ORCID Profile
0000-0001-7413-5002
Current Organisation
University of Oxford
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Publisher: Cold Spring Harbor Laboratory
Date: 16-11-2020
DOI: 10.1101/2020.11.15.383786
Abstract: Immune checkpoint blockers (ICB) exert their anti-cancer effects via CD8 + T cells, although how responses vary over sub-populations and across clones is incompletely understood. We performed single-cell RNA-sequencing of CD8 + T cells and their receptors pre- and post-ICB across eight patients, integrating results with bulk-sequencing data (n=209). We identify seven subsets with ergent responses to ICB, finding the effector cluster demonstrates the most pronounced changes. Likewise, transcriptomic response to ICB relates to clone size, with large clones demonstrating increased numbers of regulated genes of higher immunological pertinence. Cytotoxic effector clones were more likely to persist long-term following ICB and overlapped with public tumour-infiltrating lymphocyte clonotypes. Notably, pre-treatment CD8 + cytotoxicity associated with progression-free survival, highlighting the importance of the baseline CD8 + immune landscape in long-term response. This work further advances understanding of the molecular determinants of ICB response and assists in the search for peripheral prognostic biomarkers. Using single-cell and bulk RNA sequencing we explore checkpoint immunotherapy activity on peripheral CD8 + T cells in metastatic melanoma demonstrating that cell subset and clone size determine gene expression responses to treatment, and that pre-treatment cytotoxicity and clonality of peripheral CD8 + T cells is clinically prognostic.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 07-03-2014
Abstract: It is difficult to determine the mechanistic consequences of context-dependent genetic variants, some of which may be related to disease (see the Perspective by Gregersen ). Two studies now report on the effects of stimulating immunological monocytes and dendritic cells with proteins that can elicit a response to bacterial or viral infection and assess the functional links between genetic variants and profiles of gene expression. M. N. Lee et al. ( 10.1126/science.1246980 ) analyzed the expression of more than 400 genes, in dendritic cells from 30 healthy subjects, which revealed how expression quantitative trait loci (eQTLs) affect gene expression within the interferon-β and the Toll-like receptor 3 and 4 pathways. Fairfax et al. ( 10.1126/science.1246949 ) performed a genome-wide analysis to show that many eQTLs affected monocyte gene expression in a stimulus- or time-specific manner.
Publisher: Research Square Platform LLC
Date: 12-04-2022
DOI: 10.21203/RS.3.RS-1531341/V1
Abstract: Although treatment with immune checkpoint blockade (ICB) has transformed outcomes for patients with melanoma (1, 2), it frequently triggers immune related adverse events (irAEs), causing serious morbidity and presenting a major hurdle to immuno-oncology (3, 4). The degree to which germline genetic variation predisposes to irAEs is unknown. Here, studying a cohort of 214 patients receiving ICB for melanoma, we observe increased risk of severe irAEs in carriers of the minor allele of rs16906115, intronic to IL7. We find rs16906115 forms a B cell specific expression quantitative trait locus to IL7 in patients only, with risk allele carriers demonstrating increased B cell IL7 expression, immunoglobulin class switching and somatic hypermutation. Notably, increased B cell IL7 expression is independently associated with risk of irAEs. Consistent with the role of IL-7 in T cell development, risk allele carriers have distinct ICB induced CD8+ T cell subset responses, with allelic effects on gene expression and clonality. Risk allele carriers display significantly reduced CD8+ T cell mitotic responses to ICB, with skewing of T cell clonality and increased counts of large clones previously associated with disease response. These observations highlight key roles for both B cells and IL-7 in ICB response and toxicity, and demonstrate the power of agnostic human genetic studies to reveal novel determinants of response to cancer immunotherapy.
Publisher: Cold Spring Harbor Laboratory
Date: 11-05-2021
DOI: 10.1101/2021.05.11.21256877
Abstract: Treatment of severe COVID-19 is currently limited by clinical heterogeneity and incomplete understanding of potentially druggable immune mediators of disease. To advance this, we present a comprehensive multi-omic blood atlas in patients with varying COVID-19 severity and compare with influenza, sepsis and healthy volunteers. We identify immune signatures and correlates of host response. Hallmarks of disease severity revealed cells, their inflammatory mediators and networks as potential therapeutic targets, including progenitor cells and specific myeloid and lymphocyte subsets, features of the immune repertoire, acute phase response, metabolism and coagulation. Persisting immune activation involving AP-1 38MAPK was a specific feature of COVID-19. The plasma proteome enabled sub-phenotyping into patient clusters, predictive of severity and outcome. Tensor and matrix decomposition of the overall dataset revealed feature groupings linked with disease severity and specificity. Our systems-based integrative approach and blood atlas will inform future drug development, clinical trial design and personalised medicine approaches for COVID-19.
