NIHRDataInsights/HRCSData huggingface dataset:
Title: Role of non canonical haematopoietic stem cells during human blood formation
Funder: Wellcome Trust

Abstract: Blood formation ultimately relies on the function of rare haematopoietic stem cells, canonically defined as multipotent and serially transplantable (c-HSCs). Mounting evidence, primarily from mouse models, indicates that these cells are activated in situations of extreme stress (e.g. transplantation). Day-to-day haematopoiesis and responses to less severe stresses are postulated to be instead driven predominantly by cell types that do not fulfil the canonical definition of HSCs, herein termed non-canonical (nc-) HSCs. nc-HSC generation, regulation and functional relevance remain unclear because reliable models to study them are lacking, especially in human. During my current fellowship, using state-of-the-art single cell approaches, I identified and provided purification strategies for two types of human nc-HSCs. During the extension, I will i) investigate how nc-HSC are generated from c-HSCs, characterising a newly-derived model of human nc-HSC formation at the cellular, transcriptional, proteomic and epigenetic level. Focusing on erythroid differentiation, I will then ii) validate novel molecular mechanisms that drive lineage commitment of nc-HSCs; iii) define to what extent nc-HSC contribute to responses to stress. These experiments will 1) provide proof-of-principle of the functional relevance of nc-HSCs to human haematopoiesis; 2) establish a much-needed tractable experimental framework to further study their role in ageing and disease.

Lay abstract: Blood stem cells produce all blood cell types throughout life. They are very rare, yet make millions of new blood cells every second. For more than 40 years, it was thought that only one type of blood stem cell existed. Recently, work from many groups, including mine, has shown that there are different blood stem cell subtypes. Some of these subtypes are “atypical” because they do not possess all of the classical features of a blood stem cell. Here I will test the hypothesis that these atypical blood stem cells are crucial for healthy blood formation in humans. I will study how atypical blood stem cells are formed, which molecules determine their function, and what their role is when the body urgently needs new blood cells. This data will be important to discover whether these atypical blood stem cells can be targeted to treat diseases such as cancer and anaemias.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;BLOOD;GENERIC HEALTH RELEVANCE
Title: Immunogenicity test platform - in vitro and in vivo
Funder: Medical Research Council

Abstract: We will work up this platform by studying the immunogenicity of two allogenic cell products - ES-derived dopaminergic cells and iPSC derived hepatocytes, chosen because they are about to enter clinical trials in Parkinson's disease and liver failure respectively. Our proposal will involve the following work packages: 1. We will characterise the expression of innate and adaptive immune molecules by our cell products at different stages of development, and in the presence of inflammatory mediators, using PCR and flow cytometry. 2. We will define the immune response of allogeneic T cells to our cell products in mixed lymphocyte reactions and via autologous DC presentation. 3. For ES-derived dopaminergic cells we will study the effect of immunosuppressive drugs on the ability of day 16 ES-dopaminergic progenitor cells (the stage at which they are transplanted), to fully differentiate into mature dopaminergic neurons both in vitro and in vivo. 4. We will investigate the immunogenicity of iPS-derived immunogenicity using "state-of-the-art" 3D "liver on a chip" cultures. 5. We will perform in vivo studies of our cell products after transplantation in immunodeficient mice reconstituted with a human immune system, studying the host immune response using droplet based, single cell V(D)J and expression profiling (10X) of CD45+ human immune cells extracted from the transplanted tissue, draining lymph-nodes and, for comparison, blood. 6. Reverse translation - finally, we will harvest and store peripheral blood (and where relevant) CSF derived mononuclear cells, and serum, from individuals undergoing transplantation with our products in our clinical centres, with the aim of determining whether or not any unique cell/transcriptomic signatures present in our mouse models can be identified in the patient derived samples, and whether or not these signatures relate to graft rejection and or clinical outcome.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.2 CELLULAR AND GENE THERAPIES
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;BLOOD;NEUROLOGICAL
Title: Identifying critical pathways regulating autoimmunity in immuno-oncology and arthritis patients. Short title: IPADS (Immune PAthways for Drug Side-effects)
Funder: Cancer Research UK

