Inflammatory Bowel Diseases

ObjectiveThe impact of medications on COVID-19 vaccine efficacy in IBD patients is unknown, as patients with immunosuppressed states and/or treated with immunosuppressants were excluded from vaccine trials. To address this, we evaluated serological responses to COVID-19 vaccination with the SARS-CoV-2 spike (S) mRNA BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (NIH-Moderna) vaccines in IBD patients enrolled in an ongoing SARS-CoV-2 sero-survey at the Icahn School of Medicine at Mount Sinai in New York City. DesignWe obtained sera from 48 patients who had undergone vaccination with one or two vaccine doses. Sera were tested for SARS-CoV-2 anti-RBD total immunoglobulins and IgG (Siemens COV2T and sCOVG assays), anti-Spike IgG (in-house ELISA), and anti-nucleocapsid antibodies (Roche). ResultsAll IBD patients (15/15) who completed two-dose vaccine schedules achieved seroconversion to high levels. Two IBD patients with history of COVID-19 infections and who were seropositive at baseline seroconverted to high levels after the first dose. Concurrent biologic use was 85% (41/48), including 33% of patients (16) on TNF antagonist monotherapy, 42% (17) on vedolizumab monotherapy, 6% (3) on vedolizumab combination therapy with thiopurine, and 8% (4) ustekinumab; 1 patient was receiving guselkumab for psoriasis. Three patients (6%) were on oral steroids at the time of vaccination. ConclusionIBD patients receiving biologics can seroconvert with robust serological responses after complete Pfizer-BioNTech and NIH-Moderna COVID-19 vaccination. In IBD-patients with previous SARS-CoV-2 seroconversion, a single dose of either vaccine can induce high index values, mirroring findings from the general population.

Background and AimsThe pathobiology of the non-destructive inflammatory bowel disease (IBD) lymphocytic colitis (LC) is poorly understood. Our aim was to define a LC-specific transcriptome to gain insight into LC pathology, identify genetic signatures uniquely linked to LC, and uncover potentially druggable disease pathways. MethodsWe performed whole mucosa bulk RNA-sequencing of LC and CC samples from patients with active disease, and healthy controls (n=4-10 per cohort). Differential gene expression was analyzed by gene-set enrichment and deconvolution analyses to identify pathologically relevant pathways and cells, respectively, altered in LC. Key findings were validated using reverse transcription quantitative PCR and/or immunohistochemistry. Finally, we compared our sequencing data to a previous cohort of ulcerative colitis and Crohns disease patients (n=4 per group) to distinguish non-destructive from classic IBD. ResultsThe LC-specific transcriptome was defined by a limited mucosal immune response against microbiota compared to CC and classic IBD samples. In contrast, we noted a distinct induction of regulatory non-coding RNA species in LC samples. Moreover, compared to CC, we observed decreased water channel and cell adhesion molecule gene expression, which was associated with reduced intestinal epithelial cell proliferation. ConclusionsWe conclude that LC is a pathomechanistically distinct disease that is characterized by a dampened immune response despite massive mucosal immune cell infiltration. Our results point to regulatory micro-RNAs as a potential disease-specific feature that may be amenable to therapeutic intervention.

Background & AimsUlcerative colitis (UC) is an inflammatory bowel disease (IBD) where a defect in the colonic epithelial barrier elicits a chronic and unresolved inflammatory response against luminal microbiota. Mucins are heavily glycosylated proteins secreted by goblet cells that form gelatinous layers to protect the colonic epithelium. Whereas the role of the major colonic mucin, MUC2, is established in UC, few reports have analyzed MUC5B in this disease. In this study, we investigated MUC5B expression in colonic tissues and organoid cultures from UC patients and non-IBD controls. MethodsMUC5B transcripts were analyzed in colonic regions from UC patients and controls using RT-qPCR. MUC5B protein levels in colonic tissues were analyzed and quantified by immunohistochemistry. Patient-derived epithelial organoids were stained for MUC5B, E-cadherin and F-actin. Organoids were treated with interleukin 1 beta (IL-1{beta}) and MUC5B transcripts were analyzed by RT-qPCR. MUC5B proteins were assessed in IL-1{beta}-treated organoids by immunofluorescent microscopy. ResultsMUC5B transcripts and proteins were expressed in the healthy colon and their levels were decreased in UC tissues. MUC5B proteins were reduced in organoids derived from UC tissues. IL-1{beta} treatment of control organoids stimulated expression of acidic mucins, MUC5B transcripts and MUC5B proteins. MUC5B transcripts were not induced by IL-1{beta} in UC-derived organoids. ConclusionsMUC5B levels are reduced in UC colons and its expression is induced by the IL-1{beta} pro-inflammatory cytokine. These results suggest that MUC5B contributes to the protective colonic mucin layer and that this function is likely compromised in UC.

