NIHRDataInsights/HRCSData huggingface dataset:
Title: Cyclic hypoxia drives mutagenesis through increased APOBEC activity in breast cancer
Funder: Breast Cancer Now

Abstract: Background Of all people with breast cancer, those with TNBC have the worst prognosis. A wealth of evidence suggests that intermittent/cyclic hypoxia is commonplace in solid tumours and is associated with the most aggressive disease including increased metastasis. Cyclic hypoxia occurs as a result of the inefficient and poorly formed tumour vasculature. Our recent work has identified key differences in the biological response to cyclic versus stable hypoxia which likely contribute to tumourigenesis, therapy response and recurrence. Aims We propose to demonstrate that exposure to cyclic hypoxia leads to an accumulation of the APOBEC-mediated mutational signature in TNBC cells (aim 1). We will then ask how cyclic hypoxia/APOBEC3B impacts response to therapies used as standard for TNBC as well as testing novel strategies predicted by the biological response to cyclic hypoxia (aim 2). Lastly, we will develop and validate a gene signature for cyclic hypoxia/APOBEC3B and test this as a predictor of prognosis for TNBC (aim 3). Techniques and Methodology We will use sequencing (RNA-seq/WES) in TNBC cell lines and detailed bioinformatic analysis to identify and locate APOBEC-mediated mutations and changes in gene expression. Validation of gene expression changes will be carried out using standard techniques including qRT-PCR, western blotting, and immunofluorescent microscopy. In vitro assays will be carried out to determine the impact of cyclic hypoxia/APOBEC on therapy response, followed by testing in vivo. Multiplex IHC will be used to visualise key proteins in xenograft tumours. Impact on breast cancer research This proposal has the potential to identify a subtype of TNBC patients with tumours experiencing cyclic hypoxia and therefore increased APOBEC activity, therapy resistance and increased risk of recurrence. Furthermore, our mechanistic insight, particularly into changes in the cell cycle, are likely to point to novel therapeutic strategies which are urgently needed to treat this group of patients.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: STEALTH: Silent Technology to deliver Engineered Antigens for a Lethal TH1 response against mutant p53 in TNBC.
Funder: Breast Cancer Now

Abstract: Background: While Triple Negative Breast Cancer (TNBC) accounts for 15-20% of BC, it is associated with a disproportionately high number of deaths. This is underpinned by its aggressive nature, heterogeneity, and lack of targeted treatments. However, up to 90% of TNBC harbour a p53 mutation with the vast majority resulting in protein stabilisation and overexpression. This results in de novo expression of formerly cryptic self p53-determinants and provides a window of discrimination from normal cells which maintain very low basal levels of p53. Together this make mutant p53 an attractive therapeutic vaccine target. Aims: To develop a p53 therapeutic mRNA vaccine for the treatment of TNBC using a stealth-like delivery system with strategies to maximise the TH1/Cytotoxic T-cell response and/or minimise the TH2/immunosuppressive response. Techniques and methodology: p53 mRNA nanoparticles will be formulated using the RALA peptide which has been shown to facilitate delivery to APCs and elicit an effective cytotoxic T-cell response resulting in tumour cell death in a cervical cancer model vaccinated with E7-mRNA-RALA-nanoparticles. We will first interrogate the immune response to different regions of p53 to identify the optimal antigenic region eliciting a TH1 response in patient samples. In a parallel strategy we will assess the immunomodulatory function of Gemcitabine, which is known to reduce immunosuppressive TREGs and MDSCs. This will also be formulated with RALA (RAL-GEM) to overcome the associated side effects as palliative steroids must omitted. We will then assess the therapeutic efficacy of the p53 mRNA vaccine on its own or in combination with RAL-GEM against an engineered mouse model of TNBC expressing mutant p53. Impact on breast cancer research: Overall results from this study will demonstrate the efficacy of a novel vaccine for TNBC which may be applied to other diseases with p53 overexpression and/or tumour antigens.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Identification of enhancer SNPs at 14q24.1 that influence predisposition to male and female breast cancer
Funder: Breast Cancer Now

