BACKGROUND AND AIMS:Most patients with Crohn's disease (CD) who have undergone ileocolonic resection experience recurrent inflammation within 1 year after surgery. We examined the molecular basis underlying gastrointestinal inflammation in postoperative CD across 3 common anatomic locations of recurrence. METHODS:To characterize spatial transcriptomic signatures, this study utilized biopsies from the colon, neo-terminal ileum, and anastomosis of patients with postoperative CD in the PREDICT-OR study. Sample analyses were performed with 10X Genomics Visium CytAssist system V2.0, and data analyses with R. RESULTS:Histologically inflamed biopsies from all locations shared transcriptional signatures across 3 cellular niches (myeloid, B, T cells) and a specialized epithelial cell type expressing inflammation-associated genes. Differentially expressed genes overexpressed inflammatory pathway activity across the 3 locations, whereas hypoxic pathways were less apparent. In addition to genes for known treatment targets, epidermal growth factor receptor and mitogen-activated protein kinase pathways were upregulated. Cellular niches shaped inflammatory microenvironments through endoplasmic reticulum stress and extracellular matrix remodeling signaling. CONCLUSIONS:Application of spatial transcriptomics revealed a common disease signature for postoperative CD across the colon, neo-terminal ileum, and anastomosis. Inflamed biopsies from all locations demonstrated similar immune cell and inflammatory gene expression patterns as opposed to hypoxic pathways, and unique inflammatory pathways were revealed.

BACKGROUND AND AIMS:Substantial methodological and reporting heterogeneity confounds the interpretation and generalizability of transcriptomic data for inflammatory bowel disease (IBD) studies. We aimed to develop recommendations to standardize transcriptomic research in clinical trials. METHODS:A 2-part study was undertaken. A systematic review identified reports of transcriptomic analyses utilizing samples from IBD clinical trials. Studies that used global RNA assay platforms were included. Data regarding study design, methodological approaches, and reporting of transcriptomic research were extracted. The systematic review results informed a modified Research and Development/University of California Los Angeles appropriateness methodology process and the development of survey statements focused on topics with substantial methodological heterogeneity. A panel of 16 IBD translational researchers and gastroenterologists rated the appropriateness of survey statements in 2 rounds. RESULTS:The systematic review identified 37 reports that included transcriptomic analyses of samples from IBD patients. The appropriateness of 416 statements was rated by 15 panellists in the first survey. The final survey included 305 statements, of which 14 panellists rated 75% appropriate, 1% inappropriate, and 24% uncertain. The panel determined that transcriptomic analysis for multiple research objectives was appropriate at most phases of clinical development in patients with active disease. Recommendations regarding study sample size; biopsy number, location, preservation, and storage; and data analysis and reporting were also generated. CONCLUSION:The persistence of existing methodologic heterogeneity may continue to limit the value of transcriptomic research in IBD. This study provides expert recommendations to address and overcome these discrepancies and foster the inclusion of this research in clinical development.

BACKGROUND AND AIMS:Ulcerative colitis (UC) therapies lead to variable remission and response rates in patients participating in clinical trials, likely due to interindividual target variability, differences in active biological pathways, feedback, and/or resistance mechanisms. Here, we stratified patients into subtypes by characterizing heterogeneity using mucosal biopsy transcriptomics data. METHODS:Transcriptomics data from an andecaliximab phase 2/3 study in patients with UC were scored for gene signature enrichment. Eleven Reactome gene sets, moderately correlated with histological disease activity using Robarts Histopathology Index with low correlation to each other, were selected and evaluated in baseline gene expression data of ustekinumab, infliximab, and adalimumab clinical trials in patients with UC. RESULTS:Of 11 gene sets, referred to as "Metabolism and Response to Stress" (MARS) signatures, 5 correlated with "non-disease" mucosa and 6 with "disease-related" mucosa. Clustering baseline andecaliximab samples scored with MARS revealed 3 clusters with low non-disease/high disease-related, high non-disease/low disease-related, or a mixture. Importantly, these clusters did not correlate with patient demographics, clinical characteristics, or disease activity metrics. Clustering baseline data from other clinical trials (anti-interleukin-12/23 and anti-tumor necrosis factor) in patients with UC scored with MARS showed that patients in low non-disease/high disease-related baseline score clusters less likely to achieve treatment response. CONCLUSIONS:We identified and evaluated a novel, multi-dimensional signature gene set to characterize previously undefined heterogeneity in patients with UC and identify patients less likely to respond to therapy. This approach offers potential utility to define clinical trial populations, enrich for clinical responders, and identify difficult-to-treat populations for therapeutic development.

