NIHRDataInsights/HRCSData huggingface dataset:
Title: Exploring the interaction of gut microbiome, genetic and immunological factors in gastrointestinal toxicity of immune checkpoint inhibitors.
Funder: Medical Research Council

Abstract: Monoclonal antibodies targeting regulatory immune checkpoint molecules that inhibit cytotoxic T cell activation, known as immune check-point inhibitors (ICI), are being widely used for the treatment of a range of cancer types. Despite their effectiveness in improving long-term survival, treatment with ICIs can lead to severe immune-mediated adverse drug reactions (ADRs). GI adverse effects are amongst the most frequently observed ADR in patients treated with ICI, and can be life-threatening. The aim of this study is to identify individual susceptibility factors and understand mechanisms that lead to immune-mediated gastrointestinal (GI) adverse reactions in patients treated with ICIs. Using both prospective longitudinal and cross-sectional study designs, we will identify patients with and without these ADRs after the initiation of the treatment with ICIs. We propose to investigate: 1) The composition of the intestinal microbiota in treatment-naïve individuals in faecal samples to compare the diversity and abundance of the microbes between cases and controls; 2) Genetic variants in CTLA-4, CD86, PD-1, PD-L1, HLA complex and other immune-related genes and any association with GI events; 3) Measure gene expression (mRNA and miRNA) in subpopulations of circulating immune cells before and after the treatment in cases and controls; 4) Obtain the cytokine profile in serum samples in cases and controls; 5) Characterise subpopulations of the cells infiltrating inflamed tissue obtained via colonic biopsies; 6) Use single-cell RNA sequencing of infiltrating T lymphocytes and colonic epithelial cells obtained from colonic biopsies. This work will reveal important regulatory mechanisms that determine self-tolerance vs. the development of immune-mediated adverse events affecting the lower GI tract after treatment with ICIs. The mechanistic understanding will allow us to develop novel interventional strategies to improve the benefit-risk ratio of these agents.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFLAMMATORY AND IMMUNE SYSTEM
Title: Exploring the role of T cells in the immune surveillance of early renal cancer
Funder: Medical Research Council

Abstract: Context: The immune system has an important role in the recognition and elimination of malignant cells. There is clinical evidence of cancer immune surveillance in the kidney but the phenotype and functional profile of the immune cells controlling early cancer development remains unknown. Half of renal cell carcinomas (RCC) are diagnosed at early stage but the biology of early RCC is understudied. I want to improve the knowledge on immune-related disease progression events associated with early RCC. Aims: The primary aim is to explore the T cell profiles associated with progression in early RCC. The secondary aim is to investigate the impact of environmental nutrient deprivation in kidney cancer on T cell function. Methodology: Patient blood and tissue samples will be used. Primary aim: phenotypical and functional characterisation of T cell subsets associated with shift to escape in early RCC will be done using flow cytometry, immunohistochemistry (IHC), and transcriptomics. Progression-related changes in intratumoural clonal distribution of T cells will be sought after with TCR repertoire analysis. Secondary aim: phenotypic and functional characterisation of tumour T cell subsets using flow cytometry, IHC, and transcriptomics will be done on a cohort of patients that underwent non-invasive tumour metabolic assessment using hyperpolarised MRI. Scientific and medical opportunities: Innovative experimental and analytic pipelines will generate high quality outputs, contributing to one of the world's leading efforts in applied early cancer research. Elucidating T cell immune mechanisms associated with early RCC progression will lead to biomarker development, improved risk stratification, and ultimately the adoption of more personalised management decisions. While the project focuses on early RCC, a high level of translatability of methods and outputs to other disease stages, cancers, and study designs (i.e. longitudinal monitoring) is expected.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFLAMMATORY AND IMMUNE SYSTEM
Title: Immune cell development and cancer
Funder: The Francis Crick Institute

