulated miRNAs correlate to outcomes, including survival, comparing ER -positive and ER -negative tumours. Objective 2- We will identify ER /ER -modulated transcription factor binding sites upstream/ downstream of the mir-17-92 and 106a-363 transcriptional start sites using the UCSC genome browser and ChIP analyses prior to/following E2 stimulation. We will use chromosome capture assays to assess whether promoter and enhancer sequences are components of the same chromatin regions of identified interaction sites, and to identify the genomic localisation of the promoters/enhancers for the miRNA transcripts. The biological relevance of any regulatory binding will be investigated using siRNA knockdown of transcription factors and luciferase reporter assays. Objective 3- We will utilise model systems to establish the identity of the estrogen-inducible factor(s) causing inhibition of miRNA processing and determine the contribution of post-transcriptional miRNA regulation in response to ER , to oncogenesis. Methodology The proposed project uses a range of cell and molecular biology techniques, bioinformatics and tissue handling techniques, which are well established in the host laboratory. Scientific and Medical Opportunities Based on previous data, we hypothesise that post-transcriptional regulation is a general mechanism of miRNA biogenesis with relevance to breast cancer, and that an estrogen-inducible mechanism is responsible for the inhibition of miRNA processing. We aim to demonstrate the involvement of miRNA binding factors in this process, and implicate them as potential new therapeutic targets. This also has general relevance to oncology, as miRNAs are major regulators of the development and growth of many cancers, although the associated mechanisms remain poorly understood. Finally, this research will increase our knowledge of the potential role of miRNAs as biomarkers in breast cancer.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Replacement of animal models for tumour biology with a multifunctional microfluidic-based approach
Funder: National Centre for the Replacement, Refinement and Reduction of Animals in Research

Abstract: The aim of the project is to design and optimise a microfluidic device in which small biopsies of human tissue (malignant and normal) can be maintained in a biomimetic-like environment. It is proposed that these devices will be used both by pharmaceutical companies to reduce and replace drug screening and by clinicians as tools for personalising a therapeutic strategy. It is planned to investigate the pro-coagulant changes that occur in many cancers as the process is a major clinical problem and provides an ideal setting to demonstrate the widespread applicability and potential of the microfluidics platform. To investigate the reasons why a venous thromboembolism is commonly associated with tumours, tissue biopsies (2-3m3) will be maintained in a small chamber on the chip (approximately 20 ƒÝl in volume) for up to 8 days with media, or media plus drugs at clinically-relevant doses, perfusing the tissue. A major benefit of the microfluidic approach is that not only can drug combinations be tested, but also the most effective sequence of administering drugs can be rationally determined. This type of analysis is not possible in animal models as the one end point is almost always death. Additionally, normal tissue will be tested in the devices allowing side effects such as non-specific toxicity to be identified. It is proposed to establish three distinct analysis modules measuring different facets of the clotting process: coagulation, using viscosity and direct fluorescence imaging; MP release, by dual colour flow cytometry; and gene transcription using hybridisation and fluorescence detection. The modules can be used in parallel due to a switch mechanism on the chip and on multiple occasions, thus a response can be monitored over time. These integrated devices will provide data on the responses that have far greater relevance to the in vivo setting than any animal model. A key aim of the proposal is to demonstrate the robustness of the microfluidic device and compatibility of the data generated on-chip with conventional cell assays. Having established the operating parameters of the device it is proposed to test a cohort of ovarian tumour samples using a standardised chemotherapy regimen (paclitaxel plus carboplatin) alone, and in combination with a currently used VTE treatment. The results of this microfluidic trial will be correlated with the clinical outcome. Finally, a small group of tumours will be used to establish the optimal drug concentrations and dosing sequence for each tumour, i.e. a personalised treatment.


