Biology subjects

Elliott, T.

Publications and source records attributed to Elliott, T..

13 recordsLinked to original sources

bioRxiv2026

Using peptide-exchange systems to interrogate peptide-specific KIR binding to HLA Class -I

The killer-cell immunoglobulin-like receptors (KIR) are a family of activating and inhibitory HLA class I (HLA-I) binding receptors expressed on natural killer (NK) cells and subsets of T cells. The KIR detect HLA-I molecules in a peptide-dependent manner, with some KIR displaying exquisite peptide-specificity. Studying peptide recognition by KIR often uses TAP-deficient cell lines expressing single HLA-I alleles, which are heterogenous and time consuming to generate. Here, we established an alternative approach using peptide-exchange technologies hitherto developed for studying T cell recognition of HLA-I. We tested two methods; dipeptide-mediated peptide exchange and open-HLA-I, HLA-I molecules consisting of heavy chain-{beta}2m disulphide bonded dimers. We combined peptide-exchange technologies with SpyTag-SpyCatcher chemistry to allow rapid detection of KIR binding via HLA-I displayed on plates or cells. We demonstrated the fidelity of this system with peptides of known KIR specificity bound to HLA-C*05:01. We then screened a peptide library to identify novel strong KIR2DS4 binding peptides presented by HLA-C*04:01. Peptide-exchanged HLA-C was functionally competent, promoting activation of KIR2DS4+ NK cells and inhibiting activation of KIR2DL1+ NK cells. Together, we show that peptide-exchangeable HLA-I molecules are ligands for KIR, presenting a flexible, efficient system for examining the peptide-sequence dependent recognition of HLA-I by KIR.

immunology↗

bioRxiv2026

TMEM33 deletion potentiates anti-tumor CD8+ T cell immunity

Improving responses to cancer immunotherapies requires deeper insight into the cellular mechanisms governing T cell-mediated anti-tumor immunity. TMEM33 is an endoplasmic reticulum-resident transmembrane protein enriched across multiple tumor types, with reported functions in anti-viral immunity as well as calcium and lipid homeostasis, yet its role in tumor immunosurveillance remains unknown. Using murine genetic models, we demonstrate that host TMEM33 constrains anti-tumor CD8+ T cell responses. Constitutive Tmem33-/- mice exhibited delayed melanoma tumor growth and increased CD8+ T cell infiltration. Antigen-specific CD8+ compartments in tumors of Tmem33-/- mice showed TCF-1+PD-1+ progenitor-exhausted cell (Tpex) enrichment, elevated effector function and reduced exhaustion, alongside improved effector memory expansion and T-bet expression in draining lymph nodes. We highlight that TMEM33 functions intrinsically within the T cell compartment, as TMEM33 deletion (1) enhanced polyclonal activation of naive CD8+ T cells ex vivo, (2) promoted preferential Tpex accumulation among adoptively transferred naive OT-I cells in B16F10-OVA tumors and draining lymph nodes, and (3) improved the potency of ex vivo-expanded OT-I cells in controlling tumor growth during adoptive cell therapy. Finally, in a large, prospectively recruited metastatic melanoma cohort, lower TMEM33 expression in patient CD8+ T cells significantly correlated with improved survival and elevated TCF-7 (encoding TCF-1). Collectively, our findings define TMEM33 as a formerly unrecognized intrinsic determinant of tumor-directed CD8+ T cell fate that limits Tpex maintenance, and restrains cell therapy responses, suggesting that its modulation may strengthen immunotherapeutic efficacy. One sentence summaryTMEM33 intrinsically limits progenitor exhausted CD8+ T cells, scales anti-tumor responses and predicts melanoma patient survival.

immunology↗

bioRxiv2025

Atom-level mechanism of tapasin-independent peptide editing by Major Histocompatibility Complex class I molecules