Abstract: A major interest of the Immunity and Cancer Laboratory is to understand how healthy cells become cancerous. To address this question we study B cells, as they provide an ideal model system: first, their normal development is well defined; second, the most common types of human haematological malignancies are derived from the transformation of healthy B cells into cancer cells. B cells, essential cellular components of the immune system develop from hematopoietic stem cells in the bone marrow through a highly regulated process that results in the production of functional mature B cells. During the course of a T cell dependent immune response to infection, mature B cells develop further in peripheral tissues, such as spleen and lymph nodes, into memory B cells or terminally differentiate into terminally differentiated plasma cells in a reaction called germinal centre (GC). Memory B cells allow the rapid immune response re-call upon re-infection. Plasma cells produce high affinity antibodies essential for the elimination of the infectious agent. However, during the development of both memory B cells and plasma cells, healthy B cells undergo in the GC microenvironment processes of DNA mutation and recombination while rapidly dividing, and infidelity in these processes may lead to oncogenic DNA lesions. Although cancer cells may arise from healthy B cells at several stages of development, cancers derived from GC B cells or from cells that have passed the GC reaction are the most common amongst haematological malignancies in adults overall. These cancers include the vast majority of human Hodgkin and non-Hodgkin lymphomas (e.g. the aggressive diffuse large B cell and Burkitt lymphomas), and multiple myeloma (a plasma cell cancer), which is currently incurable. Using an integrative approach to immunology and cancer biology our laboratory aims to understand the mechanisms by which healthy GC B cells become cancerous. For that we primarily perform studies on three complementary research themes: (i) Identify and study subpopulations within healthy GC or post GC B cells, which due to their physiology are at a particularly high risk of becoming cancer cells, that is the so-called 'cells of origin in cancer'. (ii) Investigate the causative mutations, responsible for the progressive process of how a healthy B cell develops into a cancer cell. (iii) Assess the processes of evasion of cancer cells from immune control by determining the nature of the interplay between a developing B cell cancer and cells of the immune system.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFLAMMATORY AND IMMUNE SYSTEM
Title: Dendritic cells and innate immunity
Funder: The Francis Crick Institute

Abstract: The Immunobiology Laboratory studies receptors and signalling pathways that mobilise dendritic cells (DC) and other cells in response to infection, injury or cancer. In a related programme, the laboratory studies DC heterogeneity and ontogeny. In the last 5 years, the Immunobiology Laboratory continued earlier work on cell-intrinsic immunity to RNA viruses to show that RIG-I, a cytosolic virus sensor, can detect 5’ di-phosphate-bearing RNA, such as present in the genome of reoviruses. In addition, the lab isolated an RNA agonist for MDA5, a RIG-I-like receptor (RLR), from cells infected with a picornavirus. Finally, the lab found that antiviral RNA interference, an ancestral form of antiviral defence, is preserved in vertebrates but masked by the effects of interferons, cytokines elicited by signals from RLRs or other innate immune receptors. In a distinct line of investigation, the lab continued its studies of myeloid C-type lectin receptors that signal via Syk. The lab found that provision of one of these, CLEC-2, by DCs at the outset of an immune response causes relaxation of certain lymph node stromal cells permitting expansion of the organ. A distinct Syk-coupled C-type lectin receptor, DNGR-1, was previously found by the lab to be used by the DC1 subset of DCs to detect F-actin exposed by cells undergoing necrosis. This suggested that extracellular recognition of cytoskeletal components is an evolutionarily-ancient means of detecting tissue damage. Consistent with that notion, the lab recently found that extracellular actin elicits a response in Drosophila melanogaster akin to tissue injury. To further understand the role of extracellular actin recognition, the lab solved the structure of the DNGR-1/F-actin complex and validated the importance of F-actin detection and a pH-induced conformational change in DNGR-1 in allowing DC1s to extract antigens from cell corpses for presentation to CD8+ T cells. This process can contribute to immunity to cytopathic viruses and to cancer and, in the context of the latter, the lab found that DC activation and immune control can be subverted by prostaglandin E2 produced by tumour cells. Independently of its presence and function in differentiated DCs, DNGR-1 was additionally found by the lab to be also expressed by mouse DC precursors and was used to fate-map those cells in vivo. In an extension of the latter work, the lab demonstrated that supposedly-pure “DC” cultures widely-used for mouse immunology research contain a mixture of cells of distinct origins, some of which are better classified as macrophages (MØs). Overall, the studies of the Immunobiology Laboratory over the last quinquennium help build a global picture of the cells, receptors and signalling pathways that regulate immunity and have applications in immunotherapy of cancer and infectious diseases.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFLAMMATORY AND IMMUNE SYSTEM
Title: Measuring the impact of monoclonal antibody drugs in cancer and rheumatoid arthritis
Funder: Medical Research Council