BackgroundIntestinal barrier dysfunction is a hallmark of inflammatory bowel diseases (IBD). This condition causes intoxication and immune hyperactivation. Understanding the events underlying epithelial barrier disruption during chronic inflammation is key to developing barrier-restoring therapies. Filamentous actin (F-actin) is essential for maintaining polarity and junctional integrity. However, the contribution of F-actin dynamics to IBD-associated barrier dysfunction remains unclear. ObjectiveWe aimed to examine actin cytoskeleton integrity during chronic colitis across mouse models and human patients and identify potential regulators of cytoskeleton dynamics. DesignF-actin and junctional proteins were analyzed in three models of chronic colitis (Muc2 KO, DSS-induced colitis, adoptive transfer colitis) using confocal microscopy. Claudin-3 interactors were identified by immunoprecipitation and proteomics. Intestinal organoids were used to assess the effect of F-actin disruption on barrier integrity. Metabolomic and gene expression analyses identified candidate pathways, further validated by chemical inhibition. Biopsies from patients with ulcerative colitis (UC) were examined using transmission electron microscopy and confocal microscopy. ResultsDisrupted actin dynamics emerged as a critical driver of epithelial barrier dysfunction in chronic colitis. An imbalance between polymeric and monomeric actin impaired barrier integrity in vivo and in 3D organoids. Immunoprecipitation identified actin and associated factors as the primary interactors of claudin-3 with reduced interaction during inflammation. Ceramide metabolism was revealed as a potential regulator of F-actin and intestinal barrier. In UC patients, we confirmed concurrent disruption of junctions and F-actin. ConclusionsF-actin dysregulation contributes to barrier dysfunction in IBD and targeting its modulators, including ceramide biosynthesis, represents a novel therapeutic strategy. WHAT IS ALREADY KNOWN ON THIS TOPICO_LIEpithelial damage and increased paracellular permeability are key characteristics of inflammatory bowel diseases. C_LIO_LIParacellular permeability is partially attributed to the downregulation of junction proteins but this mechanism does not explain all clinical observations. C_LIO_LIIn the Muc2 KO mouse model of chronic colitis, F-actin organization and membrane localization of tight junction protein claudin-3 are disrupted, although protein expression levels remain unchanged. C_LI WHAT THIS STUDY ADDSO_LIF-actin dynamics is impaired in the intestinal epithelium across three different mouse models of chronic colitis and IBD patients. C_LIO_LIDisruption of F-actin dynamics leads to impaired membrane localization of tight and adherens junction proteins and increased intestinal epithelial permeability in vivo and in colonic organoids. C_LIO_LIInhibition of ceramide biosynthesis rescues F-actin polymerization and intestinal barrier integrity in mouse chronic colitis models. C_LI HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE OR POLICYO_LITargeting F-actin dynamics is a promising approach to improve gut epithelial integrity. C_LIO_LI"Ceramide-F-actin-junction" axis is proposed as one of the mechanisms behind epithelial barrier disruption in colitis. Therapeutic targeting of this axis represents a promising path for restoring gut integrity. C_LI

BackgroundCrohns disease (CD) and ulcerative colitis (UC) are highly heterogeneous, dynamic and unpredictable, with a marked disconnect between symptoms and intestinal inflammation. ObjectiveWe aimed to describe latent disease heterogeneity in IBD by identifying longitudinal faecal calprotectin (FC) and CRP patterns. DesignIn this longitudinal study, patient-level measurements of FC and CRP in two European cohorts were modelled. Latent class mixed models were used to cluster individuals with similar longitudinal profiles. Associations between cluster assignment and baseline characteristics were quantified using multinomial logistic regression. Differences in advanced therapy use across clusters were explored. Finally, we considered the overlap between FC and CRP clusters. ResultsWe included 1036 patients in the FC discovery analysis (Lothian) with a total of 10545 FC observations (median 9 per subject, IQR 6-13), and 7880 patients in the replication (Denmark). The CRP discovery analysis consisted of 1838 patients with 49364 measurements (median 20 per subject; IQR 10-36), with 10041 patients in the replication cohort. Eight distinct clusters of inflammatory behaviour over time were identified in the FC and CRP analysis. Similar patterns were observed in the replication cohort. The clusters included rapid remitters, delayed remitters, remitting-relapsing disease, and non-remitters The highest use of early advanced therapy was in the group with the lowest overall inflammation. There was broadly poor agreement between FC and CRP cluster assignment. ConclusionDistinct patterns of inflammatory behaviour over time are evident in patients with IBD. These data pave the way for a deeper understanding of disease heterogeneity in IBD.

