Biology subjects

Thomas, J. P.

Publications and source records attributed to Thomas, J. P..

6 recordsLinked to original sources

bioRxiv2026

A microbiota-responsive polyfunctional cytotoxic CD4⁺ T-cell state promotes mucosal inflammation in ulcerative colitis

Ulcerative colitis (UC) is characterised by chronic colonic inflammation with marked heterogeneity in disease severity and therapeutic outcomes. Here, we define a spatially organised, polyfunctional cytotoxic CD4 T-cell state associated with mucosal inflammation and adverse therapeutic outcomes in UC. Integrating ex vivo T-cell receptor stimulation with multi-cohort bulk and single-cell transcriptomics and multiparameter flow cytometry, we show that GZMB CD4 T cells are preferentially enriched in inflamed UC mucosa, but not peripheral blood, and co-express cytotoxic molecules, Th1- and Th17-associated cytokines and chemokines, and immunoregulatory receptors. Single-cell analyses implicate inflammatory cytokine and antigen-presentation signals in the acquisition or maintenance of this state. High-resolution spatial profiling localised this programme predominantly to Th17 cells, which were preferentially enriched within multicellular inflammatory and tertiary lymphoid structure-associated niches. Across independent patient cohorts, a transcriptional signature derived from this state increased with endoscopic disease severity and was associated with reduced response to anti-TNF and anti-IL-12/23p40 therapies. Adoptive transfer of Gzma/Gzmb-deficient rather than wild-type CD4 T cells into Rag2-deficient recipient mice markedly attenuated experimental colitis and abrogated the polyfunctional cytokine phenotype, demonstrating that granzyme-dependent effector activity is a key mechanism driving CD4+ T-cell-mediated intestinal inflammation. Finally, human host-microbiome analysis linked this programme to intestinal dysbiosis, while transfer of dysbiotic microbiota promoted the emergence of a corresponding state in vivo. Collectively, these findings define a microbiota-responsive, spatially organised polyfunctional cytotoxic CD4 T-cell programme that contributes to intestinal inflammation and is associated with disease severity and treatment resistance in UC.

immunology↗

bioRxiv2026

A dysregulated stromal remodelling programme characterises prior anti-TNF failure in ulcerative colitis

Prior anti-tumour necrosis factor (TNF) failure is associated with reduced efficacy of subsequent advanced therapies in ulcerative colitis (UC), but the biological basis of this treatment-refractory state remains unclear. We integrated clinical outcomes and baseline colonic transcriptomic data from UC patients in the UNIFI phase III trial programme with regulatory and signalling network inference, connectivity mapping, and single-cell-resolution spatial transcriptomics. Colonic transcriptomic analyses identified coordinated enrichment of extracellular matrix organisation, collagen remodelling and integrin-associated programmes, increased stromal cell representation and elevated inferred MAPK/EGFR activity in UC patients with prior anti-TNF failure. Causal network inference prioritised MAPK3 as a candidate regulator of this state, while connectivity mapping identified MEK/EGFR inhibitors as candidate perturbagens. MEK inhibition suppressed stromal pathways and reduced inferred MAPK/EGFR activity ex vivo. Spatial profiling of active UC and non-IBD colonic tissues localised these programmes to UC-enriched stromal niches. Ligand-receptor inference further identified reciprocal stromal-myeloid communication within these niches. Collectively, these findings define a stromal remodelling programme associated with prior anti-TNF failure and nominate MAPK/EGFR signalling as a potentially tractable component of treatment-refractory UC.

systems biology↗

bioRxiv2026

Cytokine interaction networks, not individual cytokines, drive anti-TNF response in Crohn's disease

Crohns disease (CD) is a chronic inflammatory condition of the gastrointestinal tract for which anti-tumour necrosis factor (anti-TNF) agents remain a first-line biologic therapy. However, remission rates are modest, and the mechanistic basis of non-response is poorly characterised. A common resistance mechanism is thought to emerge when alternative inflammatory cascades compensate for TNF inhibition, but the interactions underlying this rewiring have not been systematically characterised. We applied CytokineLink, our previously developed systems immunology framework, to single-cell RNA sequencing data from CD patients sampled before and after anti-TNF therapy. We reconstructed networks of interacting cytokines across samples stratified by treatment phase, response, and inflammation status, and identified condition-specific cytokine interactions and feedback loops, statistically validated against degree-matched random networks. We clustered the generated networks based on their inflammation, response, and treatment status. The pre-treatment inflamed non-responder network contained the largest set of unique interactions, organised around a connected module driven by IL17C targeting downstream TNF, IL6, IL1B, CXCL1/2/3/8, and CCL20. IL17C was produced by a population of non-ileal enteroendocrine cells, differentially abundant at baseline in non-responders. Gene set variation analysis in an independent cohort confirmed elevated non-responder module activity in colonic tissues of non-responders. Feedback loop analysis revealed that responder networks were characterised by persistent IL10 circuits sustained by macrophage populations and acquired tissue-remodelling interactions after therapy, whereas non-responders lost IL10 feedback loops post-treatment and gained TNF-containing motifs, including circuits signalling through the upstream activator TL1A. Our findings characterise the mechanism of anti-TNF non-response as a cytokine network, in which pre-existing epithelial-driven inflammatory modules and the failure to preserve regulatory feedback sustain TNF-independent inflammation in CD. By characterising cytokine interactions at the systems level, our approach moves beyond single-cytokine models of anti-TNF resistance to provide a mechanistic framework for understanding the biological basis of treatment failure in immune mediated diseases.