Abstract: It is now over 40 years since the first mab drugs were approved. Today six out of ten of the best selling drugs in the world are mab therapeutics. Mab drugs currently make up a third of all introduced new treatments. Despite their success, no systematic study has been done to assess how many millions of patients have taken such drugs and the extent to which they have benefited their lives. The goal of this project is to determine the impact of the best-selling mAb drugs for cancer and rheumatoid arthritis, two key disease areas where such therapy has had some of its most profound impact. In this study we will measure benefit in terms of clinical benefit (life extension and quality improvement). Previous studies have estimated benefit for a limited number of patients in a given trial. In this project we propose to multiply the estimated benefits by the number of users over a specified period.


Research activity codes: 8.2 HEALTH AND WELFARE ECONOMICS
Health categories: CANCER AND NEOPLASMS;INFLAMMATORY AND IMMUNE SYSTEM
Title: Understanding T cell immunity in anti-NMDAR encephalitis: Developing therapeutic tools for neurological autoimmunity.
Funder: Medical Research Council

Abstract: Using a model of NMDA-receptor (NMDAR) encephalitis, we will investigate the role of effector T cells in initiating antibody-mediated neurological disease. Recent evidence supports a role for T cell help in the production of antibodies to the NMDAR. We will identify antigen-specific T cell responses to the NMDA receptor in healthy controls and in patients with de novo encephalitis or neurological autoimmunity post checkpoint inhibitors. We will complete 'proof of concept' pre-clinical development of genetically engineered regulatory T cells (Tregs) to suppress pathogenic immune responses against neuronal cell surface proteins in vitro. The following hypotheses will be tested: (1) Tolerance to NMDAR derived peptides is incomplete and functional antigen-specific T cells can be identified in PBMC isolated from healthy controls and patients. (2) In the presence of checkpoint inhibitors, the frequency of NMDAR-specific T cell responses increases. (3) Human Tregs can be genetically engineered to express the myelin basic protein-specific TCR (MBP-TCR), be activated in the presence of MBP (CNS tissue restricted peptide) and demonstrate antigen-specific suppression of pathogenic effector T cell responses in vitro. T cells from healthy controls and patients will be stimulated using an NMDAR overlapping peptide pool. Peptide-specific responses, including proliferation and cytokine secretion, will be determined by CFSE assays and Luminex. MBP-TCR Tregs will be engineered by established retroviral transduction methods. To demonstrate the ability of the transduced Treg to suppress inflammation in an antigen-dependent manner we will assess suppression in vitro, by titrating doses of MBP-TCR Tregs with NMDAR peptide-specific effector T cells, stimulated with the relevant NMDAR peptide loaded target cells in the presence or absence of MBP peptide pulsed DCs. Mock-transduced Treg will be used as controls. Ethics approvals are in place for both patients and controls.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.2 CELLULAR AND GENE THERAPIES
Health categories: CANCER AND NEOPLASMS;INFLAMMATORY AND IMMUNE SYSTEM
Title: Defining the role of the IgE-Fc epsilon receptor-1 immune surveillance axis in human cutaneous squamous cell carcinoma
Funder: Medical Research Council

