BACKGROUND:Neutralizing autoantibodies against interleukin-10 can result in a phenocopy of monogenic defects of interleukin-10 signaling in children and may be associated with inflammatory bowel disease (IBD). The allele HLA-DRB1*01:03 is the strongest genetic risk factor for ulcerative colitis. METHODS:We used a cellular interleukin-10 reporter assay and a confirmatory competitive enzyme-linked immunosorbent assay to assess neutralizing interleukin-10 autoantibodies in serum samples obtained from patients with IBD in the Oxford and U.K. IBD BioResource cohorts and from persons without IBD (controls). An in vitro cytokine-release bioassay was performed in a subgroup of patients to assess interleukin-10, interleukin-23, interleukin-1β, tumor necrosis factor, and interleukin-6. We performed HLA association analysis using imputation and high-resolution sequencing. RESULTS:Interleukin-10-neutralizing autoantibodies were detected in 173 of 4909 patients with IBD (3.5%; 95% confidence interval [CI], 3.0 to 4.1) and in none of 1006 controls (P<0.001). High anti-interleukin-10 activity in serum was associated with a reduction in detectable interleukin-10 and with an exaggerated proinflammatory cytokine response, consistent with functional neutralization of interleukin-10 signaling. Anti-interleukin-10 seropositivity was strongly associated with HLA-DRB1*01:03 on the basis of imputed data from the Oxford cohort (odds ratio, 50.0; 95% CI, 16.4 to 152.3; P = 6.14×10-12) and the U.K. IBD BioResource cohort (odds ratio, 24.7; 95% CI, 14.5 to 42.1; P = 6.20×10-32) and in a high-resolution sequencing analysis of data from the Oxford cohort (odds ratio, 29.5; 95% CI, 12.2 to 71.1; P = 4.85×10-14). CONCLUSIONS:Neutralizing interleukin-10 autoantibodies were present in a subgroup of patients with IBD and were strongly associated with HLA-DRB1*01:03. (Funded by the National Institute for Health and Care Research and others.).

Abstract Background Monoclonal antibodies against tumour necrosis factor (TNF) such as Infliximab (IFX) and Adalimumab (ADA) are used as first line therapy against inflammatory bowel disease (IBD) and have proven efficacy. However, in up to 40% of IBD patients these drugs become ineffective after the first year, principally due to the development of anti-drug immunogenicity. Distinct allelic variants at the HLA DQ1 locus predispose patients to develop immunogenicity to IFX or ADA (1, 2, 3). The aim of this study is to identify peptides derived from IFX and ADA that are presented on class II MHC of antigen presenting cells, in order to determine the epitopes that may play a role in T cell mediated immunogenicity against anti-TNF therapy. This may allow rational drug re-design. Methods Monocyte-derived dendritic cells (MDDCS) from 8 different donors, as well as EBV-transformed B cell lines from 3 different donors of known HLA-type were cultured and pulsed with IFX and ADA. Unpulsed cells were used as a negative control. Cells were processed for sequential immune precipitation with HLA-DQ, HLA-DP and HLA-DR antibodies. Peptides were then purified and analysed by mass spectrometry. These were run against a database of known proteins, including IFX and ADA, using the Peaks analytical software and then mapped to the original protein. Peptides were subjected to a binding prediction algorithm, to determine the likelihood of individual peptides binding to each HLA allele combinations. Peptides were then ranked from highest to lowest binder. Results Analysis of peptides from all three MHC class II antibody fractions showed that the highest number of peptides immunoprecipitated were between 14 to 16 amino acids in length, in line with the predicted length for class II MHC proteins. Additionally, there was an enrichment of peptides predicted to bind to specific class II MHC molecules, with an average of 77% binders versus 23% non-binders for MDDCs, and 84% binders versus 16 % non-binders for B-cells, after immune precipitation. Several overlapping peptides from the variable regions of both the heavy and light chain of IFX and ADA were identified, some of which are predicted to bind to risk alleles for anti-TNF immunogenicity, including DQA1*05:01, DRB1*11:01 and HLA-DQA1*05:05 (Figures 1 and 2). Conclusion We have characterised a series of IFX and ADA derived peptides from MDDCs and B cell lines, that were pulsed with anti-TNF antibody drugs. These peptides represent candidate T cell epitopes that may play a role in eliciting anti-drug antibody responses, and these data will therefore contribute to the understanding of the molecular mechanism of anti-TNF treatment failure. References 1)Doherty R, Liao H, Satsangi J, Ternette N. Extended Analysis Identifies Drug-Specific Association of 2 Distinct HLA Class II Haplotypes for Development of Immunogenicity to Adalimumab and Infliximab. Gastroenterology. 2020, 159: 784-787. 2)Sazonovs A, Kennedy N, Moutsianas L, et al. HLA-DQA1*05 Carriage Associated With Development of Anti-Drug Antibodies to Infliximab and Adalimumab in Patients With Crohn’s Disease Gastroenterology. 2020, 158:189-199 3)Ternette N, Liao H., Satsangi J. Association of the HLA DQA1*05 allelic gene variants with immunogenicity to anti-TNF therapeutics - important differences between infliximab and adalimumab. Journal of Crohn's and Colitis. 2024