AimsAccurate determination of histological activity in ulcerative colitis (UC) is essential given its diagnostic and prognostic importance. Data on the relationship between histology and immune cell markers are limited. We aimed to evaluate the association between histological disease activity and immune cell marker concentration in colonic biopsies from patients with UC.MethodsSigmoid colon biopsies from 20 patients with UC were retrospectively assessed using the Robarts Histopathology Index (RHI). Targeted mass spectrometry determined the concentration of 18 immune cell markers (cluster of differentiation (CD) 4, CD8, CD19, CD20, CD40, CD56, CD68, CD103, forkhead box p3 (FOXP3), human leucocyte antigen, DR alpha chain (HLA-DRA), interleukin 10 (IL-10), IL-23 subunit alpha (IL-23A), IL-23 receptor (IL-23R), IL-2 receptor alpha chain (IL-2RA), Ki67, lymphocyte-activation gene 3 (LAG-3), programmed cell death protein 1 (PD-1) and PD ligand 1 (PD-L1)). The association between RHI score and immune cell marker concentration was quantified using Spearman’s rank correlation coefficient (ρ) and related 95% CIs.ResultsFourteen of the 18 immune cell marker proteins were detected, with tissue concentration ranging from 0.003 to 11.53 fmol/µg. The overall RHI score was positively correlated with CD19, CD20, CD40, FOXP3, LAG-3, PD-1 and PD-L1 concentration (ρ=0.596–0.799) and negatively correlated with CD56 concentration (ρ=−0.460). There was no significant association between RHI score and CD4, CD8, CD68, CD103, HLA-DRA or Ki67 concentration.ConclusionsThis study provides insight into the correlation between immune cell marker expression and histological disease activity and the possible molecular and immunological determinants underlying microscopic disease activity in UC.

Abstract Background Postoperative Crohn’s disease (CD) recurs in ~70% of patients ≤1 year following ileocolonic resection (ICR), as observed endoscopically. Current understanding of molecular determinants underlying histological intestinal inflammation in patients with postoperative CD recurrence is minimal. To address this issue, we used advanced spatial transcriptomic analyses on intestinal biopsy samples with matched histological and endoscopic assessments from neoterminal ileum, anastomosis, and colon of patients with CD who had undergone colonoscopy following ICR. Methods Formalin-fixed paraffin-embedded (FFPE) tissue biopsies from neoterminal ileum, anastomosis, and colon were prospectively collected from a 15-patient cross-sectional cohort with CD who underwent routine endoscopic assessment following ICR. Spatial transcriptomics was performed on samples using 10X Genomics Visium CytAssist Spatial Gene Expression for FFPE V2.0. Annotation of tissue regions of histologically active inflammation and classification of histologically inactive (Robarts Histopathology Index ≤3 with subscores of 0 for neutrophils in the lamina propria and epithelium) or active disease were performed by an expert gastrointestinal pathologist. R programming language was used for data analysis (Figure). Results Fourteen of the 43 (32.6%) FFPE biopsies had histological evidence of inflammation. Spatial transcriptomics clustering revealed a distinct transcriptional signature by the segregation of 4 clusters ("inflamed clusters") composed mostly (≥69%) of cells from samples defined by histologically active disease. Tissue regions identified as inflamed by expert pathologist annotation contributed to >46% of inflamed clusters’ composition and <15% of remaining clusters. Cell type decomposition and cellular niche analysis revealed immune (e.g., myeloid, T cells, and B cells) and epithelial cells in close proximity sharing a similar microenvironment in 3 inflamed clusters while the 4th cluster was composed of >90% epithelial cells. Differentially expressed genes from the inflamed clusters were similarly expressed across intestinal segments including inflamed anastomotic biopsies and were enriched for signalling pathways involving immune cells recruitment/activation, inflammatory signalling, extracellular matrix organisation, and oxidative stress response. Conclusion This is the first study to explore spatial transcriptomic signatures associated with histological inflammation in patients with postoperative CD recurrence. Our analysis revealed a spatial signature of cellular niches and signalling pathways arising upon histological inflammation, providing insight into therapeutic targets and biomarkers across anatomic locations and the anastomosis.