Publisher: Springer Science and Business Media LLC
Date: 09-2021
Publisher: Public Library of Science (PLoS)
Date: 08-05-2015
Publisher: Springer Science and Business Media LLC
Date: 12-2022
DOI: 10.1038/S41591-022-02095-5
Abstract: Treatment with immune checkpoint blockade (ICB) frequently triggers immune-related adverse events (irAEs), causing considerable morbidity. In 214 patients receiving ICB for melanoma, we observed increased severe irAE risk in minor allele carriers of rs16906115, intronic to IL7 . We found that rs16906115 forms a B cell-specific expression quantitative trait locus (eQTL) to IL7 in patients. Patients carrying the risk allele demonstrate increased pre-treatment B cell IL7 expression, which independently associates with irAE risk, ergent immunoglobulin expression and more B cell receptor mutations. Consistent with the role of IL-7 in T cell development, risk allele carriers have distinct ICB-induced CD8 + T cell subset responses, skewing of T cell clonality and greater proportional repertoire occupancy by large clones. Finally, analysis of TCGA data suggests that risk allele carriers independently have improved melanoma survival. These observations highlight key roles for B cells and IL-7 in both ICB response and toxicity and clinical outcomes in melanoma.
Publisher: Springer Science and Business Media LLC
Date: 07-07-2015
DOI: 10.1038/NCOMMS8545
Abstract: Neutrophils form the most abundant leukocyte subset and are central to many disease processes. Technical challenges in transcriptomic profiling have prohibited genomic approaches to date. Here we map expression quantitative trait loci (eQTL) in peripheral blood CD16+ neutrophils from 101 healthy European adults. We identify cis -eQTL for 3281 neutrophil-expressed genes including many implicated in neutrophil function, with 450 of these not previously observed in myeloid or lymphoid cells. Paired comparison with monocyte eQTL demonstrates nuanced conditioning of genetic regulation of gene expression by cellular context, which relates to cell-type-specific DNA methylation and histone modifications. Neutrophil eQTL are markedly enriched for trait-associated variants particularly autoimmune, allergy and infectious disease. We further demonstrate how eQTL in PADI4 and NOD2 delineate risk variant function in rheumatoid arthritis, leprosy and Crohn’s disease. Taken together, these data help advance understanding of the genetics of gene expression, neutrophil biology and immune-related diseases.
Publisher: Springer Science and Business Media LLC
Date: 14-07-2022
DOI: 10.1038/S41467-022-31626-4
Abstract: Natural Killer cells are innate lymphocytes with central roles in immunosurveillance and are implicated in autoimmune pathogenesis. The degree to which regulatory variants affect Natural Killer cell gene expression is poorly understood. Here we perform expression quantitative trait locus mapping of negatively selected Natural Killer cells from a population of healthy Europeans ( n = 245). We find a significant subset of genes demonstrate expression quantitative trait loci specific to Natural Killer cells and these are highly informative of human disease, in particular autoimmunity. A Natural Killer cell transcriptome-wide association study across five common autoimmune diseases identifies further novel associations at 27 genes. In addition to these cis observations, we find novel master-regulatory regions impacting expression of trans gene networks at regions including 19q13.4, the Killer cell Immunoglobulin-like Receptor region, GNLY , MC1R and UVSSA . Our findings provide new insights into the unique biology of Natural Killer cells, demonstrating markedly different expression quantitative trait loci from other immune cells, with implications for disease mechanisms.
Publisher: Springer Science and Business Media LLC
Date: 19-01-2023
DOI: 10.1038/S41467-023-35948-9
Abstract: IFNγ is an immune mediator with concomitant pro- and anti-tumor functions. Here, we provide evidence that IFNγ directly acts on intra-tumoral CD8 T cells to restrict anti-tumor responses. We report that expression of the IFNγ receptor β chain (IFNγR2) in CD8 T cells negatively correlates with clinical responsiveness to checkpoint blockade in metastatic melanoma patients, suggesting that the loss of sensitivity to IFNγ contributes to successful antitumor immunity. Indeed, specific deletion of IFNγR in CD8 T cells promotes tumor control in a mouse model of melanoma. Chronic IFNγ inhibits the maintenance, clonal ersity and proliferation of stem-like T cells. This leads to decreased generation of T cells with intermediate expression of exhaustion markers, previously associated with beneficial anti-tumor responses. This study provides evidence of a negative feedback loop whereby IFNγ depletes stem-like T cells to restrict anti-tumor immunity. Targeting this pathway might represent an alternative strategy to enhance T cell-based therapies.
Publisher: Springer Science and Business Media LLC
Date: 08-09-2013
DOI: 10.1038/NG.2756
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Benjamin Fairfax.