To Örebro University

Background: The disease course of patients with newly diagnosed ulcerative colitis (UC) is highly uncertain, and there is a lack of validated prognostic biomarkers that could aid in clinical decision making.

Methods: Newly diagnosed, mainly treatment naïve patients with UC from three large inception cohorts were used to develop and validate a serum proteomics-based risk score for prognostication of disease course during the first year from diagnosis. In the discovery cohort (n = 161) and validation cohort 1 (n = 186) an aggressive disease course was defined as the presence of any IBD-related surgery, hospital admission for active disease, treatment refractoriness towards targeted therapies (i.e. biologics, JAK-inhibitors or S1P receptor modulators), and >2 courses or high cumulative doses of systemic corticosteroids. In validation cohort 2 (n = 120), an aggressive disease course was defined as the need for a biologic, ciclosporin or surgery. 178 proteins were measured on Olink platforms, and a machine learning algorithm (i.e. regularised regression) was applied to the discovery cohort to develop an UC risk score comprising 23 proteins. The performance of the UC risk score was assessed in the two external validation cohorts. For validation cohort 2, a condensed version of the UC risk score was applied, as only 14 of the original 23 proteins were available. Cox regression estimated hazard ratios (HR) for the association between the UC risk score at diagnosis, time to escalation to targeted therapy (validation cohort I) and time to the defining episode of an aggressive disease course (validation cohort II).

Results: Based on univariate analyses, we identified 59 proteins associated with an aggressive disease course in the discovery cohort (PFDR <0.10; Figure 1A). Twenty could be validated in validation cohort 1, and nine remained in validation cohort 2 (PFDR <0.10; Figure 1B-C).

In the discovery cohort, the machine learning model showed a high predictive capacity, with an area under the curve (AUC) of 0.81 (Figure 1D) and was numerically superior compared with a clinical model comprising sex, age and CRP (AUC = 0.72). Next, the performance of the UC risk score was confirmed in the two external validation cohorts, displaying AUC:s of 0.77 (Figure 1E-F). Patients with a higher UC risk score at diagnosis had increased risk of initiating targeted therapy (HR 4.26, 95% CI 1.91–9.49; Figure 2A). The HR for having an aggressive disease course was 9.12 (95% CI 3.04–27.3; Figure 2B).

Conclusion: We develop a UC risk score for prognostication of disease course and confirmed its high predictive performance by external validation in two independent cohorts. The risk score is a promising tool for quantifying the risk of having an aggressive disease course in UC.

Background: The clinical course of inflammatory bowel disease (IBD) is highly heterogeneous. Previously we identified a protein-based prognostic signature in serum using the proximity extension assay (PEA). To enable clinical translation, further assay development is required, including the establishment of standard curves and clinically actionable cut-offs. Therefore, we aimed to develop, optimise and validate a serum-based assay that quantifies absolute protein concentrations at diagnosis to identify individuals at higher risk of an aggressive course of IBD.

Methods: Proteins were selected from the commercially available Olink inflammation and oncology II panels as well as from five custom-made multiplex panels comprising 460 proteins based on genes in 163 IBD-risk loci (the IBD Character project1). Serum from 71 newly diagnosed IBD patients (Crohn’s disease, n = 29; ulcerative colitis, n = 42) (SIC-IBD) was analysed. Proteins associated with an aggressive course: I) need for biologics, ciclosporin, or surgery for flare after initial induction or II) hospitalisation, refractoriness to targeted therapy, excessive corticosteroid use or surgery within one year, were identified using penalised logistic regression. From these proteins a focused prognostic panel was developed and analytically optimized for absolute quantification. Model performance was evaluated by nested cross-validation (area under the curve [AUC]) and externally validated in 329 treatment-naïve IBD patients from the population-based IBSEN III cohort. Time to the composite outcome was analysed by estimating hazard rations (HR) using Cox regression.