Abstract: Background: Cutaneous squamous cell carcinoma (cSCC) is the second most common skin with around 30,000 new cases per year in England. Up to 5% of cSCCs metastasise with 3-year overall survival 29% in women, 46% in men. The immune system is known to have a key role in the aetiology of cSCC. Our group and my co-supervisor's group have independently generated data implicating a novel role for the IgE-FceRI immune signalling axis in cSCC pathogenesis and progression. Aim: To characterise the FceRI-expressing cells present in cSCC and define the role of the IgE-FceRI immune surveillance axis in cSCC progression and metastatic disease. Objectives: 1. Define the composition and tissue localisation of leucocytes including FceRI+ cells in cSCC. 2: Validate and quantify FCER1A and other immune gene and protein expression as correlates for increased metastatic risk 3: Functional experiments by manipulation of the IgE-FceRI axis in vitro/in vivo. Methods: 1. Multi-parameter flow cytometry and imaging mass cytometry will define the immune cells (including FceRI+) and their spatial localisation. 2. Immunohistochemistry and targeted RNAseq in a larger cohort of archival cSCC will examine and quantify expression of FCER1A and associated selected immune genes. 3. In vitro transwell co-culture with immune cells and cSCC cell lines and mouse patient derived xenografts will be used in functional experiments in which the IgE-FceRI axis will be manipulated and downstream effects measured and compared. Scientific and medical opportunities: This project will define an exciting and novel immune signalling checkpoint that is based on compelling preliminary data. It offers the potential to discover important biomarkers for identification of high-risk primary cSCC and novel therapeutic directions for treatment of advanced cSCC whilst providing a varied, multi-disciplinary research training experience.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFLAMMATORY AND IMMUNE SYSTEM
Title: Enhancing immunogenicity in non-viral low mutation burden tumours
Funder: Medical Research Council

Abstract: Background: Current cancer immunotherapies significantly extend survival in patients with high mutation load or oncogenic viral infection, however for the majority of patients (>80%) efficacy is limited. This limited efficacy is associated with poor immunogenicity, and novel strategies to enhance tumour antigen load are urgently required. Aim: To induce anti-tumour immune response via inhibition of mRNA quality control pathways. Rationale: I hypothesize that cellular processes engaged in mRNA and protein quality control can be inhibited to increase the abundance of mutated RNA/protein, and subsequently enhance the number of mutated peptides available for HLA presentation. This then serves to increase presentation of immunogenic neoantigens, thus driving anti-tumour immune response, even in the absence of a high mutation load or oncogenic viral infection. This hypothesis is supported by my published postdoctoral work, where I demonstrated that mutated mRNAs escaping from nonsense mediated decay (NMD) are strongly associated with improved patient response to immunotherapy. These results are further supported by preclinical data. Lastly, the NMD pathway is typically hyper-activated in tumour cells (due to the burden of somatic mutations), hence allowing cancer-specific targeting without normal cell toxicity. Objectives: 1) To dissect the molecular underpinnings of NMD-escape and HLA presentation, 2) to characterise the differences in NMD pathway functionality between cancer and normal cell types, 3) to induce anti-tumour immune response via tumour specific modulation of NMD, 4) to identify other novel mRNA/protein quality control pathways associated anti-tumour immune response (e.g. UPR, no-go decay, etc). Methods: Live cell imaging, bulk tissue/single cell sequencing analysis, in vitro CRISPR KO, ex vivo tumour organoids co-culture with T cells.