Abstract: Immune checkpoint inhibitors (CPI's) such as blocking antibodies targeting CTLA4 (e.g. ipilimumab) and PD1/PDL1 (e.g. pembrolizumab) have revolutionised the treatment of metastatic cancers by offering long-term remission and possibly cure. Unfortunately, these agents are associated with serious autoimmune adverse events including death. Approximately 1 in 3 patients experience autoimmune side effects requiring treatment with systemic steroids with about 1/3 of these requiring anti-inflammatory biologics. A small but significant number of refractory patients require radical treatment such as colectomy. There is currently no way to predict which patients develop serious autoimmune toxicities nor are the cellular or molecular pathways that drive CPI-associated autoimmunity defined. Patients with refractory rheumatoid arthritis can be treated using the CTLA4-Fc fusion protein, abatacept, with the aim to therapeutically induce tolerance. Treatment is lifelong and the annual cost is ~£10,000. However, it is estimated that only 1 in 2 patients will respond to abatacept. There is currently no way to predict which patients are likely to respond to abatacept nor are the cellular or molecular pathways that mediate response clear. Current CPIs and biologics like abatacept are blunt therapies that activate many downstream cellular and molecular pathways. For CPIs, some of these will be responsible for anti-tumour efficacy whilst others will be responsible for driving autoimmunity and some for both. However, given the pleiotropic effects of immune checkpoints, it is likely that most downstream pathways are of little relevance. The same can be said of the downstream pathways induced by abatacept treatment. To dissect the critical pathways regulating autoimmunity, we will study PBMCs from patients on CPIs who either develop or do not develop autoimmune adverse events and patients treated with abatacept who either respond to therapy or not. Our novel approach uses mass cytometry, transcriptomics and mathematical modelling of cell-cell and protein-protein interaction networks to identify the critical pathways shared by those on CPI who develop autoimmunity and those on abatacept who respond to treatment compared to those who do not. By incorporating directionality of shared pathway responses (in relation to clinical outcome) we can further increase the specificity of our in silico prediction. We will then take a handful of predicted pathways forward for in vivo validation in murine models of CTLA4 blockade toxicity and rheumatoid arthritis. Defining critical causal pathways will ultimately help to stratify patients for toxicity and response on these treatments and lead to design of better therapies.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;CANCER AND NEOPLASMS
Title: Does defective wound healing contribute to immune dysregulation in both cancer and arthritis?
Funder: Cancer Research UK

Abstract: Background: Correct immune functioning is vital for the wound healing response. In response to damage and injury, immune cells mediate key roles in the co-ordination and resolution of wound repair. Failure to appropriately heal a wound leads to continued and aberrant immune activity at the damaged site. As such, failure in wound healing promotes loss of immune homeostasis and could subsequently contribute to the development of numerous pathologies. We hypothesise that an aberrant wound healing response underlies pathology in both Rheumatoid arthritis (RA) and cancer. Failure of immune homeostasis has been evidenced in both RA and cancer and as such dys-regulated immune responses underpin both pathologies. Our central hypothesis posits that a contributing factor promoting loss of immune homeostasis in both diseases is an aberrant wound healing response. This is a novel proposition and, if proven to be true, would support a step-change in our understanding of these disparate disease states. Aims: To test our novel hypothesis we will: (1) Interrogate available datasets to define whether wound-healing pathways are altered in RA and cancer. (2) Evaluate the potential of specialized pro-healing mediators to alter local immune homeostasis and limit RA and cancer onset, progression and/or severity. Methods: We will employ an in silico approach utilizing publicly available datasets to holistically assess the changes in wound-healing pathways across the time-course of disease progression in both RA and cancer. This will allow us to identify whether alterations in wound-healing signatures underpin both RA and cancer. In parallel we will employ pre-clinical mouse models of RA and breast cancer to assess the impact of administering pro-healing compounds on the initiation and severity of disease pathology. This experimental design will allow us to establish whether promoting wound healing early during disease progression can have a positive impact on disease outcome. How the results of this research will be used: The outcome of this preliminary study will establish whether RA and cancer share an underlying cause, defective wound healing. We will establish whether alterations in wound healing responses contribute to loss of immune homeostasis, and subsequent disease progression, in both RA and cancer. Not only will our results shed light on basic mechanisms supporting immune dys-regulation and disease progression in both these pathologies, but also lay the ground work for future grant applications further exploring our novel hypothesis.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;CANCER AND NEOPLASMS
Title: Synovial Hyperplasia in Rheumatoid Arthritis and Cancer (SHARC)
Funder: Cancer Research UK