Abstract Background Transcriptomic analysis has the potential to facilitate drug development and clinical decision making in inflammatory bowel disease. Current understanding of pharmacodynamic response to vedolizumab is limited by a lack of publicly available mucosal biopsy RNA samples/sequencing data and corresponding clinical information. We aimed to identify gene signatures associated with response to vedolizumab in ulcerative colitis (UC) patients by pooling data from 3 international sites. Methods Patients receiving vedolizumab for the treatment of moderate-to-severe UC at Hospital Clínic de Barcelona (IDIBAPS), Mount Sinai Hospital (MSH), and University of California, San Diego (UCSD) with baseline and post-treatment (week 14 [± 4 weeks]) mucosal biopsy RNA-sequencing data and Mayo Clinic endoscopic subscores (MCES) were eligible for inclusion. Endoscopic response was defined as an MCES <1. Demographic and clinical data were collected. Differential expressed genes (DEGs) between baseline and week 14 were identified using linear mixed models with a >1.5 or <-1.5-fold change (adjusted P-value <.05). Enrichment was performed using Reactome pathway analysis and a previously published UC gene signature (adjusted P-value <.05).1 Analyses were performed using R version 4.3.0. Results Twenty-three patients were included (IDIBAPS: n=12; MSH: n=8; UCSD: n=3). Site-specific differences in sex, surgical history, and corticosteroid use were observed (Table). Analysing data by site yielded a relatively small number of DEGs between baseline and week 14 (IDIBAPS=57 [27 up-regulated, 30 down-regulated]; MSH=0; UCSD=0) among endoscopic responders (IDIBAPS: n=5; MSH: n=7; UCSD: n=2). Combining data from the 3 sites increased the number of DEGs among endoscopic responders at week 14 (n=14) to 1162 (662 up-regulated and 500 down-regulated). The down-regulated DEGs were enriched for genes involved in 37 of 103 up-regulated Reactome pathways in UC, including neutrophil degranulation, interleukin-4 and interleukin-13 signalling, interleukin-10 signalling, and integrin cell surface interactions. The up-regulated DEGs were enriched for genes involved in 1 of 39 down-regulated Reactome pathways in UC (Drug ADME). Conclusion We defined a pharmacodynamic signature using mucosal biopsies from UC patients who had endoscopic response to vedolizumab at week 14. The signature was enriched for several, but not all, pathways involved in UC. In addition to providing insight into vedolizumab’s mechanism of action, we underscored the utility of multi-site collaboration to access data, increase statistical power, and enhance the generalizability of research findings. Reference: 1. Linggi et al. Sci Rep 2021;11:18243.

