• Biomarker
• Inflammatory Bowel Disease
• Interactions modelling
• Machine learning
• Metabolome
• Microbiome
• Translational medicine

• Humans
• Inflammatory Bowel Diseases/microbiology
• Inflammatory Bowel Diseases/metabolism
• Inflammatory Bowel Diseases/pathology
• Gastrointestinal Microbiome
• Feces/microbiology
• Metabolome
• Dysbiosis/microbiology
• Dysbiosis/metabolism

• Fibrosis
• Gastroenterology
• Inflammation
• Inflammatory bowel disease
• Monocytes

• Crohn Disease/metabolism
• Crohn Disease/pathology
• Crohn Disease/immunology
• Humans
• Fibroblasts/metabolism
• Fibroblasts/pathology
• Twist-Related Protein 1/metabolism
• Twist-Related Protein 1/genetics
• Monocytes/metabolism
• Monocytes/pathology
• Monocytes/immunology
• Fibrosis
• Male
• Nuclear Proteins/metabolism
• Nuclear Proteins/genetics
• Female
• Extracellular Matrix/metabolism
• Extracellular Matrix/pathology
• Receptors, Cell Surface/metabolism
• Receptors, Cell Surface/genetics
• Ileum/pathology
• Ileum/metabolism
• Ileum/immunology
• Cell Communication
• Adult
• Endopeptidases/metabolism
• Endopeptidases/genetics
• Animals
• Mice

• LncRNAs
• meta-analysis
• ulcerative colitis

• endoscopy
• histology
• inflammatory bowel diseases
• intestinal barrier
• ulcerative colitis

• Crohn’s disease
• PDE1A
• RNA seq
• Sema3D
• apoptosis
• autonomic nervous system
• proliferation
• smooth muscle cell

• immune landscape
• in silico analysis
• molecular subtypes
• pediatric Crohn’s disease
• weighted gene-co-expression network analysis

• Cellular phenotype
• Disease progression
• MEOX1
• Therapeutic target
• Upregulated gene

• 16S rRNA gut metagenomics
• colonic inflammation
• dextran sulfate sodium
• inflammatory bowel disease
• meat consumption
• porcine model
• ulcerative colitis

• Independent Research Fund Denmark

• anti-TNF-α inadequate responder
• mechanism
• risankizumab
• upadacitinib

Patients with inflammatory bowel disease (IBD) produce enhanced immunoglobulin A (IgA) against the microbiota compared to healthy individuals, which has been correlated with disease severity. Since IgA complexes can potently activate myeloid cells via the IgA receptor FcαRI (CD89), excessive IgA production may contribute to IBD pathology. However, the cellular mechanisms that contribute to dysregulated IgA production in IBD are poorly understood. Here, we demonstrate that intestinal FcαRI-expressing myeloid cells (i.e., monocytes and neutrophils) are in close contact with B lymphocytes in the lamina propria of IBD patients. Furthermore, stimulation of FcαRI-on monocytes triggered production of cytokines and chemokines that regulate B-cell differentiation and migration, including interleukin-6 (IL6), interleukin-10 (IL10), tumour necrosis factor-α (TNFα), a proliferation-inducing ligand (APRIL), and chemokine ligand-20 (CCL20). In vitro, these cytokines promoted IgA isotype switching in human B cells. Moreover, when naïve B lymphocytes were cultured in vitro in the presence of FcαRI-stimulated monocytes, enhanced IgA isotype switching was observed compared to B cells that were cultured with non-stimulated monocytes. Taken together, FcαRI-activated monocytes produced a cocktail of cytokines, as well as chemokines, that stimulated IgA switching in B cells, and close contact between B cells and myeloid cells was observed in the colons of IBD patients. As such, we hypothesize that, in IBD, IgA complexes activate myeloid cells, which in turn can result in excessive IgA production, likely contributing to disease pathology. Interrupting this loop may, therefore, represent a novel therapeutic strategy.

OMiCC (OMics Compendia Commons) is a biologist-friendly web platform that facilitates data reuse and integration. Users can search over 40,000 publicly available gene expression studies, annotate and curate samples, and perform meta-analysis. Since the initial publication, we have incorporated RNA-seq datasets, compendia sharing, RESTful API support, and an additional meta-analysis method based on random effects. Here, we provide a step-by-step guide for using OMiCC.

For complete details on the use and execution of this protocol, please refer to Shah et al. (2016).