Abstract: Background We identified overlapping male and female breast cancer susceptibility loci that have sex-biased risk effects. One locus, mapping to 14q24.1, confers a much larger risk of male breast cancer (MBC; OR=1.6) than female breast cancer (FBC; OR=1.08). A second locus within the same neighbourhood is associated with both MBC and FBC, but without evidence of sex-biased risk effects. Since the statistically credible causal variants are non-coding, they most likely influence the expression of one or more target-genes in a manner that permits breast cancer development. Our data implicate ZFP36L1 as a candidate target-gene. Aims We hypothesise that the breast cancer causal SNPs at 14q24.1 influence the transcriptional output of ZFP36L1 by affecting the activity of functional enhancer elements. We will identify these elements, and neighbouring “enhancer SNPs” that influence their activity. We will then perturb the activity of the enhancers and enhancer SNPs, and assess the impact upon the transcriptional output of ZFP36L1, thereby identifying candidate causal SNPs for further analysis. Finally, we will evaluate differential transcription factor binding at the candidate causal SNP sites to better illuminate the causal mechanisms of breast cancer risk mediated by these loci. Techniques and Methodology We will use STARR-seq to identify functional enhancer elements and enhancer SNPs at the 14q24.1 risk loci in cell line models of male and female mammary epithelial tissue. We will use CRISPR-perturbation to identify regulatory elements and SNPs that influence ZFP36L1 expression. SNP-proteomic methods, including LC-MS, will be used to assess transcription factor binding to candidate causal alleles. Impact on breast cancer research Understanding the molecular basis of these risk associations will provide new information about sex-specific differences in the aetiology of MBC and FBC and will contribute more broadly to our understanding of the factors that influence breast cancer predisposition in the general population.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: The identification of subtype of breast cancers with functional circadian rhythms and the evaluation of a timing based therapeutic strategy
Funder: Breast Cancer Now

Abstract: Background: The cell intrinsic circadian clocks are critical regulators of metabolism, differentiation, DNA damage response and cell cycle. Disruption to circadian clocks, for example through shift work, has been linked to increased risk of breast cancer. Our preliminary data show that circadian clock function is retained in Luminal A (ER+/HER2-) breast cancers but lost in those expressing HER2. However, unresolved questions are how the intrinsic molecular clocks are regulated in primary breast cancers and whether timing of therapy based on clock cycle may lead to improved outcomes. Aims: We will investigate why ER+/HER2- cancers remain rhythmic while HER2+ tumours have disrupted clocks and whether HER2 targeting restores clock function. We will reveal rhythmic clock target genes and pathways in Luminal type breast cancer to determine which breast cancer therapies are more likely to work in a time-of-day dependent manner. We will test a “circadian medicine” approach in cultured breast cancer cells and in mice carrying patient-derived xenograft in vivo. Techniques and methodology: Cellular clocks will be assessed by lentiviral clock reporters and real-time bioluminescence imaging. The role of ER and HER2 will be investigated by gene deletion/over-expression and small molecule compounds. CYCLOPS algorithm will be used to order time-unknown samples and identify rhythmic genes. Cell viability, proliferation, tumour size and mammosphere formation will be measured following pathway manipulations or drug treatments. This range of timely and novel approaches (such as CYCLOPS) will significantly advance this field. Impact on breast cancer research: This study will directly assess intrinsic circadian rhythms, their regulators and targets in primary breast cancers, which may provide new clock based therapeutic opportunities. The evaluation of a “circadian medicine” approach for a few well-established breast cancer drugs will provide a framework for future translational studies to improve therapies by utilising the body’s daily rhythms.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Treatment-associated macrophages to predict immunotherapy response in triple-negative breast cancer
Funder: Breast Cancer Now