BACKGROUND AND AIMSVaccine-mediated immune responses in patients with inflammatory bowel disease (IBD) may be influenced by IBD therapies. We investigated in-depth humoral and T-cell responses to SARS-CoV-2 vaccination in IBD patients following three COVID-19 vaccine doses. METHODSImmune responses of 100 SARS-CoV-2-uninfected IBD patients on varying treatments were compared to healthy controls (n=35). Anti-S1/2 and anti-RBD SARS-CoV-2-specific antibodies, CD4+ and CD8+ T-cell responses were measured at baseline and at five time-points after COVID-19 vaccination. RESULTSAnti-S1/2 and anti-RBD antibody concentrations at [~]1 month after second dose vaccination were significantly lower in anti-TNF-treated patients compared to non-TNF IBD patients and healthy controls (126.4 vs 262.1 and 295.5, p<0.0001). Anti-S1/2 antibodies remained reduced in anti-TNF treated patients before and after the third dose (285.7 vs 365.3, p=0.03), although anti-RBD antibodies reached comparable titres to non-TNF patients. Anti-RBD antibodies were higher in the vedolizumab group than controls after second dose (4.2 vs 3.6, p=0.003). Anti-TNF monotherapy was associated with increased CD4+ and CD8+ T-cell activation compared to combination anti-TNF patients after second dose, but comparable after third dose. Overall, IBD patients demonstrated similar CD4+/CD8+ T-cell responses compared to healthy controls regardless of treatment regimen. CONCLUSIONSAnti-TNFs impaired antibody concentrations when compared to non-TNF patients and controls after two vaccine doses. These differences were not observed after the third vaccine dose. However, vaccine induced SARS-CoV-2-specific T cell responses are robust in anti-TNF-treated patients. Our study supports the need for timely booster vaccination particularly in anti-TNF treated patients to minimise the risk of severe SARS-CoV-2 infection.

BackgroundKeratins, a major subgroup of intermediate filament proteins, play a critical role in maintaining epithelial barrier and intracellular epithelial integrity. Studies have demonstrated possible links between inflammatory signaling and colonic keratins type II K8, and type I K18, K19 and K20, in animal models of colitis, and in patients with Inflammatory Bowel Disease (IBD). K7 is de novo expressed in patients with the IBD subtypes Ulcerative Colitis (UC) and Crohns Disease (CD). However, the histopathological roles of colonocyte keratins across IBD, microscopic colitis (MC), and Irritable Bowel Syndrome (IBS) remain poorly understood. Given the established utility as biomarkers in cancer diagnostics, we investigated whether keratin expression patterns could be used to distinguish inflammatory and functional colonic disorders. MethodsBiobank samples from patients with IBD (n=27), MC (n=18), IBS (n=32) and healthy controls (n=31), were collected and immunohistochemically stained for K7, K8, K18, K19, and K20. Digital image analysis quantified staining intensities, which were correlated with histopathological severity scores and clinical parameters. ResultsColonic keratin expression was significantly elevated in IBD, particularly in UC, while they were decreased in MC, and unaltered in IBS. Notably, K8 and K19 expression were strongly associated with areas of severe epithelial damage in IBD. Keratin expression was most pronounced in patients who had undergone colectomy due to treatment-resistant IBD. DiscussionKeratin changes in IBD and MC but not in IBS highlight their importance in maintaining barrier homeostasis. Whether these changes are causes or consequences for these diseases will warrant further research.

ObjectiveWe investigated UK wide inactivated influenza vaccine (IIV) uptake in adults with inflammatory bowel disease (IBD), the association between vaccination against influenza and IBD flare, and the effectiveness of IIV in preventing morbidity and mortality. DesignData for adults with IBD prior to 1st September 2018 were extracted from the Clinical Practice Research Datalink (CPRD) Gold, a database of electronic health records originated during routine care of patients in the UK. It is linked to hospitalization and mortality records. We calculated the proportion of patients vaccinated against seasonal influenza in the 2018-2019 influenza cycle. To investigate vaccine effectiveness, we calculated propensity score (PS) for vaccination and undertook Cox proportional hazard regression with inverse-probability treatment weighting on PS. We employed self-controlled case series (SCCS) to investigate the association between vaccination and IBD flare. ResultsData for 13,631 IBD patients (50.4% male, mean age 52.9 years) were included. Fifty percent were vaccinated during the influenza cycle while 32.1% were vaccinated before influenza virus circulated in the community. Vaccination was associated with a non-significant reduction in hospitalisation for pneumonia (aHR (95%CI) 0.52 (0.20-1.37), including in the influenza active period (aHR (95%CI) 0.48 (0.18-1.27)). Administration of the influenza vaccine was not associated with IBD flare. ConclusionThe uptake of influenza vaccine is low in IBD patients and the majority are not vaccinated before influenza virus circulates in the community. Vaccination with the IIV is not associated with IBD flare. These findings add to the evidence to promote vaccination in patients with IBD. Key messagesO_ST_ABSWhat is already known on the topicC_ST_ABSO_LIInactivated influenza vaccine is recommended in people with IBD treated with immune suppressing drugs. C_LIO_LIConcerns about influenza vaccine causing IBD flare and lack of data on the effectiveness of influenza vaccine in people with IBD are barriers to seasonal influenza vaccination in this population. C_LI What this study addsO_LIThe uptake of seasonal influenza vaccination is low in IBD patients. C_LIO_LISeasonal influenza vaccination is not associated with IBD flare and is more likely to prevent serious complications of influenza in this population. C_LI How this study might affect research, practice, or policyO_LIThis study provides new data on the uptake, effectiveness, and safety of influenza vaccine in people with IBD and adds to the accumulating evidence to promote vaccination in this population. C_LI