Abstract Background The PROFILE study demonstrated clear benefits of early advanced therapy in luminal Crohn’s disease (CD) in the trial setting. We retrospectively evaluated the relationship between timing of onset of infliximab as first advanced therapy and disease outcomes in a real-world single centre cohort at Oxford University Hospitals NHS Trust. Methods A pharmacy database was searched to identify patients who received infliximab as first advanced therapy in CD. Electronic patient records (Cerner) were searched to capture the following: demographics, Montreal classification, timing of onset of infliximab, biochemical, endoscopic and radiological parameters. The primary outcome was persistence on therapy. Secondary outcomes were survival without surgery or hospitalisation, progression of disease phenotype and steroid use. Data was analysed using GraphPad Prism. Results 247 patients prescribed infliximab as first advanced therapy were identified (F:M = 112:135). Median duration (IQR) from diagnoses to first infliximab dose was 2.83 (0.25 – 10.02) years. 117 patients had inflammatory luminal disease at therapy onset (Montreal B1P0), with median first therapy from diagnosis of 2.67 (0.25 – 9.91) years. When reviewing all cases, and those with exclusively inflammatory luminal disease, persistence on therapy, survival without surgery and survival without hospitalisation did not vary with time to first advanced therapy (p>0.05 all comparisons, figure 1). However, in patients with luminal inflammatory CD who started therapy within 2 years of disease onset there was less disease progression, defined as extension in location, behaviour or new perianal disease (2/52 vs 10/65 chi sq 4.18 p=0.04), and a trend towards less systemic corticosteroid use (4/52 vs 13/65 chi sq 3.53 p=0.06). Conclusion Early infliximab therapy in luminal CD is associated with less disease progression and less use of systemic corticosteroids. The lack of variation in other outcomes may be due to historical case selection for advanced therapies. References Noor NM et al. PROFILE. Gastro Lancet Hep 2024 Figure 1: Persistence on therapy, surgery and hospitalisation free survival, categorised by duration from diagnosis until first infliximab dose. *luminal = Montreal B1P0