Abstract: Background Better predictive biomarkers are needed for triple-negative breast cancer (TNBC) patients to benefit from immunotherapy, but the pathologic basis of response remains elusive. The role of tumour-associated macrophages (TAMs) in determining treatment outcome has been largely overlooked, despite their diverse immunoregulatory effects. How TAMs orchestrate spatial organisation of the tumour microenvironment (TME), and how it is modified by treatment is also poorly understood, yet immunotherapy depends on perturbing cell-cell interactions. The role of macrophages in the post-treatment microenvironment (treatment-associated macrophages; TrAMs), where they are often conspicuous, is also uncertain though it may be crucial in effecting long-term response. Aims Uncover the impact of macrophages on spatial organisation of the TME and on immunotherapy response in TNBC. Techniques and Methodology I propose to use imaging mass cytometry (IMC; a technique based on isotopically pure metal reporters) to profile 44 proteins in situ at subcellular resolution in a unique sample collection from a large randomised trial of immunotherapy in TNBC, in order to characterise the phenotypic and spatial features of TAMs, as well as their dynamics under treatment. Multi-tiered image analysis will be used to understand high-dimensional tissue images at several levels of abstraction, from single-cells to multicellular complexes. By analysing samples from patients in both randomised arms of the trial (with or without immunotherapy), it will be possible to reliably infer the precise effect of immunotherapy in modifying the TME, its impact on TrAMs, and identify tissue features that predict response. Impact on breast cancer research This work will illuminate the role of macrophages as modulators of immunotherapy response in TNBC; how they orchestrate organisation of the TME and how this is modified by treatment; and identify pragmatic candidate biomarkers for further validation in future studies.


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: Improving outcomes for women with lymph node positive disease who develop resistance to endocrine therapy
Funder: Breast Cancer Now

Abstract: Background Over 75% of breast cancers are estrogen receptor positive (ER+) and have a good prognosis, largely attributed to the used of endocrine therapy (ET). Despite this, not all respond due to a variety of mechanisms. We have shown that up to one third of women with lymph-node-positive disease on ET, switch off proliferation in the primary but not in the nodes. This group of women have a poorer prognosis and currently there are no approaches to identify them and improve their outcome. Aims We aim to improve the prediction of response to ET by refining our previous BCN-funded predictor of response (EA2CliN) to include direct molecular analysis of any nodal disease. We plan to study unique cohorts of patient tissues with matched primaries and nodes who have discordant molecular responses to ET as well as nodal recurrences on ET to improve our understanding of the underlying mechanisms and identify drivers and potentially targetable mechanisms. We plan to continue the development of a genome-driven real-time tissue-based drug response assay to improve the prediction of response to therapeutic agents in resistant cancers. Techniques and Methodology EA2CliN will be used to predict response in a cohort of lymph-node positive patients from the POETIC trial treatment arm. A targeted DNA sequence and pathway focused panel and an in-situ mutation detection technique which we have validated will be used to study resistance mechanisms. Our drug response assay will use tissue explantation technology which we have developed. Impact on breast cancer research Understanding and managing endocrine resistance is one of the most important unsolved issues in breast cancer. With this proposal, we hope to improve prediction of response to ET by identifying a high-risk group of node-positive women, increase our understanding of ET resistance in metastatic disease and improve the translational potential of these findings.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS
Title: Establishing the breast cancer immunobiology and immunotherapy programme
Funder: Breast Cancer Now