BACKGROUND & AIMSAcute severe ulcerative colitis (ASUC) is a life-threatening presentation of ulcerative colitis requiring prompt treatment. Infliximab (IFX) rescue therapy can prevent colectomy in patients with ASUC. METHODSWe performed a cohort study of adult patients hospitalized with ASUC between 01/2014 - 02/2021 who received infliximab rescue therapy. Using multivariable logistic regression, baseline and longitudinal laboratory predictors of colectomy within 90 days of index hospitalization were identified and used to develop a risk prediction model and prognostic scoring system to identifying patients at risk for colectomy. Model performance was assessed using area under the receiver operator characteristic curve (AUC) analysis. RESULTS166 patients with ASUC who received infliximab rescue therapy were identified. Overall, 24.7% (n=41) underwent colectomy within 90 days. Multivariate analysis revealed that colectomy within 90 days could be predicted by having a calculated IFX clearance of >53L/d (OR 2.28, 95% CI 0.99, 5.22), a day 0 absolute C-reactive protein (CRP) > 91mg/L (OR 3.49, 95% CI 1.58 to 8.08), a decrease in CRP of < 43% from day 0 to day 3 (OR 4.13, 95% CI 1.84 to 9.94), and a decrease in CRP of < 9% from the day of IFX administration to one day post-IFX administration (OR 4.20, 95% CI 1.74 to 10.4). Using these predictors, two highly accurate prognostic scoring system were developed to identify patients at risk for requiring colectomy both prior to administering infliximab (AUC 0.76) and after administer infliximab rescue therapy (AUC 0.81). CONCLUSIONWe identified important baseline and longitudinal laboratory predictors of colectomy within 90-days among patients with ASUC receiving infliximab rescue therapy and developed accurate prognostic scores to determine risk of colectomy. These scores can be used risk-stratify patients and facilitate personalized management.

BackgroundIndividuals with inflammatory bowel disease (IBD) who are immunocompromised may have a reduced serological response to the SARS-CoV-2 vaccine. We investigated serological responses following 1st, 2nd, and 3rd doses of SARS-CoV-2 vaccination in those with IBD. MethodsA prospective cohort study of persons with IBD (n = 496) assessed serological response 1-8 weeks after 1st dose vaccination, 1-8 weeks after 2nd dose, 8 or more weeks after 2nd dose, and at least 1 week after 3rd dose. Seroconversion and geometric mean titer (GMT) with 95% confidence intervals (CI) were assessed for antibodies to the SARS-CoV-2 spike protein. Multivariable linear regression models assessed the adjusted fold change (FC) in antibody levels. ResultsSeroconversion and GMT increased from post-1st dose to 1-8 weeks post-2nd dose (81.6%, 1814 AU/mL vs. 98.7%, 9229 AU/mL, p<0.001), decreased after 8 weeks post-2nd dose (94.9%, 3002 AU/mL, p<0.001), and rebounded post-3rd dose (99.6%, 14639 AU/mL, p<0.001). Prednisone was the only IBD-related medication associated with diminished antibody response after 3rd-dose vaccination (FC: 0.07 [95% CI: 0.02, 0.20]). Antibody levels steadily decline following the 2nd (FC: 0.92 [95% CI: 0.90, 0.94] per week) and 3rd dose (FC: 0.88 [95% CI: 0.84, 0.92] per week) of the SARS-CoV-2 vaccine. ConclusionA three-dose regimen of vaccination to SARS-CoV-2 yields a robust antibody response for those with IBD across all classes of IBD therapies except for prednisone. The decaying antibody levels following the 3rd dose of the vaccine should be monitored in future studies.

Background and AimsA cohort of patients with inflammatory bowel disease (IBD) exhibit expansion of the gut pathobiont, adherent-invasive E. coli (AIEC). Loss of activity of the IBD susceptibility gene, protein tyrosine phosphatase type 2 (PTPN2), results in dysbiosis of the gut microbiota both in human subjects and mice. Further, constitutive Ptpn2 knock-out (Ptpn2-KO) mice display expansion of AIEC compared to wildtype littermates. CEACAM6, a host cell surface glycoprotein, is exploited by AIEC to attach to and enter intestinal epithelial cells (IECs). Here, we investigate the role of IEC-specific PTPN2 in restricting AIEC invasion. MethodsBiopsies from IBD patients heterozygous (CT) or homozygous (CC) for the PTPN2 SNP (single nucleotide polymorphism) rs1893217 were processed for immunohistochemistry. HT-29 intestinal epithelial cells (IEC) were transfected with control shRNA (PTPN2-CTL), or a shRNA targeted towards PTPN2 (PTPN2-KD). The rs1893217 SNP was inserted (PTPN2-KI), or a complete knock-out of PTPN2 (PTPN2- KO) was generated, with CRISPR-Cas9 gene editing of Caco-2BBe IEC lines. Adherence and invasion assays were performed with either the human IBD AIEC isolate, LF82, or a novel fluorescent-tagged mouse adherent-invasive E. coli (mAIECred) at multiplicity of infection (MOI) of 10. IL-6 and the pan-JAK inhibitor tofacitinib were administered to interrogate JAK-STAT signaling. Protein expression was determined by western blotting and densitometry. ResultsCEACAM6 expression was elevated (colon and ileum) in IBD patients carrying the PTPN2 rs1893217 SNP (CT, CC) compared to wildtype (TT) IBD patients. HT-29 and Caco-2BBe cell lines deficient in PTPN2 expressed significantly higher levels of CEACAM6. Further, PTPN2-KI and PTPN2-KO cell lines also displayed greater adherence and invasion by AIEC LF82 and higher mAIECred invasion. CEACAM6 expression was further elevated after administration of IL-6 in PTPN2-deficient cell lines compared to untreated controls. Silencing of STAT1 and 3 partially reduced CEACAM6 protein expression. Tofacitinib significantly reduced the elevated CEACAM6 protein expression and the higher AIEC adherence and invasion in PTPN2-KI and PTPN2-KO cell lines compared to DMSO controls. ConclusionOur findings highlight a crucial role for PTPN2 in restricting pathobiont entry into host cells. Our study also describes a role for the FDA-approved drug, tofacitinib (Xeljanz) in correcting the JAK-STAT- mediated over-expression of CEACAM6, used by pathobionts as an entry portal into host cells. These findings suggest a role for JAK-inhibitors in mitigating AIEC colonization in IBD-susceptible hosts.