Results: Thirteen proteins (CCL19, XPNPEP2, TGFα, VGFA, DLL1, PSGL1, OSM, CSF1, FURIN, IL-18, EpCAM, and TNFRSF9) met the pre-defined criteria and formed the final prognostic signature. In the discovery cohort, the model achieved an AUC of 0.76, with no interaction with age, sex or IBD subtype. External validation in the IBSEN III cohort yielded an AUC of 0.66 (95%CI 0.57-0.75), sensitivity 49% and specificity 70% at the discovery cohort derived optimal cut-off. Among patients classified as high risk, compared to low risk, the HR for the composite endpoint of aggressive disease course was 1.81 (P = 0.0002, Figure 1).

Conclusion: We developed and validated the first PEA-based serum panel enabling absolute quantitation of prognostic proteins for clinical use. At diagnosis, IBD-patients classified as high risk based on the 13-protein signature had an 81% higher relative risk of an aggressive disease course, supporting further evaluation.

Investigator-initiated studies that include information collected by patients are rising, but limited data is available on patient and investigator experience in this setting. The I-CARE cohort included patients with inflammatory bowel disease (IBD) monthly collecting clinical information in 15 countries for up to 6 years. We describe patients and investigators' involvement in I-CARE and identify predictors of early withdrawal due to patient non-engagement. Patients' characteristics according to the number of electronic Patient-reported outcomes (ePRO) completed during follow-up were assessed. Predictors of early withdrawal due to patient non-engagement were identified using logistic regression. The coding of outcomes reported by patients and corrections by investigators on patients' ePROs were assessed. Among 12,846 patients included by 502 investigators, 79.3% and 77.3% filled more than one ePRO and at least one ePRO within 6 months before the study end date, respectively. All ePROs were completed in 72.8% and 56.4% of patients during year 1 and 3, respectively. Male gender, younger age (< 20), being unemployed or a student, and no previous history of abdominal surgery were associated with early withdrawal. Investigators corrected 52.5% of cancer or dysplasia reported by patients compared to 10% of serious infections. Investigators added or removed a treatment sequence in 19.6% of the 6708 patients treated with biologics. These results highlight the implication of patients in research and the importance of data validation by investigators alongside the challenge and potential of collecting medical data from patients. These findings can inform similar future initiatives in other diseases. (EudraCT, Number: 2014-004728-23; ClinicalTrials.gov, Number: NCT02377258).

BACKGROUND AND AIMS: Tofacitinib and upadacitinib are Janus kinase (JAK) inhibitors that are increasingly used for the treatment of acute severe ulcerative colitis (ASUC). However, comparative analyses of safety and effectiveness have not been performed for their use in this setting.

METHODS: This multicenter, retrospective study enrolled hospitalized adult patients treated with tofacitinib or upadacitinib for ASUC between January 2019 and June 2024. The main outcomes were clinical response, clinical remission, and colectomy-free survival. Propensity-adjusted analyses using inverse probability treatment weighting (IPTW), and double robust estimations (DRE) were used to control for confounding factors.

RESULTS: In total, 111 patients (60 tofacitinib, 51 upadacitinib) were enrolled across 23 international centers. JAK inhibitors were used to induce response in 86 (77%) patients and used to maintain response after adequate intravenous steroid response in 25 (23%). The median follow up was 31 weeks (IQR 13-64). Between days 3-7 after treatment initiation, upadacitinib was associated with greater response rates 84% vs.54%,p=0.02 but response/remission were comparable at day 98 (45%/36% vs 55/48%) and day 182 (29/29% vs. 39/34%). Sub-analyses for JAK inhibitor use as salvage therapy (tofacitinib (n=35) vs. upadacitinib (n=31)) showed similar effectiveness outcomes across both groups. The probabilities of colectomy-free survival at days 98/182 for tofacitinib and upadacitinib were 79%/75% and 80%/78%, respectively, with no significant differences in the comparison of survival curves, p=0.99. Treatment failure rates (where JAK inhibitor was used to maintain remission) were similar at days 98 and 182. The frequency of adverse events was comparable.

CONCLUSION: Tofacitinib and upadacitinib appear to have similar effectiveness and safety profiles when used for the treatment of ASUC.

Background: Minimally invasive biomarkers that can reliably distinguish adults with inflammatory bowel disease (IBD) from symptomatic controls are still lacking. We investigated whether serum lipidomics can provide a reproducible diagnostic signature for IBD and how such a signature performs in relation to relevant inflammatory markers.