Abstract Background Ulcerative colitis (UC) therapies lead to variable remission in participants in clinical trials likely due to interindividual variability, differences in active biological pathways, feedback, and/or resistance mechanisms. We sought to characterise these differences using mucosal biopsy transcriptomics datasets from two recent UC clinical trials. Methods Two clinical trial datasets including patients with moderate to severe UC with mucosal biopsy RNA-Sequencing analysis were used: a phase 2/3 study of andecaliximab (anti-matrix metalloproteinase-9, NCT02520284) and a phase 3 study of ustekinumab (anti-interleukin-12/23, UNIFI, NCT02407236). Samples were scored for enrichment of ~5200 MSigDB signatures using Geneset Variation Analysis and were evaluated for correlation to the sample Robarts Histopathology Index (RHI) (Figure). Results From the andecaliximab baseline and follow-up samples, 11 Reactome pathways were specifically selected that were moderately correlated with RHI (r=~0.4) and had low correlation to each other (r<0.7). The 11 genesets, called Metabolism and Response to Stress (MARS) signatures, can generally be sorted into 2 categories: 5 metabolism-related and 6 related to stress response. Clustering of baseline andecaliximab samples scored with MARS signatures revealed 3 major sample groups (baseline and follow-up samples). Group 1 had low metabolism/high stress scores, group 2 had high metabolism/low stress scores, and group 3 had a mixture of samples that had high metabolism/low stress and low metabolism/high stress. Group 2 was associated with a lower proportion of current smokers (p=.04), and group 3 had a higher proportion of immunomodulator failure (p=.03), but not associated with disease duration or prior biologic use. Group 2 had lower Geboes score for epithelial neutrophils (p=.02), lamina propria neutrophils (p=.002), and inflammatory infiltrate (p=.03), while eosinophils increased (p=.01). To evaluate prediction of response to therapy, we evaluated the UNIFI dataset baseline samples using the MARS signatures and identified 4 groups. Group 2 had low metabolism/high stress response, group 3 had high metabolism/low stress response, and groups 1 and 4 had a mixture. The mucosal healing response rate was 3- to 4-fold lower for group 2 than other groups (5.3% [group 2] and 19%, 23%, and 21% for other groups, p=.0009). Conclusion We describe the MARS signatures which characterise the heterogeneity of participants with UC clinical trials and identify participants most likely to respond to ustekinumab at baseline. These signatures may be generally useful to predict patient response, match therapeutics to patient profiles, or identify pathways to target in difficult-to-treat patients.

BACKGROUND:Clinical trials of novel therapies for the treatment of ulcerative colitis (UC) may benefit from immune cell profiling, however implementation of this methodology is limited in the multicenter trial setting by necessity of timely (within 6 to 8 h) isolation and processing of peripheral blood mononuclear cells (PBMC) from whole blood samples. Becton Dickinson Vacutainer CPT™ Cell Preparation Tubes (CPT™) limit required processing prior to shipping to a central lab to an initial centrifugation step within 24 h of sample collection. As shipping may delay final processing beyond 24 h, we analyzed cell viability and T cell composition in whole blood stored in CPT™ to determine if their use may accommodate processing delays typical for multicenter clinical trials.METHODS:Whole blood samples from 3 patients with UC were collected in CPT™ (15 tubes/patient) and PBMC were processed at various timepoints (24-96 h). Cell viability and T cell composition (26 types) were evaluated by flow cytometry. Variability between technical and biological replicates was evaluated in the context of cell-type abundance, delayed processing time, and data normalization.RESULTS:Total cell viability was <50% when processing was delayed to 48 h after collection and was further reduced at later processing timepoints. The effect of delayed processing on cell abundance varied widely across cell types, with CD4+, CD8+, naïve effector CD8+, and Tcm CD4 + T cells displaying the least variability in abundance with delayed processing. Normalization of cell counts to cell types other than total T cells corrected for the effect of delayed processing for several cell types, particularly Th17.CONCLUSIONS:Based on these data, processing of PBMC in CPT™ should ideally be performed within 48 h. Delayed processing of PBMC in CPT™ may be considered for cell types that are robust to these conditions. Normalization of cell abundance to different parental cell-types may reduce variability in quantitation and should be used in conjunction with the expected effect size to meet the experimental goals of a multicenter clinical trial.

