The genetics of Crohn's disease and ulcerative colitis--status quo and beyond

Mendelian randomization study of circulating leukocytes counts reveals causal associations with inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic recurrent IBD, whose cause involves the interaction between genetic and environmental factors. Although there is a recognized link between immune response and IBD, the causal relationship between circulating immune cell counts and IBD remains controversial. This study aimed to elucidate the causal relationship between genetically predicted circulating immune cell counts and IBD. We conducted a bidirectional 2-sample Mendelian randomization (MR) study using aggregated statistics from genome-wide association studies. The causal relationship between 5 circulating leukocytes cells (monocytes, lymphocytes, eosinophils, basophils and neutrophils) counts and IBD, including ulcerative colitis (UC) and Crohn disease (CD) was analyzed. Horizontal pleiotropy test and heterogeneity test were used to ensure the stability of the results. Our findings indicated that monocytes, lymphocytes, eosinophils, and basophils count were not significantly associated with IBD, however, elevated circulating neutrophils count was significantly associated with higher risk of IBD [odds ratio (OR) = 1.0017; 95% confidence interval (CI) = 1.0004-1.003; P = .009] and UC [OR = 2.465; 95% CI = 1.236-4.916; P = .01]. In addition, we also found that IBD [OR: 12.07; 95% CI = 1.909-76.316; P = .008] and CD [OR = 1.014; 95% CI = 1.004-1.023; P = .005] were significantly associated with higher circulating neutrophils count in reverse MR. This MR study provides genetic evidence for the causal relationship between the genetically predicted increase in circulating neutrophils count and the risk of IBD (UC and CD). This finding stresses the need for further exploring physiological functions of neutrophils in order to develop effective strategies against IBD.

Zatariamultiflora hydroalcoholic extract: A triple-blind randomized controlled trial on immune genes, inflammation, and ulcerative colitis symptoms

ETHNOPHARMACOLOGICAL RELEVANCE

Zataria multiflora Boiss. (Shirazi thyme) is traditionally used for digestive disorders and inflammatory conditions. Despite its known anti-inflammatory, immunomodulatory, and antioxidant properties, there is limited clinical evidence on its efficacy for ulcerative colitis (UC).

AIM OF THE STUDY

To evaluate the effectiveness of Zataria multiflora Boiss. (Z. multiflora) extract in alleviating UC symptoms, reducing inflammatory markers, and modulating immune-related gene expression.

MATERIALS AND METHODS

In a multicenter, randomized, placebo-controlled, triple-blind trial in Iran, 92 participants received Z. multiflora extract (6 mg/kg/day) or a placebo for two months. Inflammatory markers and gene expression were analyzed from blood samples. Disease activity was assessed using the Partial Mayo Score (p-Mayo) and the Gastrointestinal Symptom Rating Scale (GSRS). Data were analyzed with SPSS software.

RESULTS

The Z. multiflora group showed significant reductions in C-reactive protein (CRP) (p < 0.001), Interleukin-17 (IL-17) (p = 0.001), Interferon-gamma (IFN-γ) (p = 0.002), Nuclear Factor kappa B (NF-κB) (p = 0.002), T-box Transcription Factor T-bet (T-bet) (p = 0.006), and Retinoic Acid-Related Orphan Receptor gamma t (ROR-γt) (p < 0.001). No significant changes were observed in Erythrocyte Sedimentation Rate (ESR) (p = 0.25), GATA Binding Protein 3 (GATA3) (p = 0.09), and Forkhead Box P3 (FOXP3) (p = 0.17). Symptoms such as heartburn, acid reflux, bloating, diarrhea, and fecal urgency improved (p < 0.05). The GSRS score improved (p < 0.001), while the p-Mayo score did not show a significant change (p = 0.24).

CONCLUSION

Z. multiflora extract significantly alleviated UC symptoms and reduced inflammatory markers, indicating its potential as a complementary treatment for UC. However, the study was limited by its short intervention period and the absence of biopsy analysis to assess local tissue effects. Further longitudinal studies are required to validate these findings and determine long-term efficacy.

Antibiotic usage within the first year of life has a protective effect against ulcerative colitis in South Korea: A nationwide cohort study

BACKGROUND

Antibiotic usage in early life has been proposed as a risk factor for inflammatory bowel disease, especially Crohn's disease. However, most studies were conducted in Western countries.