Abstract: Background Rheumatoid arthritis (RA) is an autoimmune disease that progresses from a systemic breach of self-tolerance to joint inflammation and bone erosion. Identification of the trigger or ‘second hit’ required for progression to joint disease could reveal novel therapeutic targets to limit or prevent joint damage. The rheumatoid joint is characterised by proliferation of synovial fibroblasts; this causes synovial hyperplasia. This is accompanied by an influx of inflammatory immune cells. Osteoarthritis is characterised by a more transient synovial hyperplasia that occurs in the absence of overt inflammation. This dysregulated proliferation of synovial fibroblasts in arthritic joints resembles the unchecked proliferation of tumour cells but rarely develops into a synovia sarcoma. Identification of the factors that are either present within the synovium that limit tumour development, or are lacking but required for tumour development, could reveal novel pathways to limit tumour growth. Aims We aim to address two key questions: First, is synovial hyperplasia sufficient to drive joint damage and, second, can we identify molecular pathways that limit the development of uncontrolled cell division and tumour development in synovial fibroblasts. Methods First, we will create a strong evidence base for synovial hyperproliferation in arthritic joints. Publically available data on fibroblasts from RA and OA patients will be compared with those from fibro-sarcomas to identify key candidate genes and pathways that may 1. underlie the dysregulated proliferation of synovial fibroblasts and 2. explain the lack of tumour development in synovial fibroblasts. Second, we will develop a mouse model to address the role of synovial hyperplasia in driving joint damage and inflammation. We will develop cell transfer models to track fibroblasts isolated from control mice of those with synovial hyperplasia. We will determine the impact of the transplanted fibroblasts on synovial hyperplasia, joint inflammation, and damage in either resting joints or in the context of inflammatory arthritis. By either over-expressing or silencing genes identified in our bioinformatics studies, we will determine the role these genes play in disease development. How will the results of the research be used? By addressing our key questions, we will determine whether synovial hyperplasia may act as the second hit in RA, creating opportunities for early identification or intervention in individuals at risk of RA. Furthermore, by identifying which molecules involved in cell proliferation are either overlapping or are distinct in dysregulated synovial fibroblasts and fibro-sarcomas, we will potentially reveal novel pathways involved in the tumour development.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;CANCER AND NEOPLASMS
Title: Molecular regulation of NK cell functional maturation by the transcription factor BACH2
Funder: Medical Research Council