Patients treated with immune checkpoint inhibitors (ICIs) may develop ICI-associated enterocolitis, for which there is no approved treatment. We aimed to systematically review the efficacy and safety of medical interventions for the prevention and treatment of ICI-associated enterocolitis. MEDLINE, EMBASE, and the Cochrane Library were searched to identify randomized controlled trials (RCTs), cohort and case–control studies, and case series/reports, evaluating interventions (including corticosteroids, biologics, aminosalicylates, immunosuppressants, and fecal transplantation) for ICI-associated enterocolitis. Clinical, endoscopic, and histologic efficacy endpoints were evaluated. The Grading of Recommendations, Assessment, Development, and Evaluation criteria were used to assess overall quality of evidence. A total of 160 studies (n = 1514) were included (one RCT, 3 retrospective cohort studies, 156 case reports/case series). Very low quality evidence from one RCT suggests budesonide is not effective for prevention of ICI-associated enterocolitis in ipilimumab-treated patients (relative risk 0.93 [95% confidence interval 0.56, 1.56]). Very low quality evidence suggests that corticosteroids, infliximab, and vedolizumab may be effective for treatment of ICI-associated enterocolitis by inducing clinical response and remission. No validated indices for measuring disease activity were used. Biologic treatment was used in 42% (641/1528) of patients, as reported in 97 studies. ICIs were discontinued in 65% (457/702) of patients, as reported in 63 studies. Current treatment recommendations for ICI-associated enterocolitis are based on very low quality evidence, primarily from case reports and case series. Large-scale prospective cohort studies and RCTs are needed to develop prophylactic and therapeutic treatments to minimize interruption or discontinuation of oncological therapies.

Publicly available ulcerative colitis (UC) gene expression datasets from observational studies and clinical trials include inherently heterogeneous disease characteristics and methodology. We used meta-analysis to identify a robust UC gene signature from inflamed biopsies. Eight gene expression datasets derived from biopsy tissue samples from noninflammatory bowel disease (IBD) controls and areas of active inflammation from patients with UC were publicly available. Expression- and meta-data were downloaded with GEOquery. Differentially expressed genes (DEG) in individual datasets were defined as those with fold change > 1.5 and a Benjamini–Hochberg adjusted P value < .05. Meta-analysis of all DEG used a random effects model. Reactome pathway enrichment analysis was conducted. Meta-analysis identified 946 up- and 543 down-regulated genes in patients with UC compared to non-IBD controls (1.2 and 1.7 times fewer up- and down-regulated genes than the median of the individual datasets). Top-ranked up- and down-regulated DEG were LCN2 and AQP8 . Multiple immune-related pathways (e.g., ‘Chemokine receptors bind chemokine’ and ‘Interleukin-10 signaling’) were significantly up-regulated in UC, while ‘Biological oxidations’ and ‘Fatty acid metabolism’ were downregulated. A web-based data-mining tool with the meta-analysis results was made available ( https://premedibd.com/genes.html ). A UC inflamed biopsy disease gene signature was derived. This signature may be an unbiased reference for comparison and improve the efficiency of UC biomarker studies by increasing confidence for identification of disease-related genes and pathways.

Background: Currently, 2 coprimary end points are used by health authorities to determine the effectiveness of therapeutic interventions in patients with Crohn's disease (CD): symptomatic remission (patient-reported outcome assessment) and endoscopic remission (ileocolonoscopy). However, there is lack of accepted biomarkers to facilitate regulatory decision-making in the development of novel therapeutics for the treatment of CD. Methods: With support from the Helmsley Charitable Trust, Critical Path Institute formed the Crohn's Disease Biomarkers preconsortium (CDBpC) with members from the pharmaceutical industry, academia, and nonprofit organizations to evaluate the CD biomarker landscape. Biomarkers were evaluated based on biological relevance, availability of biomarker assays, and clinical validation data. Results: The CDBpC identified the most critical need as pharmacodynamic/response biomarkers to monitor disease activity in response to therapeutic intervention. Fecal calprotectin (FC) and serum C-reactive protein (CRP) were identified as biomarkers ready for the regulatory qualification process. A number of exploratory biomarkers and potential panels of these biomarkers was also identified for additional development. Given the different factors involved in CD and disease progression, a combination of biomarkers, including inflammatory, tissue injury, genetic, and microbiome-associated biomarkers, will likely have the most utility. Conclusions: The primary focus of the Inflammatory Bowel Disease Regulatory Science Consortium will be development of exploratory biomarkers and the qualification of FC and CRP for IBD. The Inflammatory Bowel Disease Regulatory Science Consortium, focused on tools to support IBD drug development, will operate in the precompetitive space to share data, biological samples for biomarker testing, and assay information for novel biomarkers.