Research activity codes: 5.1 PHARMACEUTICALS;5.9 RESOURCES AND INFRASTRUCTURE (TREATMENT DEVELOPMENT)
Health categories: CANCER AND NEOPLASMS
Title: Assessing RNA helicase p68 (Ddx5) as a biomarker in the deregulation of microRNAs in prostate cancer
Funder: Prostate Cancer UK

Abstract: The onset and progression of prostate cancer (PCa) is driven by the transcriptional function of the androgen receptor (AR). Ablation of androgens is a therapeutic modality in early stages of disease; however, PCa can progress to a castrate resistant (CRPCa) phenotype. Currently, there are no curative therapeutic agents available. A better understanding of the molecular events by which PCa can progress to CRPCa may lead to the identification of novel therapeutic targets, improving the survival rate for patients. MicroRNAs are small non-coding RNAs that act as translational suppressors, thereby regulating protein production. Several studies identified microRNAs dysregulated in PCa, indicating a role for them in the pathogenesis of the disease. We previously reported the DEAD box RNA helicase p68 (DdX5) as a novel co-activator of AR regulated transcriptional activity. Ours and other studies support the idea that dysregulation of p68 expression and/or function plays an important role in cancer development. p68 is also known to play a role in microRNA processing as part of the Drosha complex, and is required for the maturation of a subset of microRNAs. A small number of these microRNAs (and targets), are shown to be dysregulated in PCa and modulate AR and PSA expression. However, their roles in the development of CRPCa are largely undefined. These findings suggest an insight for a new approach to PCa treatment by studying the upstream pathways (modulated by p68), important in regulating aberrant microRNA expression, and the possible identification of novel microRNA ‘signature’ biomarkers of PCa progression to CRPCa.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: Psychosexual support following prostate cancer surgery: feasibility and outcomes of a couple-based intervention
Funder: Prostate Cancer UK

Abstract: Even with careful prostate surgery, men find it difficult to have an erection. Our previous research shows that couples are not often supported to cope with the effects of surgery on their sexual relationships. In this study, we will design a way of supporting couples, and test how well it works. We will decide what the support should include (e.g. duration, frequency and timing of the support). We will do this by looking at available literature on the subject. We will recruit 68 couples to the study, half will receive standard care and the other half will be invited to attend six sessions of psychosexual support with specially trained professionals (trained by men affected by prostate conditions and a cancer/couple support specialist). Before and after the support, men and their partners will be asked to complete questionnaires which measure quality-of-life, emotional needs, and their relationship. We will ask the couples to fill out the questionnaires again six-months later to see if the support has long-term benefits. At the end of the study we will also interview 10 couples to find out their views of the support, and another 10 couples about standard treatment. When we have tested this support, we expect to see men and their partners tell us that their quality of life has improved, and they have higher satisfaction with their relationship. We will calculate the overall cost of providing this support, and the benefits it has on reducing the need for other health-care services (like GP use).


Research activity codes: 7.1 INDIVIDUAL CARE NEEDS
Health categories: CANCER AND NEOPLASMS
Title: Focal therapy for prostate cancer using irreversible electroporation
Funder: Prostate Cancer UK

Abstract: Current treatments for early prostate cancer use radiation or surgery to treat the whole prostate. This causes damage to surrounding structures that control erections and urine flow. This leads to leakage of urine and poor sexual function. Our group has shown that treating only the areas of cancer, with heat, cold or laser-light, can lead to a much lower rate of these side-effects. The cancer control rates however, can vary and are not consistent. We think we can do better, perhaps by using a different type of energy called irreversible electroporation. This causes the walls of cells to forms holes in them so that they are killed. This new type of treatment seems to be more precise and well-controlled than others we have used. We believe that the reason for this is that the treatment does not rely on creating an extreme of temperature (either very hot or very cold) – something that the body is very good at resisting. Moreover, the treatment takes just a few minutes and can be carried out as an out-patient. We are recognised as the leading group in the world at evaluating new technology in a thorough manner. It is this that we wish to do with a grant from Prostate Action. We are proposing a trial in which we will establish once and for all whether this technology has any merit in treating the prostate. If NANOKNIFETM shows promise we would plan to seek funding to evaluate it in a randomised setting.


Research activity codes: 6.5 RADIOTHERAPY AND OTHER NON-INVASIVE THERAPIES
Health categories: CANCER AND NEOPLASMS