Abstract: The Breast Cancer Immunology Team (BCIT) has been established to build immunology and immunotherapy-related research in breast cancer across the translational spectrum, right through from pre-clinical mouse modelling, to analysis of clinical samples from patients through the ICR’s cross-divisional Centre for Translational Immunotherapy (CTI), which is also led by Alan Melcher. The work of the BCIT is divided into two projects that have strong links with the Breast Cancer Now Unit at KCL and with other Teams in the Breast Cancer Now Toby Robins Research Centre at the ICR. 1. Investigating the Functional Immunology of HORMAD1 as a Tumour Associated Antigen This project complements and builds on the work of Anita Grigoriadis and Yin Wu at KCL on the biology of HORMAD1. This project aims to: • Determine the potential antigenicity of HORMAD1 using population-based as well as specific class I HLA predictions. • Test naïve T cell priming against HORMAD1 • Investigate T cell receptor reactivity against HORMAD1 • Generate an oncolytic virus encoding HORMAD1 2. Developing Oncolytic Virus Therapy for Breast Cancer This project builds on the expertise within the Melcher/Harrington group investigating oncolytic virus (OV) based immunotherapy including in combination with targeted small molecules, previously in melanoma and head and neck cancer but now brought to the field of breast cancer. This project links to the work of Sheeba Irshad at KCL and aims to: • Investigate the sensitivity of human and mouse breast cancer to OV in vitro • Demonstrate the efficacy of OV in breast cancer in vivo • Determine the immunogenicity of OV in vivo • Assess immunogenic OV-based treatment in human preclinical models


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.1 PHARMACEUTICALS
Health categories: CANCER AND NEOPLASMS
Title: Modelling tumour ecosystem dynamics to optimise therapy choice
Funder: Breast Cancer Now

Abstract: The implementation of personalised precision breast cancer medicine in the clinic has been slow. As a result, breast cancer therapy selection is not optimised to the molecular profile of the tumour ecosystem and consequently many receive ineffective therapies. This heterogeneity in response, which is associated with prognosis, is most striking in patients with early breast cancer treated with systemic anticancer treatment before surgery (neoadjuvant therapy). In 32% of cases, no cancer is detected at surgery after completion of neoadjuvant treatment: this is a biomarker of therapy effectiveness and is associated with a high cure rate. However, in 55% of patients, extensive cancer is still present, indicative of therapy failure and this has a poor prognosis. The vision of this work is to develop a molecular and computational framework for a new generation of adaptive clinical trials that exploit on-therapy dynamic tumour ecosystem biology as captured through serial integrative high dimensional profiling to inform therapy choice. We will aim to tackle the challenges underlying the high therapy failure rate, as measured by survival outcomes, observed in breast cancer patients treated with neoadjuvant therapy by firstly characterising the relationship between the pre-therapy tumour ecosystem and post-therapy response to develop a clinically implementable machine learning predictor of response to therapy. Following this we will characterise tumour and microenvironment evolutionary trajectories during therapy to develop a clinically implementable predictor of response that integrates data from the pre and on-therapy tumour ecosystem to identify therapy failure early and accurately. The output will be a first-in-kind machine learning framework that models early changes in tumour biology as it is perturbed by therapy to predict response to therapy.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: CANCER AND NEOPLASMS
Title: A realist process evaluation of robotic surgery: integration into routine practice and impacts on communication collaboration and decision making
Funder: Department of Health (England)

Abstract: The aim of this project is to understand how and in what circumstances robotic surgery produces both intended and unintended outcomes. This will be achieved through a process evaluation running alongside ROLARR (RObotic versus LAparoscopic Resection for Rectal cancer) a randomised controlled trial (RCT) comparing laparoscopic and robotic rectal cancer surgery for the curative treatment of rectal cancer. Realist evaluation (Pawson & Tilley 1997) which is concerned with understanding for whom and in what circumstances complex interventions work and involves building testing and refining the theories of how the intervention is supposed to work provides an overall framework for the study. In Phase 1 grey literature will be reviewed to identify theories concerning (i) how robotic surgery becomes embedded into surgical practice; (ii) how robotic surgery impacts on communication teamwork and decision making in the OT and how this is affected by the process through which the technology is introduced; and (iii) subsequent impacts on outcomes such as operation duration conversion to open surgery and complications. These candidate theories will be refined and added to through interviews conducted with staff at different levels of the organisation across ten NHS hospital Trusts that are using robotic surgery for rectal cancer resection (both Trusts that are participating in the trial and those that are not) along with a review of documentation associated with the introduction of robotic surgery. In Phase 2 a multi-site case study will be conducted across four NHS hospital Trusts (three that are participating in the trial and one that is not) to test and refine the candidate theories. Data will be collected using multiple methods. Observation using the structured observation tool OTAS (Observational Teamwork Assessment for Surgery; Undre et al. 2007) and video recordings of operations will be combined with ethnographic observation and interviews. In Phase 3 interviews will be conducted at the four case sites with staff representing a range of surgical disciplines to assess the extent to which the results of Phase 2 are generalisable and to refine the resulting theories to reflect the experience of a broader range of surgical disciplines. Findings will be fed back to all four case sites in interactive sessions feedback from which will assist in the production of actionable guidance concerning how to support integration of robotic surgery into surgical practice and how to ensure effective communication and teamwork when undertaking robotic surgery.