Background and AimsEven in the absence of inflammation, persistent symptoms in Crohns disease (CD) are prevalent and negatively impact quality of life. We aimed to determine whether quiescent CD patients with persistent symptoms (qCD+symptoms) have changes in microbial structure and functional potential compared to those without symptoms (qCD-symptoms). MethodsWe performed a prospective multi-center observational study nested within the SPARC IBD study. CD patients were included if they had evidence of quiescent disease as defined by fecal calprotectin level < 150 mcg/g. Persistent symptoms were defined by the CD-PRO2 questionnaire. Active CD (aCD), diarrhea-predominant irritable bowel syndrome (IBS-D), and healthy controls (HC) were included as controls. Stool samples underwent whole genome shotgun metagenomic sequencing. ResultsA total of 424 patients were analyzed, including 39 qCD+symptoms, 274 qCD-symptoms, 21 aCD, 40 IBS-D, and 50 HC. Patients with qCD+symptoms had a less diverse microbiome, including significant reductions in Shannon diversity (P<.001) and significant differences in microbial community structure (P<.0001), compared with qCD-symptoms, IBS-D, and HC. Further, patients with qCD+symptoms showed significant enrichment of bacterial species that are normal inhabitants of the oral microbiome, including Klebsiella pneumoniae (q=.003) as well as depletion of important butyrate and indole producers, such as Eubacterium rectale (q=.001), Lachnospiraceae spp. (q<.0001), and Faecalibacterium prausnitzii (q<.0001), compared with qCD-symptoms. Finally, qCD+symptoms showed significant reductions in bacterial tnaA genes, which mediate tryptophan metabolism, as well as significant tnaA allelic variation, compared with qCD-symptoms. ConclusionThe microbiome in patients with qCD+symptoms show significant changes in diversity, community profile, and composition compared with qCD-symptoms. Future studies will focus on the functional significance of these changes. What You Need to KnowO_ST_ABSBackgroundC_ST_ABSPersistent symptoms in quiescent Crohns disease (CD) are prevalent and lead to worse outcomes. While changes in the microbial community have been implicated, the mechanisms by which altered microbiota may lead to qCD+symptoms remain unclear. FindingsQuiescent CD patients with persistent symptoms demonstrated significant differences in microbial diversity and composition compared to those without persistent symptoms. Specifically, quiescent CD patients with persistent symptoms were enriched in bacterial species that are normal inhabitants of the oral microbiome but depleted in important butyrate and indole producers compared to those without persistent symptoms. Implications for Patient CareAlterations in the gut microbiome may be a potential mediator of persistent symptoms in quiescent CD. Future studies will determine whether targeting these microbial changes may improve symptoms in quiescent CD.