Abstract Background The HLA allele DQA1*05 was initially identified as a risk factor for the development of anti-drug antibodies in patients undergoing infliximab and adalimumab treatment for Crohn's disease1. We found in our extended analyses that DQA1*05:01 is associated with the development of antibodies to infliximab only, while DQA1*05:05 is associated with immunogenicity to both drugs in the original cohort2. These observations were confirmed for adalimumab in the SERENE trial3. Here we present data from the Oxford OASIS study, which comprised 899 patients receiving both infliximab or adalimumab. Participants had a median age of 38 years at the start of the treatment. 279 patients were diagnosed with ulcerative colitis (UC), 599 with Crohn's disease (CD), and 20 with unclassified inflammatory bowel disease. Methods We interrogated the HLA allele associations of a 'primary loss of response (LOR)', defined as no documented clinical response ever recorded, with a drug treatment for less than 12 months, and a 'secondary loss of response', defined as the documentation of clinical response to either drug followed by later, documented LOR. Kaplan-Meier curves were used to examine the proportional hazard hypothesis and demonstrated the differences of immunogenicity rates between different HLA types. Further, log-rank tests were applied using R package 'survival' (10.32614/CRAN.package.survival) to compute the hazard ratios (HR) between two categories, and to estimate their 95% confidence intervals (CI) and p-values. Results Our analysis confirmed that HLA-DQA1*05:01 was associated with primary LOR to infliximab (HR=1.8, 95% CI=[0.911, 3.55], p=0.0368), while not associated with LOR to adalimumab (HR=0.754, 95% CI=[0.439, 1.29], p=0.338). Conversely, LOR to adalimumab was associated HLA DQA1*05:05 (HR=1.96, 95% CI=[1.05, 3.65], p=0.0086), while we did not see significant correlation with loss of response to infliximab (HR=1.49, 95% CI=[0.782, 2.83], p=0.178). When both alleles were grouped together as HLA-DQA1*05, a significant association of LOR was only detected for infliximab, and the significant association of adalimumab with HLA DQA1*05:05 would be obscured. Conclusion Our findings from the OASIS study reveal distinct association of HLA-DQA1*05:01 with LOR to infliximab, and HLA DQA1*05:05 with LOR to adalimumab, highlighting that these alleles cannot be considered or grouped together for HLA association studies as previously practised1. These results underscore the necessity of 4-digit high-resolution HLA typing to distinguish between closely related alleles and accurately identify treatment-specific immunogenicity risks3,4. Furthermore, the co-inheritance of other HLA alleles may also play an important role, warranting additional investigation2. References 1.Sazonovs A, Kennedy NA, Moutsianas L, et al. HLA-DQA1*05 Carriage Associated With Development of Anti-Drug Antibodies to Infliximab and Adalimumab in Patients With Crohn's Disease. Gastroenterology. Jan 2020;158(1):189-199. doi:10.1053/j.gastro.2019.09.041 2.Powell Doherty RD, Liao H, Satsangi JJ, Ternette N. Extended Analysis Identifies Drug-Specific Association of Two Distinct HLA Class II Haplotypes for Development of Immunogenicity to Adalimumab and Infliximab. Gastroenterology. Apr 7 2020;doi:10.1053/j.gastro.2020.03.073 3.Reppell M, Zheng X, Dreher I, et al. HLA-DQA1*05 associates with anti-TNF immunogenicity and low adalimumab trough concentrations in inflammatory bowel disease patients from the SERENE UC and CD studies. J Crohns Colitis. Aug 20 2024;doi:10.1093/ecco-jcc/jjae129 4.Ternette N, Liao H, Satsangi J. Association of the HLA DQA1*05 allelic gene variants with immunogenicity to anti-TNF therapeutics - important differences between infliximab and adalimumab. J Crohns Colitis. Nov 16 2024;doi:10.1093/ecco-jcc/jjae172

The immune–epithelial–stromal interactions underpinning intestinal damage in celiac disease (CD) are incompletely understood. To address this, we performed single-cell transcriptomics (RNA sequencing; 86,442 immune, parenchymal and epithelial cells; 35 participants) and spatial transcriptomics (20 participants) on CD intestinal biopsy samples. Here we show that in CD, epithelial populations shifted toward a progenitor state, with interferon-driven transcriptional responses, and perturbation of secretory and enteroendocrine populations. Mucosal T cells showed numeric and functional changes in regulatory and follicular helper-like CD4 + T cells, intraepithelial lymphocytes, CD8 + and γδ T cell subsets, with skewed T cell antigen receptor repertoires. Mucosal changes remained detectable despite treatment, representing a persistent immune–epithelial ‘scar’. Spatial transcriptomics defined transcriptional niches beyond those captured in conventional histological scores, including CD-specific lymphoid aggregates containing T cell–B cell interactions. Receptor–ligand spatial analyses integrated with disease susceptibility gene expression defined networks of altered chemokine and morphogen signaling, and provide potential therapeutic targets for CD prevention and treatment.