Nat. Med.; 10.1038/nm.4307; corrected online 11 April 2017 In the version of this article initially published, there were two typographical errors in the Abstract. The unnecessary 'h' in the line “Furthermore, h according to.....” has been deleted. The line “OSM is thus a potential biomarker of and therapeutic target for IBD,.

The signaling network downstream of the ErbB family of receptors has been extensively targeted by cancer therapeutics; however, understanding the relative importance of the different components of the ErbB network is nontrivial. To explore the optimal way to therapeutically inhibit combinatorial, ligand-induced activation of the ErbB-phosphatidylinositol 3-kinase (PI3K) axis, we built a computational model of the ErbB signaling network that describes the most effective ErbB ligands, as well as known and previously unidentified ErbB inhibitors. Sensitivity analysis identified ErbB3 as the key node in response to ligands that can bind either ErbB3 or EGFR (epidermal growth factor receptor). We describe MM-121, a human monoclonal antibody that halts the growth of tumor xenografts in mice and, consistent with model-simulated inhibitor data, potently inhibits ErbB3 phosphorylation in a manner distinct from that of other ErbB-targeted therapies. MM-121, a previously unidentified anticancer therapeutic designed using a systems approach, promises to benefit patients with combinatorial, ligand-induced activation of the ErbB signaling network that are not effectively treated by current therapies targeting overexpressed or mutated oncogenes.

3974 The role of the EGFR family in cancer is well documented. To date most of the attention has been focused on EGFR and ErbB2. We have taken a systems approach to understanding ErbB signaling and built a comprehensive computational model of the pathway. Simulations revealed ErbB3 as an ultra-sensitive node in the ErbB pathway and suggested it as a better target for therapeutic intervention. Historically, ErbB3 has not been considered as an attractive target because of its impaired kinase activity and low expression in tumors although recent publications suggest a key role in promoting resistance to EGFR and ErbB2 targeted therapeutics. Human monoclonal IgG2 antibodies against ErbB3 were then developed and tested in multiple orthogonal assays for the ability to modulate ErbB3 activity and one candidate, MM-121, was chosen to move forward into pre-clinical testing. MM-121 demonstrated potent inhibition of heregulin-induced signaling events in human cancer cell lines. When MM-121 efficacy was assessed in vivo, MM-121 showed a dose-dependent ability to inhibit tumor growth in multiple xenograft models of human cancer, including ovarian, renal cell, pancreatic and prostate cancer. Pharmacodynamic analysis of samples from these studies showed that chronic MM-121 administration resulted in inhibition of ErbB3 activity which correlated with efficacy. In vitro antibody binding studies suggested that MM-121 binds to ErbB3 receptors from mouse, rat, cynomolgus monkey and human with a similar affinity. In order to design an efficacious and safe dosing regimen, pre-clinical studies were carried out in mouse, rat and cynomolgus monkey. These studies suggest that MM-121 can safely be administered at serum levels that produce in good inhibition of ErbB signaling and efficacy in xenograft models of cancer. Cumulatively, these data support that MM-121 could have significant clinical benefit for the treatment of cancer and warrant proceeding forward into phase 1 clinical trials.