Methods: Untargeted lipidomic profiling was conducted on serum from the Swedish SIC-IBD inception cohort, comprising adults referred for suspected IBD, symptomatic controls, as well as healthy controls. Candidate diagnostic lipids were identified using supervised machine-learning models in the discovery cohort and then evaluated in the independent, population-based Norwegian IBSEN III inception cohort of treatment-naïve adults. We examined the diagnostic performance of the lipidomic signature in combination with high-sensitivity C-reactive protein (hs-CRP) and fecal calprotectin (FCP).

Results: The discovery cohort included 96 IBD patients, 66 non-IBD symptomatic controls, and 48 healthy controls, whereas the validation cohort comprised 349 patients with IBD and 198 symptomatic controls (Table 1). In the discovery cohort, a serum signature of hs-CRP and the two top lipids, lactosyl ceramide (d18:1/16:0) and phosphatidylcholine (O-44:5), demonstrated a high diagnostic performance (area under the curve [AUC] 0.80, 95% CI 0.73-0.87) compared with hs-CRP alone (AUC 0.70, 95% CI 0.63-0.79). When applied to the validation cohort, hs-CRP combined with the serum lipid signature significantly enhanced discrimination between IBD and symptomatic controls (AUC 0.79, 95% CI 0.75-0.83) compared with hs-CRP alone (AUC 0.68, 95% CI 0.64-0.73; P < 0.0001). As illustrated in Figure 1, among patients with available stool samples, combining FCP with hs-CRP and the lipid signature numerically improved diagnostic accuracy (AUC 0.89, 95% CI 0.86-0.92) compared with FCP alone (AUC 0.86, 95% CI 0.83–0.90).

Conclusion: We identified and externally validated a serum lipidomic signature that improves the diagnostic prediction of IBD when combined with hs-CRP. Although the blood-based model of hs-CRP, lactosyl ceramide (d18:1/16:0), and phosphatidylcholine (O-44:5) did not outperform FCP alone, it approached its diagnostic performance and further enhanced accuracy when integrated with FCP. These findings support added value these lipids and may offer insights into lipid-related pathways underlying IBD pathogenesis.

Background: Substantial variation exists in early inflammatory bowel disease (IBD) disease management. Biomarkers predicting disease trajectories may enable personalised treatment. The NORDTREAT strategy-trial was designed to compare “top-down” treatment with standard clinical care in patients at increased risk of an aggressive IBD course, as defined by the prognostic NORDTREAT protein signature.

Methods: NORDTREAT (NORdic inflammatory bowel disease TREATment; NCT05180175) was a randomised, multicentre, biomarker-strategy design, open-label, controlled trial conducted across 15 Nordic hospitals. Following screening, eligible adult with newly diagnosed IBD were randomised (1:1) to either access or non-access to the protein signature. In the access arm, patients displaying a high-risk profile received “top-down” (anti-TNF +/- immunomodulator) treatment, whereas low-risk patients were excluded. The non-access arm received standard care with stepwise treatment escalation at the investigator’s discretion (“clinical management”). The primary endpoint was corticosteroid-free clinical and endoscopic remission at week 52, with surgery considered treatment failure. Secondary endpoints included endoscopic remission, cumulative corticosteroid exposure, and serious adverse events. Analyses were performed in the intention to treat population.

Results: 313 IBD patients (CD, n = 133 and UC/IBD-unclassified, n = 180) were randomised between February 2022 and March 2024. Median time from diagnosis to enrolment was 7 days. Among access-arm patients (n = 157), 24 (15%) had a high-risk profile. In the non-access arm, 29/156 (19%) patients were found after trial completion to have had a high-risk profile at baseline and of these 16 (55%) received advanced therapy after a median period of 15 days. The primary endpoint was achieved in 10/24 (42%) “top-down” and 8/29 (27%) “clinical management” patients (absolute difference 15%; 95%CI -11-41, p = 0.26). Endoscopic remission rates at week 52 were comparable (53% vs 53%, p = 0.99). Median cumulative cortisone equivalents was 1232 mg in top-down vs 1651 mg in standard care, p = 0.07). Table 1 provides information on serious adverse events. Post-hoc analyses showed numerically higher rates of achieving the primary endpoint in CD, 50% vs 11% (p = 0.09) UC, whereas rates were comparable in UC 36% vs 35% (p = 0.97).