Research activity codes: 8.1 ORGANISATION AND DELIVERY OF SERVICES;7.3 MANAGEMENT AND DECISION MAKING
Health categories: CANCER AND NEOPLASMS
Title: Identification of therapeutic targets in acute myeloid leukaemia expressing the mutant RAS oncogene
Funder: Division for Social Care and Health Research (Wales)

Abstract: Cancers including acute myeloid leukaemia (AML) have a high morbidity and mortality rate and are a significant healthcare challenge, particularly with respect to prevention and early treatment. Mutational activation of RAS is observed in 15-25% AML. To understand the contribution of this oncogene to the development of leukaemia we previously devised an experimental model based on normal blood progenitor/stem cells which enabled us to analyse the effects of mutant RAS expression on their blood cell development. These studies showed that RAS disturbs the development of blood cells and also promotes the growth of immature blood cells – the hallmarks of leukaemia. Recently, we have also shown that mutant RAS promotes the production of reactive oxygen species (ROS) and we have established that this contributes to the pro-proliferative effects of RAS. It is established that ROS promotes the activity of kinases which are central to the pathogenesis of all cancers. We propose to identify the kinases which can be specifically attributed to the excessive production of ROS by these cells. To do this we will use a technique called PepChip kinomic array profiling which allows us to measure the hundreds of kinases which are expressed in the human genome. We propose to: I. Identify the RAS target kinases by using PepChip kinomic array profiling of normal human primary cells transduced with mutant NRASG12D (compared with equivalent controls). We will perform similar experiments in the presence of ROS inhibitors/antioxidants to determine the ROS-specific kinome profile. II. Confirm the role of putative critical kinases on haematopoietic differentiation and proliferation and establish their clinical relevance in AML patient material. This knowledge will aid in the development of new and novel therapeutic approaches aimed at restoring normal developmental capacity. Further, this study may identify prognostic indicators AML.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS
Title: Investigation of biochemical fingerprints for early diagnosis of lung cancer
Funder: Division for Social Care and Health Research (Wales)

Abstract: Lung cancer is the most common cancer worldwide with 1.3 million deaths recorded per annum and the second most common cancer in the UK with 34,500 deaths annually. Survival time for lung cancer patients is poor with over 90% dying within five years of diagnosis. The reason for such a poor prognosis is that patients are usually diagnosed a late stage of the disease mainly because lung cancer symptoms such as coughing and blood in phlegm are frequently dismissed by long-term smokers as simply being a consequence of smoking. Mortality figures and treatment costs would be greatly improved if lung cancer could be diagnosed at an early stage and there is a strong argument for a national screening programme for people high-risk for lung cancer. We lead a national study called Medlung involving hospitals across England and Wales recruiting lung cancer patients and high-risk people to provide sputum for our research into developing a technology for early diagnosis of lung cancer. This studentship will evaluate the diagnostic technology we are developing and help us elucidate the biochemicals that are changed in cells of tumours compared to normal healthy lung tissue.


Research activity codes: 4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: CANCER AND NEOPLASMS