Peptide binding to major histocompatibility complex class I molecules (MHC-I) and their presentation to cytotoxic immune cells is a keystone of the adaptive immune system. The selection of MHC-I bound peptides is facilitated by the chaperone tapasin, which allows MHC-I to iteratively sample peptides until they are loaded with optimal binding peptides, known as peptide editing. However, some MHC-I allotypes can select high affinity binding peptides independently of tapasin, and the molecular mechanism(s) for such peptide editing are unknown. Here, we used enhanced sampling molecular dynamics simulations of peptide-deficient MHC-I to investigate tapasin-independent peptide editing. Our simulations revealed transient disruption of hydrogen bonds between MHC-I and the peptide backbone could allow for peptide editing, a process we term "active displacement". Destabilisation of interactions with the peptide backbone, necessitates sequence-specific sidechain interactions to maintain peptide binding. Our active displacement model predicts surface expression levels for multiple MHC-I allotypes and accounts for the presentation of an immunogenic mutant KRAS-G12D neoepitope by HLA-C*08:02, but not by closely related HLA-C*05:01. Together our data provide a molecular mechanism for tapasin-independent MHC-I peptide editing, influencing the surface immunopeptidome and anti-tumour immunity. Significance StatementMajor histocompatibility complex class I molecules (MHC-I) bind and present peptides to specialised killer cells of the immune system. These immune cells can unleash their cytotoxic effector functions if they recognise the peptide-MHC-I complex. Which peptides are presented by MHC-I is therefore highly important. Peptide selection is usually assisted by the tapasin protein, although some MHC-I molecules can select peptides independently of tapasin, but it is not known how this occurs. Here, we provide an atomistic description of the tapasin-independent peptide selection mechanism. Our mechanism applies to multiple MHC-I allotypes and illustrates how an immunogenic peptide is presented by one MHC-I molecule, but not by another closely related molecule. This new insight provides a rational basis for therapeutic treatments.

immunology↗

bioRxiv2024

Comparative analysis of protein expression between oesophageal adenocarcinoma and normal adjacent tissue

Oesophageal adenocarcinoma (OAC) is the 7th most common cancer in the United Kingdom and remains a significant health challenge. This study presents a proteomic analysis of seven OAC donors complementing our previous neoantigen identification study of their human leukocyte antigen (HLA) immunopeptidomes. Using label-free mass spectrometry proteomics, we compared OAC tumour tissue to matched normal adjacent tissue (NAT) to identify differentially expressed proteins. We identified differential expression of a number of proteins previously linked to OAC and other cancers. We observed enrichment of processes and pathways relating RNA processing and the immune system. Our findings also offer insight into the role of the protein stability in the generation of the neoantigen we previously identified. These results provide independent corroboration of existing oesophageal adenocarcinoma biomarker studies that may inform future diagnostic and therapeutic research.

cancer biology↗

bioRxiv2024

Comparative analysis of transcriptomic and proteomic expression between two non-small cell lung cancer subtypes

Non-small cell lung cancer (NSCLC) is frequently diagnosed at an advanced stage and has poor survival. NSCLC subtypes require different treatment regimes, hence there are extensive efforts to find more precise and non-invasive differential diagnostics tools. Complementing these efforts, we examined two NSCLC subtypes for differences that may inform treatment options and identify potential novel therapeutic pathways. Here we present a comparative analysis of transcriptomic and proteomic expression in tumours from a cohort of 22 NSCLC patients: 8 squamous cell carcinoma (LUSC), 14 adenocarcinoma (LUAD). We examined differential gene and differential protein expression between LUSC and LUAD, and between NSCLC subtypes and either PBMCs or normal adjacent lung tissue (NAT). We found that both NSCLC subtypes shared common differences in gene expression to PBMC relating to developmental and structural changes, and common protein expression differences to NAT relating to protein translation and RNA related processing and splicing. Between NSCLC subtypes we found differential gene expression relating to cell differentiation for LUSC and cellular structure and immune response regulation for LUAD. Differential protein expression between NSCLC subtypes related to extracellular structure for LUSC and metabolic processes, including glucose metabolism for LUAD. Many of our observations of differentially expressed genes and proteins between NSCLC subtypes support and inform existing observations, aiding both basic and clinical research seeking to identify subtype biomarkers or druggable targets.