•

OMiCC (OMics Compendia Commons) is a free web-based tool for gene expression data reuse

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

• Crohn’s disease
• Inflammatory bowel disease
• transcription factor
• transcriptome
• ulcerative colitis

• CCAAT-Enhancer-Binding Protein-beta
• Colitis, Ulcerative/diagnosis
• Crohn Disease/diagnosis
• Humans
• Inflammatory Bowel Diseases/genetics
• Interferon Regulatory Factor-2/genetics
• Lectins, C-Type
• Receptors, Cell Surface/genetics
• Transcription Factors/genetics
• Transcriptome

• G0701898 Medical Research Council
• MR/S034919/1 Medical Research Council
• 2017/25/B/NZ5/02783 Polish National Science Centre
• 2858546 European Union's Seventh Framework Programme
• European Union’s Seventh Framework Programme

Improved mucosal immune profiling in active and quiescent colonic inflammatory bowel disease (IBD) is needed to develop therapeutic options for treating and preventing flares. This study therefore aimed to provide a comprehensive mucosal characterization with emphasis on immunological host response of patients with active ulcerative colitis (UC active), UC during remission (UC remission) and active colonic Crohn’s disease (CD active).

Colonic biopsies from 47 study subjects were collected for gene expression and pathway analyses using the NanoString host-response panel, including 776 genes and 56 immune-related pathways.

The majority of mucosal gene expression and signaling pathway scores were increased in active IBD (n=27) compared to healthy subjects (n=10). However, both active IBD and UC remission (n=10) demonstrated decreased gene expression and signaling pathway scores related to autophagy, alpha kinase-1 and IL-17 signaling pathways compared to healthy subjects. Further, UC remission was characterized by decreased scores of several signaling pathways linked to homeostasis along with increased mononuclear cell migration pathway score as compared to healthy subjects. No major differences in the colonic mucosal gene expression between CD active (n=7) and UC (n=20) active were observed.

This study indicates that autophagy, alpha kinase-1 and IL-17 signaling pathways are persistently downregulated in UC irrespective of disease activity. Further, UC patients in remission present a unique mucosal environment, potentially preventing patients from reaching and sustaining true homeostasis. These findings may enable better comprehension of the remitting and relapsing pattern of colonic IBD and guide future treatment and prevention of flares.

• Swedish Foundation For Strategic Research
• Julins Foundation
• Bengt Ihre Fellowship
• Wilhelm and Martina Lundgren foundation
• the Mag-tarmfonden
• Svenska Läkarsällskapet
• the Calder foundation

• National Natural Science Foundation of China

• Colon Cancer
• DNA Mismatch Repair
• Gut Microbiota
• Inflammation

• Animals
• Carcinogenesis/genetics
• Colonic Neoplasms/genetics
• Colorectal Neoplasms, Hereditary Nonpolyposis/genetics
• Colorectal Neoplasms, Hereditary Nonpolyposis/metabolism
• Colorectal Neoplasms, Hereditary Nonpolyposis/pathology
• DNA Mismatch Repair
• Humans
• Inflammation
• Mice
• Microbiota
• Receptor, Transforming Growth Factor-beta Type II/genetics
• Receptor, Transforming Growth Factor-beta Type II/metabolism

• P30 CA013330 NCI NIH HHS
• R01 CA222358 NCI NIH HHS
• R01 CA248536 NCI NIH HHS

• antigen presentation
• intestinal epithelium
• major histocompatibility class II
• organoids
• polyinosinic:polycytidylic acid Poly(I:C)
• tofacitinib
• tumor necrosis factor (TNF)
• ulcerative colitis

In recent years it has become apparent that the epithelium is highly involved in inflammatory bowel disease (IBD) pathophysiology. The majority of gene expression studies of IBD are generated from heterogeneous biopsies, providing no distinction between immune cells, the epithelium and other mucosal cells. By using laser capture microdissection (LCM) coupled with RNA sequencing, we aimed to characterize the expressional changes of the isolated colonic epithelial monolayer from ulcerative colitis (UC) and Crohn’s disease (CD) patients compared to healthy controls (HC). The analysis identified 3706 genes as differentially expressed between active IBD epithelium and HC. Weighted gene co-expression network analysis was used to stratify genes into modules, which were subsequently characterized using enrichment analysis. Our data show a distinct upregulation of the antigen presentation machinery during inflammation, including major histocompatibility complex class II molecules (e.g. HLA-DPA1, HLA-DPB1, HLA-DRA) and key transcription factors/activators (STAT1, IRF1, CIITA). We also see an epithelial downregulation of retinoic acid-responsive nuclear receptors (RARA, RARB, RXRA), but upregulation of retinoid-metabolizing enzymes (RDH11, ALDH1A2, ALDH1A3), which together suggest a perturbation of epithelial vitamin A signaling during active IBD. Lastly, we identified a cluster of stress-related genes, including activator protein 1 components JUNB and ATF3, as significantly upregulated in active UC but not in CD, revealing an interesting aspect of IBD heterogeneity. The results represent a unique resource for enhanced understanding of epithelial involvement in IBD inflammation and is a valuable tool for further studies on these processes.