BackgroundReal-world data are receiving attention from regulators, biopharmaceuticals and payors as a potential source of clinical evidence. However, the suitability of these data to produce evidence commensurate with randomized controlled trials (RCTs) and the best practices in their use remain unclear. We sought to compare the real-world effectiveness of Tofacitinib in the treatment of IBD against efficacy rates published by corresponding RCTs. MethodsElectronic health records at the University of California, San Francisco (UCSF) were queried and reviewed to identify 86 Tofacitinib-treated IBD patients through 4/2019. The primary endpoint was treatment effectiveness. This was measured by time-to-treatment-discontinuation and by the primary endpoints of RCTs in Ulcerative Colitis (UC) and Crohns Disease (CD). Endpoints were measured and analyzed following a previously published protocol and analysis plan. Findings86 patients (68 with UC, 18 with CD) initiated Tofacitinib for IBD treatment. Most of the data needed to calculate baseline and follow-up disease activity indices were documented within the EHR(77% for UC, 91% for CD). Baseline characteristics of the UCSF and RCT cohorts were similar, except for a longer disease duration and 100% treatment failure of Tumor Necrosis Factor inhibitors in the former. None of the UCSF cohort would have met the RCT eligibility criteria due to multiple reasons. The rate of achieving the RCT primary endpoints were highly similar to the published rates for both UC(16%, P=0{middle dot}5) and CD (38%, P=0{middle dot}8). However, treatment persistence was substantially higher: 69% for UC (week 52) and 75% for CD (week 26). InterpretationAn analysis of routinely collected clinical data can reproduce published Tofacitinib efficacy rates, but also indicates far greater treatment durability than suggested by RCTs including possible benefit in CD. These results underscore the value of real-world studies to complement RCTs. FundingThe National Institutes of Health and UCSF Bakar Institute Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSTofacitinib is the most recently approved treatment for Ulcerative Colitis. Data related to treatment efficacy for either IBD subtype is generally limited, whether from controlled trials or real-world studies. A search of clinicaltrials.gov was performed in January 2019 for completed phase 2 or 3, interventional, placebo-controlled clinical trials matching the terms "Crohns Disease" OR "Ulcerative Colitis" in the conditions field, and matching "Placebo" AND "Tofacitinib" OR "CP-690,550") in the Interventions field. We identified three Phase 3 trials for UC (OCTAVE trials, all initially reported in a single article in 2016) and three Phase 2 trials of CD (two published in the same article in 2017, one reported in 2014). The Phase 3 UC trials reported 57{middle dot}6% pooled clinical response rate in the Tofacitinib-assigned groups after 8 weeks (induction), and a 37{middle dot}5% pooled remission rate among eligible induction trial responders in the Tofacitinib-assigned groups at 52 weeks. The 2017 CD trial reported a 70{middle dot}8% pooled rate of response or remission in the Tofacitinib-assigned groups after 8 weeks, and a 47{middle dot}6% pooled rate of response or remission among enrolled induction-trial responders at 26 weeks. A bias assessment of both UC and CD trials indicated a high risk of attrition bias and unclear risk of bias related to conflicts of interest. We also performed a search of pubmed.gov in January 2019 using search terms ("Colitis" OR "Crohns") AND ("Tofacitinib" OR "CP-690,550") OR "real-world" to identify cohort studies of Tofacitinib efficacy in routine clinical practice. No studies meeting these criteria were identified. Added value of this studyThis is one of the early studies to closely compare the results of clinical trials with the continuously-updated data captured in the electronic health records, and the very the first to assess the efficacy-effectiveness gap for Tofacitinib. We found that none of the patients treated at our center thus far would have qualified for the clinical trial based on published eligibility criteria. We found that the drug appeared to perform similarly to its efficacy when using the endpoints reported in clinical trials, but treatment persistence was significantly greater than would have been expected from the reported trial outcomes: 69% for UC at week 52 and 75% for CD at week 26. Implications of all the available evidenceTofacitinib is an effective treatment for the Ulcerative colitis and may be efficacious for Crohns disease. Controlled trials may not be representative of real-world cohorts, may not be optimally designed to identify efficacious drugs, and may not accurately predict patterns of use in clinical practice. Further studies using real-world data as well as methods to enable their proper use are needed to confirm and continuously monitor the efficacy and safety of drugs, both for on- and off-label use.

Symptoms after SARS-CoV-2 primary vaccination among patients with inflammatory bowel disease (IBD) are generally of similar frequency, severity, and duration to those reported in the general population. The symptom profile after a 3rd mRNA vaccine dose in the predominantly immune-compromised IBD population is unknown. We aimed to assess symptomology after a 3rd or booster dose of mRNA vaccination in adults with IBD. We surveyed participants of the Coronavirus Risk Associations and Longitudinal Evaluation in IBD (CORALE-IBD) post-vaccination registry for symptom frequency and severity after a 3rd mRNA vaccine dose in an observational cohort study. In total, 524 participants (70% female, mean age 45 years) reported a third dose of mRNA vaccination through October 11, 2021. Overall, 41% reported symptoms after a third dose, with symptoms generally more frequent and more severe among participants younger than 55 years. The most frequent postvaccination symptoms were injection site pain (39%), fatigue or malaise (34%), and headache (23%). These symptoms were all less frequently reported after dose 3 than after dose 2. Gastrointestinal symptoms were reported by 8.8%, which was slightly more frequent than after dose 2 (7.8%). Those with severe symptoms after dose 2 were more likely to have severe symptoms after dose 3. These findings can reassure the IBD patient and provider communities that the likelihood and distribution of symptoms after a third mRNA vaccine dose are generally similar to those after a second dose, and that the frequency of postvaccination symptoms after dose 3 are generally lower than after dose 2.