Abstract Background Anti-TNF therapy is established as a mainstay in IBD management. Recent data raise controversies regarding efficacy of these agents, sustainability of response, and identification of factors that may influence outcomes, including dose escalation and need for long-term concurrent immunosuppression (Lancet Gastro.Hep.2019;4:341). Methods We report a retrospective cohort study of 699 IBD patients on anti-TNF at our centre between 2005-2022. Clinical data were obtained from patient records and pharmacy database (TABLE 1). Primary outcomes were overall loss of response (LOR) at any timepoint; and secondary LOR (after an initial clinical response to therapy). Cox regression analysis was performed to identify variables independently affecting outcome. Kaplan-Meyer survival curves were constructed to demonstrate overall response rates (persistence on drug) and secondary LOR (Figure 1a-d). Dose adjustments were made proactively in a Virtual Clinic. Results 204 patients had a diagnosis of ulcerative colitis (UC), 481 Crohn’s Disease (CD) and 14 IBD-unclassified. 126 patients received both infliximab (IFX) and adalimumab (ADA). Median duration on IFX was 42 months (range 0-204); median duration on ADA was 48.5 months (range 0-180). 48% of patients on IFX underwent dose escalation, as did 40% on ADA. Overall, 58 patients (7.6%) remained on treatment at 120 months. Overall survival rates for IFX at 12 months were 83% (82%CD vs. 82%UC); and at 36 months were 71% (69%CD vs. 74%UC). Overall survival rates for ADA at 12 months were 84% (89%CD vs. 59%UC); and at 36 months were 72% (78% CD vs. 42% UC) (Figure 1a-b). Secondary LOR rates for IFX at 12 months were 6% (5%CD vs. 9%UC); and at 36 months were 16% (15%CD vs.19%UC). Secondary LOR rates for ADA at 12 months were 7% (5%CD vs. 19%UC); and at 36 months were 16% (12% CD vs. 42% UC) (Figure 1c-d). There was no difference in survival analysis for IFX between CD and UC. On Cox regression analysis, for IFX, immunomodulation was associated with reduction in overall LOR (HR=0.48, p=1.07e-05) but not secondary LOR (HR=0.78, p=0.31) (Figure 1e-f). For ADA, outcomes were better for CD vs. UC for both overall LOR (HR=0.35, p=3.29e-07) and secondary LOR (HR=0.35, p=9.99e-05). Conclusion We demonstrate encouraging response rates in the first three years of therapy, with a small proportion remaining on therapy beyond 120 months. Survival rates on IFX were similar for UC and CD, but for ADA were significantly lower in UC. Secondary LOR was not affected by immunomodulation. Further analysis of relation to drug levels, dose escalation and genotyping is underway. This work was supported by The Leona M & Harry B Helmsley Charitable Trust.

The success of checkpoint inhibitors (CPIs) for cancer has been tempered by immune-related adverse effects including colitis. CPI-induced colitis is hallmarked by expansion of resident mucosal IFNγ cytotoxic CD8+ T cells, but how these arise is unclear. Here, we track CPI-bound T cells in intestinal tissue using multimodal single-cell and subcellular spatial transcriptomics (ST). Target occupancy was increased in inflamed tissue, with drug-bound T cells located in distinct microdomains distinguished by specific intercellular signaling and transcriptional gradients. CPI-bound cells were largely CD4+ T cells, including enrichment in CPI-bound peripheral helper, follicular helper, and regulatory T cells. IFNγ CD8+ T cells emerged from both tissue-resident memory (TRM) and peripheral populations, displayed more restricted target occupancy profiles, and co-localized with damaged epithelial microdomains lacking effective regulatory cues. Our multimodal analysis identifies causal pathways and constitutes a resource to inform novel preventive strategies.