cancer biology↗

bioRxiv2024

Proteogenomics guided identification of functional neoantigens in non-small cell lung cancer

Non-small cell lung cancer (NSCLC) has poor survival even with modern checkpoint inhibitor therapies. Personalised vaccines based on short peptide neoantigens containing tumour mutations are an attractive precision medicine strategy, but identifying therapeutically relevant neoantigens remains challenging, with existing methods yielding positive responses in only 6% of candidates tested. We developed an immunopeptidomics approach to improve neoantigen identification in 24 NSCLC patients (15 adenocarcinoma, 9 squamous cell carcinoma). We directly identified one neoantigen and using whole exome sequencing, transcriptomics and mass spectrometry-based immunopeptidomics, we filtered predicted neoantigens based on observed cohort HLA peptide presentation. This approach achieved positive functional responses in 5 of 6 patients tested (83% success rate) with 13% of putative neoantigens (9 out of 70) eliciting strong responses. Bayesian modelling of our initial rules-based neoantigen selection further revealed patient specific peptide presentation patterns and propensities. Our findings demonstrate that incorporating donor specific HLA peptide presentation data substantially improves neoantigen identification success rates and immune response specificity, advancing personalised cancer vaccine development.

immunology↗

bioRxiv2023

Single-cell immune multi-omics and repertoire analyses in pancreatic ductal adenocarcinoma reveal differential immunosuppressive mechanisms within different tumour microenvironments

Pancreatic ductal adenocarcinoma (PDAC) has an extremely poor prognosis. Understanding the multiple mechanisms by which the tumour evades immune control, and how these mechanisms may be disrupted is critical to developing targeted immunotherapies. Previous studies have shown that higher lymphocyte infiltration is associated with better survival, and here we investigated what mediates these differences. We performed a comprehensive analysis of PDAC-associated immune cells using single cell multi-omics coupled with re-analysis of public PDAC scRNA-seq datasets. We introduce novel single-cell and repertoire analyses that have uncoupled diverse roles and contributions of various immune cell populations within different tumour microenvironments (TMEs). They revealed clear distinctions in the clonal characteristics among different patient groups, provided valuable insights into the mechanisms of immune cell migration and tissue adaptation underlying these disparities. These results point to differential CD4 polarisation of intra-tumoural T cells, differential B cell differentiation, GC reactions, antigen presentation pathways, and distinct cell-cell communication between the myeloid-enriched and adaptive-enriched groups. Overall, we identified two major distinct themes for future immune intervention within PDAC patients between those with higher adaptive versus myeloid immune cell infiltration.

immunology↗

bioRxiv2023

Integration of Avidity and Differentiation is enabled by CD8+ T-cell sensing of IFN-γ

The most effective responses to intracellular pathogens have a breadth of T-cell clones with different affinities for their cognate peptide, and a diversity of functional phenotypes, from effector to long-lived memory cells. While high- and low-affinity T-cells are inherently skewed towards becoming effector and memory, respectively, overall, both functional subsets exploit a wide range of affinities. How the breadth of affinities and functionalities are coordinated is therefore unclear. In this study, we provide evidence that direct sensing of the cytokine IFN-{gamma} by CD8+ T-cells is a factor controlling the integration of T-cell affinity and differentiation during infection. IFN-{gamma} increases the expansion of low-affinity T-cells, allowing them to overcome the selective advantage of high-affinity T-cells. Concomitantly, IFN-{gamma} reinforces high-affinity T-cell entry into the memory pool. As a result, direct IFN-{gamma} sensing by CD8+ T-cells increases the avidity of the memory response. This comes at the expense of the primary T-cell response, for which IFN-{gamma} decreases the avidity, leading to sub-optimum immunity to infection. IFN-{gamma} sensing by CD8+ T-cells is paracrine, provided by a distinct subset of CD8+ T-cells called Virtual Memory T-cells, an antigen inexperienced subset that harbors memory features. Overall, we propose that IFN-{gamma} and Virtual Memory T-cells fulfil a critical immunoregulatory role by enabling the coordination of T-cell avidity and fate.