BackgroundCrohns disease (CD) is a chronic inflammatory disorder of the gastrointestinal tract characterized by high post-operative recurrence (POR) rates, reaching up to 90% within one year. Current clinical and endoscopic predictors show limited accuracy. ObjectiveThis study aimed to identify molecular mechanisms associated with POR at the time of surgery through integrated transcriptomic and bacteriomic analyses of ileal tissue. DesignIleal samples were obtained during surgery from 20 patients with CD and 10 inflammatory bowel disease-free controls, with an independent validation cohort of 49 patients with CD. POR was evaluated every six months using ileocolonoscopy and defined by Rutgeerts score. Host gene expression and tissue-associated microbiome profiles were integrated using correlation and pathway enrichment analyses to uncover host-microbe interactions linked to POR. ResultsIn the inflamed mucosa of patients who developed endoscopic POR, we identified a novel immune interaction involving the Porphyromonadaceae family, mainly Parabacteroides gordonii, which was slightly depleted. This depletion was associated with downregulation of epithelial barrier and tissue repair genes, including TFF1 and LSR, findings confirmed in the validation cohort. Porphyromonadaceae abundance positively correlated with short-chain fatty acid levels, particularly propionate. Additionally, omics integration revealed an association between Xanthomonadaceae and increased expression of ITGAM, a gene involved in neutrophil activation. ConclusionThese results highlight microbial-host gene interactions associated with POR. The pathogenic ITGAM-driven immune signature and the protective Porphyromonadaceae-TFF1-propionate axis supporting epithelial integrity may enable microbiome-informed prognostic tools and therapeutic strategies for CD POR. O_LIWhat is already known on this topic: Post-operative recurrence in Crohns disease is linked to microbial dysbiosis, particularly reduced diversity and expansion of Enterobacteriaceae. However, how microbial changes translate into host molecular mechanisms driving POR remains unclear. C_LIO_LIWhat this study adds: This prospective multi-omic study identifies a disrupted Porphyromonadaceae-SCFA-epithelial barrier axis and the participation of neutrophil responses in patients who develop POR at surgery time. C_LIO_LIHow this study might affect research, practice or policy: The findings provide mechanistic targets for microbiome-informed risk stratification and prevention of POR. They support development of microbial or metabolite-based interventions aimed at restoring epithelial barrier function after surgery. C_LI

Inflammatory bowel disease (IBD) treatments and pregnancy can independently modulate immune responses, but the combined effects on SARS-CoV-2 vaccine-induced immunity are poorly understood. This study explores the efficacy of SARS-CoV-2 vaccination and placental antibody transfer among pregnant women with IBD on biologic therapies. This observational study included pregnant women with and without IBD from the PIANO and PREVENT-COVID studies and their neonates. We assessed anti-SARS-CoV-2 neutralizing antibody titers (NT50) in maternal and cord blood post-vaccination using a pseudotype neutralization assay and calculated placental transfer ratios. A total of 32 pregnant women participated, and 27 were exposed to a biologic medication during pregnancy. Neutralizing antibody titers were similar between biologic-treated and non-treated groups, and biologic-exposed women demonstrated robust placental transfer of neutralizing antibodies. Corticosteroid use during pregnancy was significantly associated with reduced placental transfer efficiency, although this effect was not significant in a sensitivity analysis excluding patients treated with immunomodulators. Vaccination timing and previous SARS-CoV-2 infection impacted maternal and cord antibody levels, with higher titers observed in those vaccinated before pregnancy or infected during pregnancy. Overall, our findings suggest that pregnant women with IBD on biologic therapies mount effective SARS-CoV-2 neutralizing antibody responses similar to their non-biologic-exposed counterparts, with efficient placental transfer. These findings reassure the safety and efficacy of SARS-CoV-2 vaccination in this population, though further research is needed to explore the long-term protective effects of transferred antibodies in neonates. Corticosteroid use, immunomodulator use, and vaccination timing may influence antibody dynamics, underscoring the need for tailored clinical management in this vulnerable population.

BACKGROUND & AIMSAnti-tumor necrosis factor (anti-TNF) is a mainstay of inflammatory bowel disease (IBD) therapy but fails in many patients. Although TNF has pro-inflammatory effects, depletion of TNF receptor 1 (TNFR1) paradoxically exacerbates chronic colitis. Because colitis induces remodeling of mesenchymal cell populations, which provide a niche for epithelial stem cells involved in mucosal healing, we hypothesized that TNFR1 promotes colonic mesenchymal cell diversity and stem cell niche function. METHODSMesenchymal TNFR1 function was studied using TNFR1-/-, platelet derived growth factor receptor alpha (PDGFR)-Cre;TNFR1fl/fl mice, and mixed-genotype mesenchymal-epithelial co-cultures. Mesenchymal cell diversity and gene function were assessed using single-cell RNA-Seq of primary colonic myofibroblasts (CMFs) and via anti-integrin A6 (ITGA6) antibody treatment and exogenous R-spondin 3 (RSPO3) supplementation. RESULTSTNFR1-/- mesenchyme exhibits reduced cell diversity, with specific depletion of specialized TNF- and interferon-signaling pericryptal cell-type. Deletion of TNFR1 in the pericryptal mesenchyme diminished the (PDGFR)+ CMF population and reduced RSPO3 expression, but increased ITGA6 expression relative to controls (TNFR1+/-). Moreover, inhibition of ITGA6 reversed the proliferative and migratory phenotype of TNFR1-/- CMFs and restored expression of PDGFR and RSPO3. Co-cultures of colonoids with TNFR1-/- CMFs resulted in downregulation of stem cell marker expression; this was rescued by supplementation with RSPO3. Supporting the role for mesenchymal TNFR1 in regulating colonic epithelial stem cells, mice deficient for TNFR1 in PDGFR+ cells showed a 40% loss of Lgr5+ stem cells, consistent with the global TNFR1-deficient mouse. CONCLUSIONTNFR1-mediated signaling regulates specification and function of colonic mesenchyme, performing an integral role in the maintenance of the crypt stem cell population.