• Colitis, Ulcerative/metabolism
• Colon/pathology
• Crohn Disease/pathology
• Gene Expression
• Humans
• Inflammation/pathology
• Inflammatory Bowel Diseases/metabolism
• Intestinal Mucosa/metabolism

• Norges Forskningsråd
• the Liaison Committee between the Central Norway Regional Health Authority and NTNU
• The joint research committee (FFU) between St. Olav University Hospital and NTNU

Crohn’s disease (CD) is a chronic intestinal inflammation considered to be a major entity of inflammatory bowel diseases (IBDs), affecting different segments of the whole gastrointestinal tract. Peripheral serotonin (5-HT), a bioactive amine predominantly produced by gut enterochromaffin cells (ECs), is crucial in gastrointestinal functions, including motility, sensitivity, secretion, and the inflammatory response. These actions are mediated by a large family of serotonin receptors and specialized serotonin transporter (SERT) located on a variety of cell types in the gut. Several studies indicate that intestinal 5-HT signaling is altered in patients with inflammatory bowel disease. Paraformaldehyde-fixed intestinal tissues, obtained from fifteen patients with Crohn’s disease were analyzed by immunostaining for serotonin, Langerin/CD207, and alpha-Smooth Muscle Actin (α-SMA). As controls, unaffected (normal) intestinal specimens of seven individuals were investigated. This study aimed to show the expression of serotonin in dendritic cells (DCs) and myofibroblast which have been characterized with Langerin/CD207 and α-SMA, respectively; furthermore, for the first time, we have found the presence of serotonin in goblet cells. Our results show the correlation between different types of intestinal cells in the maintenance of the inflammatory state in CD linked to the recall of myofibroblasts.

Studies of the mucosal transcriptomic landscape have given new insight into the pathogenesis of inflammatory bowel disease (IBD). Recently, the predictive biomarker potential of gene expression signatures has been explored. To further investigate the mucosal gene expression in IBD, we recruited a cohort of treatment naïve patients and compared them to both symptomatic and healthy controls.

Altogether, 323 subjects were included: Crohn’s disease (N = 75), ulcerative colitis (N = 87) and IBD unclassified (N = 3). Additionally, there were two control groups: symptomatic controls (N = 131) and healthy controls (N = 27). Mucosal biopsies were collected during ileocolonoscopy and gene expression in inflamed and non-inflamed mucosa was explored. Gene expression profiling was performed using Agilent G3 Human Gene Expression 860K v3 One-Color microarray. We recorded information about treatment escalation to anti-TNF agents or surgery, and anti-TNF response, to explore predictive opportunities of the mucosal transcriptome.

Gene expression profiles in symptomatic controls in whom IBD had been excluded resembled that of IBD patients and diverged from that of healthy controls. In non-inflamed Crohn’s disease and ulcerative colitis, gene set enrichment analysis revealed dysregulation of pathways involved in basic cellular biological processes. Mitochondria-associated pathways were dysregulated both in non-inflamed and inflamed Crohn’s disease and ulcerative colitis (>2.6 normalized enrichment scores <−1.8). Gene expression signatures of Crohn’s disease and ulcerative colitis did not predict time for treatment escalation (p = 0.175). No significant association was found between gene expression signatures and anti-TNF response.

Non-inflamed samples are probably superior to inflamed samples when exploring gene expression signatures in IBD and might reveal underlying mechanisms central for disease initiation. The gene expression signatures of the control groups were related to if they were symptomatic or not, which may have important implications for future study designs.

• IBD-CHARACTER

Recent studies reported the responses of ustekinumab (UST) for the treatment of Crohn's disease (CD) differ among patients, while the cause was unrevealed. The study aimed to develop a prediction model based on the gene transcription profiling of patients with CD in response to UST.