Abstract: Natural killer (NK) cells are cytotoxic innate lymphocytes that form a critical first line of defence against cancer and infection. Unlike CD8+ T cells, recognition of cancer cells by NK cells is independent of neo-antigens and potentiated by defects in antigen presentation, making them attractive as mechanistically distinct targets to CD8+ T cells for cancer immunotherapy. Clinical responses to NK cell-targeted immunotherapies have thus far been modest identifying a need to better understand molecular mechanisms that restrict their function. NK cells exist in a variety of different states, called functional maturation states. These have important implications for their ability to control infections and cancer. We lack an understanding of negative regulators of NK cell functional maturation, though identifying such mechanisms may provide new therapeutic targets for NK cell-based immunotherapies. BACH2 is a transcriptional repressor whose expression is predominantly restricted to lymphocytes. New data indicates that BACH2 is an intrinsic negative regulator of NK cell functional maturation with consequences for homeostasis and anti-tumour immunity. The purpose of this work is to establish the function of BACH2 in NK cells, testing the hypothesis that it is a critical negative regulator of NK cell functional maturation and testing its consequences for homeostasis and immune responses to infection and cancer. Our proposed study is organised into three aims: 1. We will determine how BACH2 affects NK cells function under normal conditions, and during influenza infection, where NK cells can contribute to both clearance and immunopathology. 2. We will examine the effect of BACH2 in restraining NK cell responses to cancer. 3. We will map the genome-wide epigenetic and transcriptional changes that occur with NK cell functional maturation and examine the component of the NK cell functional maturation programme controlled by BACH2.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;CANCER AND NEOPLASMS
Title: Investigating the effect of inflammatory cytokines on cross-presentation in a murine melanoma model
Funder: Wellcome Trust

Abstract: Our understanding of how the immune system shapes the development of cancer is constantly improving as we continue to employ better experimental models. In particular, we are interested in how cytotoxic T cells, known as “resident killer” cells of the immune system, are capable of entering tumour tissues to suppress malignant cell growth. Acquisition of mutations allows tumour cells to become insensitive to soluble molecules called cytokines, which function within the vicinity of the tumour to promote T cells to recognize and attack tumour cells. Inflammatory cytokines further activate professional antigen presenting cells which can in turn initiate T cells specific for the tumour to proliferate and persist. However, it is not known whether insensitivity to cytokines due to tumour mutations will alter the function of immune cells. We propose to explore this biology using a murine model of melanoma which best replicates immune cell activity in the tumour. We aim to better understand how these mutations dampen anti-tumour immunity, and hope that our results can provide the basis for novel therapies which work to re-shape immune responses against tumours.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;CANCER AND NEOPLASMS
Title: Characterising the Tumour-Associated Regulatory T Cell Niche
Funder: Wellcome Trust

Abstract: The maintenance of tissue homeostasis is dependent on the function of stem cells (SCs) and tissue-resident immune cells. How tissue-resident immune cells influence SCs is poorly understood. Regulatory T cells (Tregs) are a specialised T cell subset that plays a significant role in regulating inflammatory responses. Emerging evidence suggests that subsets of Tregs stably residing in barrier tissue sites (e.g. skin) are highly implicated in tissue regeneration and cancer. Our group has demonstrated that a subset of skin-resident Tregs localise to SCs, and are functionally required for skin regeneration. Skin-resident Tregs express the Notch ligand, Jagged-1 (Jag1), as a critical receptor that augments SC function. Additionally, several studies have functionally linked Jag1 to the maintenance of cancer stem cells (CSCs). This research aims to understand how Treg-specific expression of Jag1 regulates the tumour associated Treg niche and affects skin tumour progression. We will primarily utilise in vivo model systems, but also cell culture, multi-colour flow cytometry and advanced molecular profiling, including RNA-sequencing, qPCR analysis, and tissue histopathology techniques. Upon completing this PhD project, we hope to better understand the underlying Treg-mediated regulatory mechanism of CSCs in skin cancers.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;CANCER AND NEOPLASMS
Title: Investigation of hypoxia-sensing mechanisms in immune regulation
Funder: Wellcome Trust