Objectives We aimed to determine whether changes in acute severe colitis (ASC) management have translated to improved outcomes and to develop a simple model predicting steroid non-response on admission. Design Outcomes of 131 adult ASC admissions (117 patients) in Oxford, UK between 2015 and 2019 were compared with data from 1992 to 1993. All patients received standard treatment with intravenous corticosteroids and endoscopic disease activity scoring (Ulcerative Colitis Endoscopic Index of Severity (UCEIS)). Steroid non-response was defined as receiving medical rescue therapy or surgery. A predictive model developed in the Oxford cohort was validated in Australia and India (Gold Coast University Hospital 2015–2020, n=110; All India Institute of Medical Sciences, New Delhi 2018–2020, n=62). Results In the 2015–2019 Oxford cohort, 15% required colectomy during admission vs 29% in 1992–1993 (p=0.033), while 71 (54%) patients received medical rescue therapy (27% ciclosporin, 27% anti-tumour necrosis factor, compared with 27% ciclosporin in 1992–1993 (p=0.0015). Admission C reactive protein (CRP) (false discovery rate, p=0.00066), albumin (0.0066) and UCEIS scores (0.015) predicted steroid non-response. A four-point model was developed involving CRP of ≥100 mg/L (one point), albumin of ≤25 g/L (one point), and UCEIS score of ≥4 (1 point) or ≥7 (2 points). Patients scoring 0, 1, 2, 3 and 4 in the validation cohorts had steroid response rates of 100, 75.0%, 54.9%, 18.2% and 0%, respectively. Scoring of ≥3 was 84% (95% CI 0.70 to 0.98) predictive of steroid failure (OR 11.9, 95% CI 10.8 to 13.0). Colectomy rates in the validation cohorts were were 8%–11%. Conclusions Emergency colectomy rates for ASC have halved in 25 years to 8%–15% worldwide. Patients who will not respond to corticosteroids are readily identified on admission and may be prioritised for early intensification of therapy.

BACKGROUND:Patient-reported outcome measures [PROMs] are key to documenting outcomes that matter most to patients and are increasingly important to commissioners of health care seeking value. We report the first series of the ICHOM Standard Set for Inflammatory Bowel Disease [IBD]. METHODS:Patients treated for ulcerative colitis [UC] or Crohn's disease [CD] in our centre were offered enrolment into the web-based TrueColours-IBD programme. Through this programme, e-mail prompts linking to validated questionnaires were sent for symptoms, quality of life, and ICHOM IBD outcomes. RESULTS:The first 1299 consecutive patients enrolled [779 UC, 520 CD] were studied with median 270 days of follow-up (interquartile range [IQR] 116, 504). 671 [52%] were female, mean age 42 years (standard deviation [sd] 16), mean body mass index [BMI] 26 [sd 5.3]. At registration, 483 [37%] were using advanced therapies. Median adherence to fortnightly quality of life reporting and quarterly outcomes was 100% [IQR 48, 100%] and 100% [IQR 75, 100%], respectively. In the previous 12 months, prednisolone use was reported by 229 [29%] patients with UC vs 81 [16%] with CD, p <0.001; 202 [16%] for <3 months; and 108 [8%] for >3 months. An IBD-related intervention was reported by 174 [13%] patients, and 80 [6%] reported an unplanned hospital admission. There were high rates of fatigue [50%] and mood disturbance [23%]. CONCLUSIONS:Outcomes reported by patients illustrate the scale of the therapeutic deficit in current care. Proof of principle is demonstrated that PROM data can be collected continuously with little burden on health care professionals. This may become a metric for quality improvement programmes or to compare outcomes.

Background & Aims The pathogenesis of immune checkpoint inhibitor (ICI)–colitis remains incompletely understood. We sought to identify key cellular drivers of ICI-colitis and their similarities to idiopathic ulcerative colitis, and to determine potential novel therapeutic targets. Methods We used a cross-sectional approach to study patients with ICI-colitis, those receiving ICI without the development of colitis, idiopathic ulcerative colitis, and healthy controls. A subset of patients with ICI-colitis were studied longitudinally. We applied a range of methods, including multiparameter and spectral flow cytometry, spectral immunofluorescence microscopy, targeted gene panels, and bulk and single-cell RNA sequencing. Results We demonstrate CD8+ tissue resident memory T (TRM) cells are the dominant activated T cell subset in ICI-colitis. The pattern of gastrointestinal immunopathology is distinct from ulcerative colitis at both the immune and epithelial-signaling levels. CD8+ TRM cell activation correlates with clinical and endoscopic ICI-colitis severity. Single-cell RNA sequencing analysis confirms activated CD8+ TRM cells express high levels of transcripts for checkpoint inhibitors and interferon-gamma in ICI-colitis. We demonstrate similar findings in both anti–CTLA-4/PD-1 combination therapy and in anti–PD-1 inhibitor-associated colitis. On the basis of our data, we successfully targeted this pathway in a patient with refractory ICI-colitis, using the JAK inhibitor tofacitinib. Conclusions Interferon gamma–producing CD8+ TRM cells are a pathological hallmark of ICI-colitis and a novel target for therapy.