The GSE112366 dataset, which contains 86 CD and 26 normal samples, was downloaded for analysis. Differentially expressed genes (DEGs) were identified first. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were administered. Least absolute shrinkage and selection operator regression analysis was performed to build a model for UST response prediction.

A total of 122 DEGs were identified. GO and KEGG analyses revealed that immune response pathways are significantly enriched in patients with CD. A multivariate logistic regression equation that comprises four genes (HSD3B1, MUC4, CF1, and CCL11) for UST response prediction was built. The area under the receiver operator characteristic curve for patients in training set and testing set were 0.746 and 0.734, respectively.

This study is the first to build a gene expression prediction model for UST response in patients with CD and provides valuable data sources for further studies.

• Crohn's disease
• LASSO regression
• machine learning model
• ustekinumab

• Alternative splicing
• Crohn’s disease
• Post-transcriptional regulation

• environmental factors
• incidence
• industrialization
• inflammatory bowel disease
• urbanization

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.

• biomarkers
• epigenetics
• obstructive sleep apnea
• systematic review

• Broad Foundation
• Kenneth Rainin Foundation
• Consejo Nacional de Investigaciones Científicas y Técnicas
• Agencia Nacional de Promoción Científica y Tecnológica

Treatment of inflammatory bowel disease (IBD) is challenging, with a series of available drugs each helping only a fraction of patients. Patients may face time-consuming drug trials while the disease is active, thus there is an unmet need for biomarkers and assays to predict drug effect. It is well known that the intestinal epithelium is an important factor in disease pathogenesis, exhibiting physical, biochemical and immunologic driven barrier dysfunctions. One promising test system to study effects of existing or emerging IBD treatments targeting intestinal epithelial cells (IECs) is intestinal organoids (“mini-guts”). However, the fact that healthy intestinal epithelium is in a physiologically hypoxic state has largely been neglected, and studies with intestinal organoids are mainly performed at oxygen concentration of 20%. We hypothesized that lowering the incubator oxygen level from 20% to 2% would recapitulate better the in vivo physiological environment of colonic epithelial cells and enhance the translational value of intestinal organoids as a drug testing platform. In the present study we examine the effects of the key IBD cytokines and drug targets TNF/IL17 on human colonic organoids (colonoids) under atmospheric (20%) or reduced (2%) O₂. We show that colonoids derived from both healthy controls and IBD-patients are viable and responsive to IBD-relevant cytokines at 2% oxygen. Because chemokine release is one of the important immunoregulatory traits of the epithelium that may be fine-tuned by IBD-drugs, we also examined chemokine expression and release at different oxygen concentrations. We show that chemokine responses to TNF/IL17 in organoids display similarities to inflamed epithelium in IBD-patients. However, inflammation-associated genes induced by TNF/IL17 were attenuated at low oxygen concentration. We detected substantial oxygen-dependent differences in gene expression in untreated as well as TNF/IL17 treated colonoids in all donors. Further, for some of the IBD-relevant cytokines differences between colonoids from healthy controls and IBD patients were more pronounced in 2% O₂ than 20% O₂. Our results strongly indicate that an oxygen concentration similar to the in vivo epithelial cell environment is of essence in experimental pharmacology.

• cytokines
• epithelium
• inflammatory bowel diseases
• interleukin 17
• organoids
• oxygen
• tumor necrosis factor

• Chemokine Receptors
• Dopaminergic Regulation
• G Protein–Coupled Receptors Heteromers
• Gut Tropism
• Inflammatory Bowel Diseases
• Inflammatory Colitis
• T Cell Migration

• Amino Acid Sequence
• Animals
• CD4-Positive T-Lymphocytes/immunology
• Cell Movement
• Cell Proliferation
• Colitis/immunology
• Colitis/pathology
• Gastrointestinal Tract/immunology
• Gastrointestinal Tract/pathology
• Humans
• Inflammation/immunology
• Inflammation/pathology
• Inflammatory Bowel Diseases/immunology
• Inflammatory Bowel Diseases/pathology
• Integrin beta1/metabolism
• Jurkat Cells
• MAP Kinase Signaling System
• Mice, Inbred C57BL
• Models, Biological
• Peptides/chemistry
• Phosphorylation
• Protein Multimerization
• Receptors, CCR/deficiency
• Receptors, CCR/metabolism
• Receptors, Dopamine D5/deficiency
• Receptors, Dopamine D5/metabolism
• Signal Transduction
• Tropism
• Mice