Research activity codes: 6.2 CELLULAR AND GENE THERAPIES
Health categories: CANCER AND NEOPLASMS;INFLAMMATORY AND IMMUNE SYSTEM
Title: Defining non-redundant functions of glycogen synthase kinase (GSK)-3 alpha and GSK-3 beta in T cell subsets that control tumour growth
Funder: Medical Research Council

Abstract: T cells play a key role in eliminating infected cells and tumours. Understanding how these lymphocytes are regulated is key to our fundamental understanding of immunity and to the design of therapeutic strategies that exploit their activity, such as those used in cancer immunotherapy. We have shown that the ubiquitous, unconventional kinase, Glycogen Synthase Kinase (GSK)-3 negatively regulates CD8 T cell function, limiting effector functions and promoting immune checkpoints. Importantly, inhibiting GSK-3 produces striking enhancement of tumour rejection in animal models and suggests therapeutic approaches to enhance immunotherapy. CD4+ T cells also mediate tumour rejection but how GSK-3 acts in this heterogenous subset of T cells is unknown. There are two highly related isoforms of GSK-3, alpha and beta, encoded by separate genes. Using mice in which either Gsk3a or Gsk3b (or both genes) are deleted in T cells, we have shown non-redundant activity of the two isoforms, based on rejection of lung or brain tumours. We will use these mice and tumour models to identify the CD4+ T cell subset(s) whose activity is modulated by GSK-3 inactivation, resulting in tumour rejection. We will identify tumour infiltrating subsets of cells and determine how the migration of CD4+ T cell subsets is regulated in vitro and using adoptive transfer models into tumour bearing models. Our data shows that GSK-3b inactivation favours rejection of lung tumours whereas GSK-3a deletion favours tumour immunity in the brain. We will determine whether this represents differences in the tumour or in differential requirements for T cell subsets at these anatomical locations. Furthermore, we will use these GSK-3 cKO mice to identify pathways regulated by the two GSK-3 isoforms in CD4+ T cells, integrating proteome and gene expression data from the CD4+ subsets mediating tumour rejection. Key components of these pathways are potential molecular targets for future cancer immunotherapy strategies.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFLAMMATORY AND IMMUNE SYSTEM
Title: Transcriptional regulation and therapeutic modulation of cytotoxic function in tumour-infiltrating CD4+ T cells
Funder: Medical Research Council

Abstract: Recent cancer immunotherapy approaches have been focused on boosting or re-invigorating cytotoxic CD8+ T cell function. However, the proportion of patients that do not respond to therapy remains high and some tumours lack MHC I expression. There is growing recognition that CD4+ T helper cells can also acquire cytotoxic effector function, and that these cells form a key component of the response to cancer and viral infection. However, we lack information on the factors required for the differentiation and function of cytotoxic CD4+ T cells (CD4+ TCTX), especially in tumours. We have found that acquisition of cytotoxic function in tumour-infiltrating CD4+ T cells requires the transcriptional repressor Blimp-1 and is antagonised by Bcl6. We have also discovered that although Blimp-1 is necessary for GzmB transcription, GzmB protein production in TEFF is inhibited unless TREG are depleted from the tumour microenvironment. We propose to combine genomics and tumour immunology approaches to identify regulatory mechanisms that control the differentiation and function of cytotoxic CD4+ T cells in tumours and how these mechanisms may be targeted to enhance the function of these cells in tumour immunity. We have three research objectives: 1. Understand how Blimp-1 and Bcl6 regulate the differentiation of CD4+ cytotoxic precursors in tumours by applying CUT&Tag and scATAC-seq techniques to genetically modified tumour models. 2. Characterise and modulate a checkpoint that restrains GzmB protein production in CD4+ cytotoxic precursors using blocking antibodies and gene editing in tumour models. 3. Determine whether the Blimp-1/Bcl6 axis can be targeted to promote acquisition of cytotoxic CD4+ T cell function using tumour models and patient-derived xenografts. This work will provide knowledge of the factors that control cytotoxic CD4+ T cell function and identify targets through which the activity of these cells can be harnessed in patients.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: CANCER AND NEOPLASMS;INFLAMMATORY AND IMMUNE SYSTEM