ABSTRACTBackground & aimsWe aimed to determine whether changes in ulcerative colitis management have translated to improved outcomes, in order to develop a simple model to predict steroid non-response on admission.MethodsOutcomes of 131 adult ASC admissions (117 patients) in Oxford, UK between 2015-19 were compared with prospectively collected data from 1992-3. All patients received standard treatment with intravenous corticosteroids and endoscopic disease activity scoring (UCEIS). Steroid non-response was defined as receiving rescue medical therapy or surgery. A predictive model created in the Oxford cohort was validated in Australia and India (110 hospitalised patients Gold Coast University Hospital 2015-20; 62 hospitalised patients AIIMS, New Delhi 2018-20).ResultsIn the 2015-19 Oxford cohort, 71 (54%) patients received medical rescue therapy (27% ciclosporin, 27% anti-TNF), compared to 27% ciclosporin in 1992-3, p=0.0015. Only 15% required colectomy during admission vs 29% in 1992-3 (p=0.033). Admission CRP, albumin, and UCEIS scores predicted steroid non-response (FDR p=0.00066, 0.0066 and 0.015). A four-point model was developed involving CRP ≥100mg/L (1 point), albumin ≤25g/L (1 point), UCEIS ≥4 (1 point) or ≥7 (2 points). Scoring 0 or 4 was 100% predictive of steroid response and non-response, respectively, in all three cohorts. Patients scoring 3-4 had 83% risk of steroid non-response in Oxford and 84% (0.70-0.98) in the validation cohorts – OR 11.9 (10.8-13).ConclusionColectomy rates for ASC have halved in 25 years, while use of rescue medical therapy has doubled. Patients who are highly unlikely to respond to parenteral steroid treatment alone may be readily identified on admission, to be prioritised for early intensification of therapy.WHAT YOU NEED TO KNOWBackground and contextAcute severe colitis (ASC) requires hospitalisation and, frequently, colectomy. The accepted management of ASC is three-five days of intravenous steroids followed by protocolised response assessment.New findingsMedical rescue therapy has doubled and the colectomy rate halved in 25 years. A predictive index identifying steroid non-response was derived and validated in three independent centres in three countries.LimitationsA need remains to demonstrate that earlier rescue medical therapy for patients predicted to be steroid non-responders will further improve outcomes.ImpactThe outcome of ASC has substantially improved in the past 25 years, with the potential for further improvement by identifying patients on admission for early escalation of therapy.

Background Immune checkpoint blockers (ICBs) activate CD8 + T cells, eliciting both anti-cancer activity and immune-related adverse events (irAEs). The relationship of irAEs with baseline parameters and clinical outcome is unclear. Methods Retrospective evaluation of irAEs on survival was performed across primary ( N = 144) and secondary ( N = 211) independent cohorts of patients with metastatic melanoma receiving single agent (pembrolizumab/nivolumab—sICB) or combination (nivolumab and ipilimumab—cICB) checkpoint blockade. RNA from pre-treatment and post-treatment CD8 + T cells was sequenced and differential gene expression according to irAE development assessed. Results 58.3% of patients developed early irAEs and this was associated with longer progression-free (PFS) and overall survival (OS) across both cohorts (log-rank test, OS: P < 0.0001). Median survival for patients without irAEs was 16.6 months (95% CI: 10.9–33.4) versus not-reached ( P = 2.8 × 10 −6 ). Pre-treatment monocyte and neutrophil counts, but not BMI, were additional predictors of clinical outcome. Differential expression of numerous gene pathway members was observed in CD8 + T cells according to irAE development, and patients not developing irAEs demonstrating upregulated CXCR1 pre- and post-treatment. Conclusions Early irAE development post-ICB is associated with favourable survival in MM. Development of irAEs is coupled to expression of numerous gene pathways, suggesting irAE development in-part reflects baseline immune activation.