Conclusion: A biomarker-guided “top-down” approach did not increase corticosteroid-free clinical and endoscopic remission at week 52 compared with standard care. However, a possible benefit was seen in CD, suggesting that early “top-down” could improve outcomes in this subgroup of patients even in the era of widespread use of advanced therapies.

Background: IgG autoantibodies against integrin αvβ6 have been associated with preclinical ulcerative colitis (UC),1,2 but data on their emergence and validation are still scarce. Therefore, we aimed to establish and validate a cutoff of anti-αvβ6 for predicting future UC across two independent preclinical cohorts. Additionally, we examined their development in early-life, assessed the influence of genetic-, environmental risk factors and inflammation on anti-αvβ6.

Methods: Within large population-based cohorts (n > 180,000), prediagnostic blood samples from individuals who later in life were diagnosed with UC were compared with age- and sex-matched controls who remained UC-free during follow-up (Figure 1). To explore early-life presence and genetic and shared environmental influences, we analysed serum from ABIS, a population-based birth cohort (n = 17,055) and the Swedish Twin Registry (n > 97,000). Anti-αvβ6 levels were measured using an in-house automated fluorescence enzyme immunoassay. Relative estimates of proteins were measured on the Olink platform3.

Results: In the discovery cohort (Table 1), anti-αvβ6 antibodies differentiated preclinical UC from controls (area under the curve [AUC]=0.68). Applying the model to the validation cohort yielded an AUC of 0.79, with a sensitivity of 46% and a specificity of 93%, at the optimal cut-off (109 UA/l) derived from the discovery cohort. Predictive capacity increased closer to diagnosis but remained significant for samples collected ≥20 years before UC diagnosis (AUC=0.67). In the birth cohort, anti-αvβ6 levels at birth appeared elevated in children who later developed UC (OR = 2.13; 95%CI, 0.84-5.38), likely reflecting transplacental antibody transfer, but also after 5 years (OR = 2.58; 95%CI, 0.83-8.03) and 8 years (OR = 2.50; 95%CI, 0.30-21.00). When assessing the level of agreement within twin pairs, low intra-class correlation coefficients were observed irrespective of zygosity and disease status, suggesting limited influence of genetic and shared environmental exposures. However, anti-αvβ6 levels differed across smoking categories in the preclinical cohorts, but inclusion of smoking status added little to model performance (AUC=0.82). By calculating a composite proteomic score, a progressive increase in the score was observed from the lowest to highest quartile of αvβ6 levels in preclinical UC, whereas most controls were found in the lowest quartiles for both the proteomic score and autoantibody levels.

Conclusion: Anti-αvβ6 autoantibodies represent a reproducible biomarker for preclinical UC. Their early-life presence, environmental modulation, and correlation with immuno-inflammatory proteins highlight their potential utility for risk stratification.

Background: Paediatric inflammatory bowel disease (IBD), comprising the subtypes Crohn’s disease (CD) and ulcerative colitis (UC), is believed to result from an interplay between genetic predisposition and environmental exposures. Examining exposome metabolome may help to identify environmental exposures, including host-derived metabolites, with potential relevance in paediatric IBD.

Methods: Relative concentrations of metabolites were measured in serum samples from treatment-naïve patients with IBD (N = 80) and symptomatic, non-IBD controls (N = 37) included in the IBSENIII cohort (Table 1). Ultra-high-performance liquid chromatography–mass spectrometry (UHPLC-MS) was performed. Authentic standards or the Human Metabolome Database were used for annotation. Associations with IBD, with CD (N = 53), and with UC including IBD-unclassified (N = 27), were assessed using logistic regression while adjusting for sex, age, and BMI. In addition, correlations with serum proteins (proximity extension assay technology) were examined. A false discovery rate (PFDR) threshold of < 0.1 was applied.