immunology↗

bioRxiv2022

Identification of neoantigens in esophageal adenocarcinoma

Esophageal adenocarcinoma (EAC) has a relatively poor long-term survival and limited treatment options. Promising targets for immunotherapy are short peptide neoantigens containing tumor mutations, presented to cytotoxic T-cells by human leukocyte antigen molecules (HLA). Despite an association between putative neoantigen abundance and therapeutic response across cancers, immunogenic neoantigens are challenging to identify. Here we characterized the mutational and immunopeptidomic landscapes of tumors from a cohort of seven patients with EAC. We directly identified one HLA-I presented neoantigen from one patient, and report functional T-cell responses from a predicted HLA-II neoantigen in a second patient. The predicted class II neoantigen contains both HLA I and II binding motifs. Our exploratory observations are consistent with previous neoantigen studies in finding that neoantigens are rarely directly observed, and an identification success rate following prediction in the order of 10%. However, our identified putative neoantigen is capable of eliciting strong T-cell responses, emphasizing the need for improved strategies for neoantigen identification.

cancer biology↗

bioRxiv2021

Immunopeptidomic analysis of influenza A virus infected human tissues identifies internal proteins as a rich source of HLA ligands

CD8+ and CD4+ T cells provide cell-mediated cross-protection against multiple influenza strains by recognising epitopes bound as peptides to human leukocyte antigen (HLA) class I and -II molecules respectively. Two challenges in identifying the immunodominant epitopes needed to generate a universal T cell influenza vaccine are: A lack of cell models susceptible to influenza infection which present population-prevalent HLA allotypes, and an absence of a reliable in-vitro method of identifying class II HLA peptides. Here we present a mass spectrometry-based proteomics strategy for identifying viral peptides derived from the A/H3N2/X31 and A/H3N2/Wisconsin/67/2005 strains of influenza. We compared the HLA-I and -II immunopeptidomes presented by ex-vivo influenza challenged human lung tissues. We then compared these with directly infected immortalised macrophage-like cell line (THP1) and primary dendritic cells fed apoptotic influenza-infected respiratory epithelial cells. In each of the three experimental conditions we identified novel influenza class I and II HLA peptides with motifs specific for the host allotype. Ex-vivo infected lung tissues yielded few class-II HLA peptides despite significant numbers of alveolar macrophages, including directly infected ones, present within the tissues. THP1 cells presented HLA-I viral peptides derived predominantly from internal proteins. Primary dendritic cells presented predominantly viral envelope-derived HLA class II peptides following phagocytosis of apoptotic infected cells. The most frequent viral source protein for HLA-I and -II was matrix 1 protein (M1). This work confirms that internal influenza proteins, particularly M1, are a rich source of CD4+ and CD8+ T cell epitopes. Moreover, we demonstrate the utility of two ex-vivo fully human infection models which enable direct HLA-I and -II immunopeptide identification without significant viral tropism limitations. Application of this epitope discovery strategy in a clinical setting will provide more certainty in rational vaccine design against influenza and other emergent viruses. Author SummaryInfluenza infections present a significant global health challenge. High rates of mutation require reformulation of vaccines annually. Vaccines are designed to induce antibody responses to the surface proteins of the influenza virus, but the contribution of T cells to overall immunity is unclear. Here, we used several totally human laboratory models to show how the viral proteins are presented to the T cells to induce immunity. We found that CD8 T cells, which kill infected cells, and CD4 T cells which support the CD8 T cells as well as the antibody-producing B cells, mainly see proteins from inside the viral particle, not the surface ones which are targeted by antibodies. These internal viral proteins are more similar between different viral strains than the surface proteins, and therefore suggest that vaccines designed to induce T cell responses could be better protective if they target internal viral proteins.