systems biology↗

bioRxiv2026

Epithelial regulatory networks link non-coding genetic variation to clinical heterogeneity in ulcerative colitis

Ulcerative colitis (UC) is a genetically heterogeneous disease causing chronic intestinal inflammation. Genome-wide association studies have linked numerous non-coding single nucleotide polymorphisms (SNPs) to UC, yet how these variants relate to intestinal epithelial function and clinical outcomes remains largely unknown. To address this, we aimed to reconstruct patient-specific epithelial signalling and regulatory networks perturbed by non-coding SNPs and to dissect patient heterogeneity in a large UC phase III trial. We analysed genotype data from 452 participants in the etrolizumab phase III HICKORY cohort using the integrated SNP network platform (iSNP) to map the downstream effects of non-coding SNPs and identify transcription factors (TFs) they perturb in each patient. TFs were filtered to retain those with differential regulatory activity in UC epithelial cells, patients were stratified by these TF profiles, and clusters were correlated with etrolizumab outcomes. We identified 14 SNP-propagated TFs with differential epithelial regulatory activity. Unsupervised clustering stratified patients into subgroups differing in disease severity and treatment response: two clusters had the highest severity and lowest remission and response rates, whereas two others had the best outcomes. iSNP-based clustering improved endoscopic healing prediction (p = 0.03), with trends for clinical response and histological endoscopic mucosal improvement. This systems genomics framework links patient-specific non-coding SNPs to epithelial signalling and regulatory networks in UC and captures clinically meaningful heterogeneity associated with treatment outcomes. It supports genetics-informed precision medicine and improved clinical trial design in inflammatory bowel disease and beyond.

systems biology↗

bioRxiv2024

Decoding Cytokine Networks in Ulcerative Colitis to Identify Pathogenic Mechanisms and Therapeutic Targets

Ulcerative colitis (UC) is a chronic inflammatory disorder of the gastrointestinal tract characterised by dysregulated cytokine signalling. Despite the advent of advanced therapies targeting cytokine signalling, treatment outcomes for UC patients remain suboptimal. Hence, there is a pressing need to better understand the complexity of cytokine regulation in UC by comprehensively mapping the interconnected cytokine signalling networks that are perturbed in UC patients. To address this, we undertook systems immunology modelling of single-cell transcriptomics data from colonic biopsies of treatment-naive and treatment-exposed UC patients to build complex cytokine signalling networks underpinned by putative cytokine-cytokine interactions. The generated cytokine networks effectively captured known physiologically relevant cytokine-cytokine interactions which we recapitulated in vitro in UC patient-derived colonic epithelial organoids. These networks revealed new aspects of UC pathogenesis, including a cytokine subnetwork that is unique to treatment-naive UC patients, the identification of highly rewired cytokines across UC disease states (IL22, TL1A, IL23A, and OSM), JAK paralogue-specific cytokine-cytokine interactions, and the positioning of TL1A as an important upstream regulator of TNF and IL23A as well as an attractive therapeutic target. Overall, these findings open up several avenues for guiding future cytokine-targeting therapeutic approaches in UC, and the presented methodology can be readily applied to gain similar insights into other immune-mediated inflammatory diseases (IMIDs). One Sentence SummaryA systems immunology map of cytokine interaction networks in ulcerative colitis reveals novel insights into disease pathogenesis, with potential to guide future cytokine-targeting therapeutic strategies.

systems biology↗

bioRxiv2021

Extracellular vesicles produced by the human commensal gut bacterium Bacteroides thetaiotaomicron affect host immune pathways in a cell-type specific manner that are altered in inflammatory bowel disease

The gastrointestinal (GI) tract is inhabited by a complex microbial community, which contributes to its homeostasis. Disrupted microbiome can cause GI-related diseases, including inflammatory bowel disease, therefore identifying host-microbe interactions is crucial for better understanding gut health. Bacterial extracellular vesicles (BEVs), released into the gut lumen, can cross the mucus layer and access underlying immune cells. To study cross-kingdom communication between BEVs and host, we focused on the influence of BEVs, generated by Bacteroides thetaiotaomicron (VPI-5482), on host immune cells. Using single-cell RNA sequencing data and host-microbe protein-protein interaction networks, we examined the potential effect of BEVs on dendritic cells, macrophages and monocytes with particular focus on the Toll-like receptor (TLR) pathway. We identified biological processes affected in each immune cell type, and also cell-type specific processes (e.g myeloid cell differentiation). The TLR pathway analysis highlighted that BEV targets differ among cells and even between the same cells in healthy versus disease (ulcerative colitis) conditions. Our in silico findings were validated in BEV-monocyte co-cultures demonstrating the requirement for TLR4 in BEV-elicited NF-{kappa} B activation. This study demonstrates that both cell-type and health condition influence BEV-host communication. The results and the pipeline can facilitate BEV-based therapy development for the treatment of IBD.

bioinformatics↗