Abstract: CD4+CD25+Foxp3+ regulatory T cells (Tregs) are central to immune regulation and are a promising therapy for the treatment of autoimmunity and transplant rejection, where I am currently leading a clinical trial. Adaptive immune responses are regulated by environmental factors including hypoxia which reduces the activity of prolyl hydroxylase domain (PHD) enzymes thereby activating Hypoxia Inducible Factor (HIF) transcription factors. Effects on cytotoxic T cell activity have been reported, but the interplay between hypoxic signalling and Treg function is less clear. We have recently investigated this PHD/HIF axis using novel tetracycline-inducible PHD knockdown mice. Preliminary data suggest a previously unreported role for PHD2 and HIF-2a in the modulation of Treg activity. I now propose to characterise further the relationship between the PHD/HIF pathway and Treg activity, and to identify therapeutic targets that may be harnessed to modulate Treg function. Effects of further genetic (and pharmacological) manipulations will be tested in sensitive Treg functional assays and transplantation models. The cellular and metabolic mechanisms will be investigated in detail through phenotypic, transcriptomic and metabolic profiling. Overall, these data will broaden our understanding of the relationship between oxygen-sensing mechanisms and immune regulation which I am ultimately well placed to translate to the clinical setting.

Lay abstract: How does the immune system respond to changes in oxygen levels? Our immune system has an astounding ability to respond to infections while remaining tolerant towards our own cells. This equilibrium is maintained when we are healthy. However, a breakdown can result in an immune imbalance and the inability to respond appropriately to infections and tumours, as well as the development of autoimmune diseases. The factors responsible for this balance are not yet fully understood, but may be related to how T cells respond to low levels of oxygen. In order to investigate this, I will use genetically altered cells that behave as if they are in a low oxygen environment. Studying the way in which these cells perform will provide valuable insight into diseases of immune dysfunction and open up the possibilities for manipulating immune cells to produce better outcomes for patients with transplants, autoimmune diseases, and perhaps cancer.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;CANCER AND NEOPLASMS
Title: Elucidating How Tissue Resident Regulatory T cells Contribute to Epithelial Stem Cell Homeostasis and Tissue Regeneration
Funder: Wellcome Trust

Abstract: The maintenance of tissue homeostasis is dependent on the function of tissue-resident immune cells and the differentiation capacity of tissue-resident stem cells (SCs). How immune cells influence the function of SCs is largely unknown. Regulatory T-cells (Tregs) in skin preferentially localize to hair follicles (HFs), which house a major subset of SCs (HFSCs). Recently, we have functionally dissected the role of Tregs in HFSC biology. Lineage-specific depletion revealed that Tregs promote HF regeneration by augmenting HFSC function. Transcriptional and phenotypic profiling of skin Tregs identified expression of the Notch ligand family member, Jagged-1 (Jag1). Expression of Jag1 on Tregs facilitated HFSC function and efficient HF regeneration. To mechanistically dissect how Jag1 expression on Tregs is induced and how these cells represent a unique skin-resident population, we will initially perform comprehensive discovery approaches, at both the population and single cell level. We will also define the mechanistic contribution of Jag1+ Tregs in SC mediated regeneration in both healthy skin and skin tumors. Given that several new therapies for cancer and chronic inflammatory diseases are focused on augmenting the function of Tregs, it is imperative that we have a comprehensive understanding of the biology of Tregs in tissues.

Lay abstract: The maintenance of tissue homeostasis is dependent upon the immune cells present in that tissue, but also the ability of stem cells (SCs) to self-renew. How immune cells influence the function of SCs is largely unknown. In the skin, resides an immune cell population known as Regulatory T-cells (Tregs). Conventionally, these cells act by suppressing other over-activated tissue immune cells. We have recently shown that Tregs in skin are required for efficient function of skin SCs, and that they exert their function via expression of a receptor, called Jagged-1 (Jag1). Herein, we dissect how Jag1 expressing Tregs influence skin SCs both during normal skin function and during skin cancer. We hope that by understanding how Jag1+ Tregs work in tissues, we can better understand how SC- mediated diseases and cancer progression occurs. And in doing so, we can develop better-targeted therapies for these diseases.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;CANCER AND NEOPLASMS