Results: We observed positive association of aryl sulfate (phenol sulfate; PFDR=0.03) with IBD versus symptomatic controls (Figure 1). Within the IBD population, aryl sulfate was positively correlated with several serum proteins, including CCL20 (r = 0.48, PFDR=0.004), MCP-3 (r = 0.47, PFDR=0.004), and TNF-α (r = 0.45, PFDR=0.001). We observed inverse associations of four perfluoroalkyl substances (PFAS); (linear-perfluorooctane sulfonate (PFOS-L), branched-perfluorohexanesulfonate (PFHxS-B), perfluorooctanoate (PFOA), and branched-perfluorooctane sulfonate (PFOS-B)) with IBD, UC, or both. In IBD, PFOA, PFOS-L, PFHxS-B positively correlated with Delta/Notch-like epidermal growth factor (EGF)-related receptor (DNER) protein levels. The secondary bile acid 6-ketholithocholic acid was inversely associated with UC, while the primary bile acids glycochenodeoxycholic acid-3-O-sulfate, cholic acid and glycocholic acid were positively associated with UC (all PFDR<0.1).

Conclusion: Several metabolites including aryl sulfate were associated with paediatric IBD and correlated with inflammation-related proteins. These findings confirm recent results from preclinical Crohn’s disease1 and may point towards a role of aryl sulfate at IBD diagnosis.

Background: Consistent alterations in DNA methylation across the genome have been well-characterised in inception cohorts of North European patients with inflammatory bowel disease [1-3]; these data implicate inherited determinants, active inflammation and the exposome in shaping the methylome. We have recruited a unique group of 155 twin pairs discordant for IBD to allow exploration of the interplay between these factors.

Methods: Whole blood from twins discordant for diagnosis of IBD was profiled using methylation microarrays (Figure) in two cohorts (UK-1 & Scandinavia-2). We performed analysis of both cohorts with epigenome-wide association study (EWAS), investigation of methylation Shannon’s entropy, methylation variance, and the epigenetic age. Analysis of the methylation correlates of disease activity in cohort 1 (UK) was performed. Additionally, smoking-related methylation was explored.

Results: The discovery cohort (UK-1) included 64 di- and monozygotic twin pairs while the replication cohort (Scandinavia-2) included 91 sex-matched IBD-discordant twin pairs. The mean age in both cohorts was 53 years and the mean disease duration was 24 years. IBD-discordant twin pairs differed in Shannon’s entropy at individual probes (located in/near IL10RA, IL2RA, IL18RAP, VMP1, CEP72/AHRR), of which three replicated (cg11498228-ARHGEF10, cg07664915-KCTD13/MAPK3, cg20859708-NAA35), and many were located in IBD GWAS regions (such as FOXP1, LPP, MICA). The entropy findings from IBD GWAS regions were partially confirmed in monozygotic twins alone (e.g., TNXB in MHC class III region, bootstrap p.fdr<10-118), despite near-perfect controlling for genetics and early-life exposome. Sites highlighted by differential variance analysis included IBD genes, such as TAS1R3, GALNT2 and CACNA1H (all q-values<5×10-6). No epigenetic age acceleration was identified in patients with IBD. Clinical activity of IBD exhibited a number of associations with the whole blood methylome, including a negative correlation between methylation at a key IBD site RPS6KA2 with faecal calprotectin (Table). In patients with IBD and controls, cross-cohort smoking EWAS replicated multiple smoking-related sites at genome-wide significance, many of which located in AHRR and ALPI loci, both of which are implicated in IBD.

Conclusion: Methylation level at individual probes related to IBD activity and showed IBD-associated differences in methylation entropy and variance between twins despite shared genetics and early-life exposome, adding new context for understanding established IBD loci and strengthening their role.

References:

1. Ventham et al. Integrative epigenome-wide analysis demonstrates that DNA methylation may mediate genetic risk in inflammatory bowel disease. Nat Commun. 2016;7:13507.

2. Kalla et al. Analysis of Systemic Epigenetic Alterations in Inflammatory Bowel Disease: Defining Geographical, Genetic and Immune-Inflammatory influences on the Circulating Methylome. J Crohns Colitis. 2023;17(2):170-184.

3. Ventham et al. Genome-Wide Methylation Profiling in 229 Patients With Crohn's Disease Requiring Intestinal Resection: Epigenetic Analysis of the Trial of Prevention of Post-operative Crohn's Disease (TOPPIC). Cell Mol Gastroenterol Hepatol. 2023;16(3):431-450.