immunology↗

bioRxiv2021

Fluctuations in TCR and pMHC interactions regulate T cell activation

Adaptive immune responses depend on interactions between T cell receptors (TCRs) and peptide major-histocompatibility complex (pMHC) ligands located on the surface of T cells and antigen presenting cells (APCs) respectively. As TCRs and pMHCs are often only present at low copy-numbers their interactions are inherently stochastic, yet the role of stochastic fluctuations on T cell function is unclear. Here we introduce a minimal stochastic model of T cell activation that accounts for serial TCR-pMHC engagement, reversible TCR conformational change and TCR aggregation. Analysis of this model indicates that it is not the strength of binding between the T cell and the APC cell per se that elicits an immune response, but rather the information imparted to the T cell from the encounter, as assessed by the entropy rate of the TCR-pMHC binding dynamics. This view provides an information-theoretic interpretation of T cell activation that explains a range of experimental observations. Based on this analysis we propose that effective T cell therapeutics may be enhanced by optimizing the inherent stochasticity of TCR-pMHC binding dynamics.

immunology↗

bioRxiv2018

Protective low avidity anti-tumour CD8+ T cells are selectively attenuated by regulatory T cells

Regulatory T cells (Treg) play a major role in the suppression of protective anti-tumour T cell responses. In the CT26 BALB/c murine model of colorectal carcinoma, Tregs differentially suppress responses to two characterised CD8+ T epitopes, AH1 and GSW11, which results in an absence of detectable IFN-{gamma} producing GSW11- specific T cells in the spleen and lymph nodes of tumour challenged mice. Activation of GSW11-specific T cells correlates with protection against tumour growth. Here we show that GSW11-specific T cells are in fact induced in Treg-replete, CT26-bearing mice, where they make up the majority of tumour infiltrating CD8+ lymphocytes, but exhibit a dysfunctional exhausted phenotype. This dysfunctional phenotype is induced early in the anti-tumour response in draining lymph nodes, spleens and tumours and is significantly more pronounced in GSW11-specific T cells compared to other tumour-specific T cell responses. Depletion of Tregs prior to tumour challenge significantly reduces the induction of exhaustion in GSW11-specific T cells and correlates with altered T cell receptor (TcR) usage. Moreover, the avidity of GSW11- specific TcRs that expanded in the absence of Tregs was significantly lower compared to TcRs of cytotoxic T lymphocyte (CTL) populations that were diminished in protective anti-tumour responses. This indicates that Tregs suppress the induction of protective anti-tumour T cell responses and may signify that the induction of low avidity T cells, while being more susceptible to exhaustion are the most efficacious in tumour rejection.

immunology↗

bioRxiv2018

Cities of the future, visualizing climate change to inspire actions

Combating against climate change requires unified action across all sectors of society. However, this collective action is precluded by the consensus gap between scientific knowledge and public opinion. A growing body of evidence suggests that facts do not persuade people to act. Instead, it is visualization - the ability to simulate relatable scenarios - is the most effective approach for motivating behavior change. Here, we exemplify this approach, using current climate projections to enable people to visualize cities of the future, rather than describing intangible climate variables. Analyzing city pairs for 520 major cities of the world, we characterize which cities will most closely resemble the climate conditions of which other major cities by 2050. On average, most cities will resemble cities that are over 1000km south, and 22% of cities will experience climate conditions that are not currently experienced by any existing major cities. We predict that Londons climate in 2050 will resemble Barcelonas climate today, Madrid will resemble to Marrakesh, Moscow to Sofia, Seattle to San Francisco, Stockholm to Budapest, Tokyo to Changsha, etc. Our approach illustrates how complex climate data can be packaged to provide tangible information. By allowing people to visualize their own climate futures, we hope to empower citizens, policy makers and scientists to visualize expected climate impacts and adapt decision making accordingly.

scientific communication and education↗