• agonal factors
• brain cell types
• gene co-expression
• gene expression
• post-mortem brain studies

• IFN-γ
• disease modeling
• iPSC-derived human intestinal organoids

• Apoptosis/drug effects
• Apoptosis/genetics
• Cell Line
• Claudins/genetics
• Claudins/metabolism
• Gene Expression Profiling/methods
• Humans
• Indoleamine-Pyrrole 2,3,-Dioxygenase/genetics
• Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism
• Induced Pluripotent Stem Cells/drug effects
• Induced Pluripotent Stem Cells/metabolism
• Interferon-gamma/pharmacology
• Intestinal Mucosa/cytology
• Intestinal Mucosa/drug effects
• Intestinal Mucosa/metabolism
• Models, Biological
• Oligonucleotide Array Sequence Analysis/methods
• Organoids/cytology
• Organoids/drug effects
• Organoids/metabolism

• P01 DK046763 NIDDK NIH HHS

• Crohn’s disease
• inflammatory bowel diseases
• serotonin
• serotonin reuptake transporter
• ulcerative colitis

• Human intestinal organoids
• ISG15
• innate immunity

Diet plays a substantial role in the pathogenesis and management of ulcerative colitis (UC), and epidemiologic studies indicate an association between red meat intake and increased risk of UC development. Therefore, we evaluated the effect of a red meat diet on dextran sulfate sodium (DSS)-induced colitis in pigs. Weaned pigs (42 days old) were fed either a control diet or a diet substituted with 15% minced, cooked and dried beef from experimental day 0 to 14. From day 14 to 18, half of the pigs on each diet received a daily oral dose of DSS. Dietary red meat aggravated the severity of colitis based on clinical signs of disease (negative performance score) and histopathological parameters in the colon such as erosion/ulceration and the overall inflammation score but no negative effects were observed on systemic health or small intestinal permeability. Importantly, dietary meat also caused a potential beneficial reduction in the colonic expression of the pro-inflammatory cytokines IL-17A and IL-6, the pro-inflammatory enzyme PTGS2 and in the chemokine IL-8. The present study emphasizes the potential of diet to modulate mucosal inflammation and that a red meat diet might be a risk factor for the development of inflammatory bowel disease.

• dextran sulfate sodium
• diet
• gene expression
• histology
• inflammation
• inflammatory bowel disease
• porcine

• Biological agent
• Crohn’s diseases
• Inflammatory bowel disease
• Ulcerative colitis

• Biological Products/therapeutic use
• Gastrointestinal Microbiome
• Humans
• Inflammatory Bowel Diseases/drug therapy
• Inflammatory Bowel Diseases/microbiology
• Interleukin Inhibitors/therapeutic use

Inflammatory bowel disease is known to be associated with a genetic predisposition involving multiple genes; however, there is growing evidence that abnormal interactions with environmental factors, particularly epigenetic factors, can also significantly contribute to the development of inflammatory bowel disease (IBD). Although many genome-wide association studies have been performed to identify the genetic changes underlying the pathogenesis of Crohn’s disease, the role of epigenetic alterations based on molecular complications arising from Crohn’s disease (CD) is poorly understood. We employed an unbiased approach to define DNA methylation alterations in colonoscopy samples from patients with CD using the HumanMethylation450K BeadChip platform. Technical and functional validation was performed by methylation-specific PCR (MSP) and bisulfite sequencing of a validation set of 207 patients with CD samples. Immunohistochemistry (IHC) analysis was performed in the representative sample sets. DNA methylation profile in CD revealed that 135 probes (24 hypermethylated and 111 hypomethylated probes) were differentially methylated. We validated the methylation levels of 19 genes that showed hypermethylation in patients with CD compared with normal controls. We uniquely identified that the fragile histidine triad (FHIT) gene was hypermethylated in a disease-specific manner and its protein level was downregulated in patients with CD. Pathway analysis of the hypermethylated candidates further suggested putative molecular interactions relevant to IBD pathology. Our data provide information on the biological and clinical implications of DNA hypermethylated genes in CD, identifying FHIT methylation as a promising new biomarker for CD. Further study of the role of FHIT in IBD pathogenesis may lead to the development of new therapeutic targets.

• Crohn’s disease (CD), hypermethylation
• DNA methylation profile
• gene network

• Golimumab
• drug monitoring
• mucosal healing
• trough levels