Surveillance colonoscopy reduces colorectal cancer (CRC) risk in inflammatory bowel disease (IBD), but anecdotal evidence suggests a link between surveillance colonoscopy and symptoms flare, which may affect patient compliance with CRC surveillance. We investigated the effects of surveillance colonoscopy in quiescent IBD using a national database to conduct a retrospective, propensity score-matched (PSM) cohort study of 1,717 patients with IBD and 1,717 patients without IBD who underwent colonoscopy. Strict inclusion criteria were used to select patients with quiescent IBD undergoing surveillance colonoscopy. We demonstrated that patients with quiescent IBD prior to colonoscopy received significantly more post-colonoscopy steroid prescriptions compared to matched controls (OR 1.46 [1.20, 1.77], p<0.001). Steroid prescriptions were more likely in patients with IBD at longer follow-up intervals, suggesting a delayed mechanism of onset for post-colonoscopy inflammation. No significant differences between groups were observed for the other outcomes of post-procedure emergency room and hospital visits or enteric infections. Our results suggest a potential risk of symptom exacerbation, evidenced by increased steroid prescriptions, following surveillance colonoscopy. Given that nearly 25% of patients with IBD do not receive surveillance colonoscopy at the recommended intervals, active post-procedure symptoms may be a contributing factor that warrants further investigation.

Background and aimsInflammatory Bowel Diseases (IBD) are chronic inflammatory conditions influenced heavily by environmental factors. DNA methylation is a form of epigenetic regulation linking environmental stimuli to gene expression changes and inflammation. Here, we investigated how DNA methylation of the TNF promoter differs between inflamed and uninflamed mucosa of IBD patients, including anti-TNF responders and non-responders. MethodsWe obtained mucosal biopsies from 200 participants (133 IBD and 67 controls) and analyzed TNF promoter methylation using bisulfite sequencing, comparing inflamed with uninflamed segments, in addition to paired inflamed/uninflamed samples from individual patients. We conducted similar analyses on purified intestinal epithelial cells from bowel resections. We also compared TNF methylation levels of inflamed and uninflamed mucosa from a separate cohort of 15 anti-TNF responders and 17 non-responders. Finally, we sequenced DNA methyltransferase genes to identify rare variants in IBD patients and functionally tested them using rescue experiments in a zebrafish genetic model of DNA methylation deficiency. ResultsTNF promoter methylation levels were decreased in inflamed mucosa of IBD patients and correlated with disease severity. Isolated IECs from inflamed tissue showed proportional decreases in TNF methylation. Anti-TNF non-responders showed lower levels of TNF methylation than responders in uninflamed mucosa. Our sequencing analysis revealed two missense variants in DNMT1, one of which had reduced function in vivo. ConclusionsOur study reveals an association of TNF promoter hypomethylation with mucosal inflammation, suggesting that IBD patients may be particularly sensitive to inflammatory environmental insults affecting DNA methylation. Together, our analyses indicate that TNF promoter methylation analysis may aid in the characterization of IBD status and evaluation of anti-TNF therapy response.

Clonal hematopoiesis of indeterminate potential (CHIP) is the presence of somatic mutations in myeloid and lymphoid malignancy genes in the blood cells of individuals without a hematologic malignancy. Inflammation is hypothesized to be a key mediator in the progression of CHIP to hematologic malignancy and patients with CHIP have a high prevalence of inflammatory diseases. This study aimed to identify the prevalence and characteristics of CHIP in patients with inflammatory bowel disease (IBD). We analyzed whole exome sequencing data from 587 Crohns disease (CD), 441 ulcerative colitis (UC), and 293 non-IBD controls to assess CHIP prevalence and used logistic regression to study associations with clinical outcomes. Older UC patients (age>45) harbored increased myeloid-CHIP mutations compared to younger patients (age[&le;]45) (p=0.01). Lymphoid-CHIP was more prevalent in older IBD patients (p=0.007). Young CD patients were found to have myeloid-CHIP with high-risk features. IBD patients with CHIP exhibited unique mutational profiles compared to controls. Steroid use was associated with increased CHIP (p=0.05), while anti-TNF therapy was associated with decreased myeloid-CHIP (p=0.03). Pathway enrichment analyses indicated overlap between CHIP genes, IBD phenotypes, and inflammatory pathways. Our findings underscore a connection between IBD and CHIP pathophysiology. Patients with IBD and CHIP had unique risk profiles especially among older UC patients and younger CD patients. These findings suggest distinct evolutionary pathways for CHIP in IBD and necessitate awareness among IBD providers and hematologists to identify patients potentially at risk for CHIP-related complications including malignancy, cardiovascular disease and acceleration of their inflammatory disease.