AIMS

We evaluated the association between antibiotic usage and the incidence of inflammatory bowel disease in the Asian population.

METHODS

This nationwide population-based retrospective cohort study included 2,941,889 South Korean infants born between 2007 and 2015, using the National Health Insurance Service database. We assessed whether antibiotic use was associated with the incidence of inflammatory bowel disease. Additionally, we conducted sensitivity analyses, considering protopathic bias and dietary variables. The Cox proportional hazards model was used.

RESULTS

Among 2,941,889 infants, 2,566,390 (87 %) used antibiotics within a year after birth. Antibiotic usage within a year, number of antibiotic classes, and cumulative days of usage were shown to decrease the risk of ulcerative colitis. This association was particularly prominent with earlier antibiotic exposure. Penicillin was the only antibiotic class related to the reduced risk. The results were robust after adjusting for dietary variables and considering protopathic effect.

CONCLUSIONS

Antibiotic exposure during the first year of life, particularly at a younger age, is linked to a reduced risk of early-onset ulcerative colitis in South Korea.

Maternal diet in pregnancy and the risk of inflammatory bowel disease in the offspring: a prospective cohort study

BACKGROUND

Diet has been hypothesized as a risk factor for the development of inflammatory bowel disease (IBD).

OBJECTIVE

The objective of this study was to explore associations between maternal diet diversity and quality in pregnancy and the offspring's risk of IBD.

METHODS

We used data from a nationwide cohort study on 85,129 Norwegian children followed from birth (1999-2009) with information on maternal diet in pregnancy from validated food frequency questionnaires. Hazard ratios (HRs) for IBD, Crohn disease (CD), and ulcerative colitis (UC) by maternal diet diversity, quality, and intake amounts of individual food groups were adjusted for maternal BMI, parental IBD, and sociodemographic factors. Sensitivity analyses were adjusted for the child's early-life diet quality and antibiotic treatment. Dietary exposures were classified into tertiles, comparing low (reference) with medium, and high levels.

RESULTS

During a mean follow-up time of 16.1 y (1,367,837 person-years of follow-up), 268 children developed IBD (CD, n = 119; UC, n = 76; IBD-unclassified, n = 73). High compared with low diet diversity in pregnancy was associated with a lower risk of UC in the offspring [adjusted HR (aHR) 0.46, 95% confidence interval: 0.25, 0.87], with consistent findings after further adjustment for the child's early-life diet quality and antibiotic treatment. High compared with low diet diversity in pregnancy yielded aHRs of 0.81 for CD (0.51-1.28) and 0.75 for any IBD (0.55-1.02) in the offspring. A high compared with low diet quality in pregnancy or intakes of specific food groups were not associated with the offspring's risk of IBD or its subtypes.

CONCLUSIONS

Our findings suggest that a higher maternal diet diversity in pregnancy may be associated with a lower risk of UC in the offspring.

Cell-type-resolved chromatin accessibility in the human intestine identifies complex regulatory programs and clarifies genetic associations in Crohn's disease

Crohn's disease (CD) is a complex inflammatory bowel disease resulting from an interplay of genetic, microbial, and environmental factors. Cell-type-specific contributions to CD etiology and genetic risk are incompletely understood. Here we built a comprehensive atlas of cell-type- resolved chromatin accessibility comprising 557,310 candidate cis-regulatory elements (cCREs) in terminal ileum and ascending colon from patients with active and inactive CD and healthy controls. Using this atlas, we identified cell-type-, anatomic location-, and context-specific cCREs and characterized the regulatory programs underlying inflammatory responses in the intestinal mucosa of CD patients. Genetic variants that disrupt binding motifs of cell-type-specific transcription factors significantly affected chromatin accessibility in specific mucosal cell types. We found that CD heritability is primarily enriched in immune cell types. However, using fine- mapped non-coding CD variants we identified 29 variants located within cCREs several of which were accessible in epithelial and stromal cells implicating cell types from additional lineages in mediating CD risk in some loci. Our atlas provides a comprehensive resource to study gene regulatory effects in CD and health, and highlights the cellular complexity underlying CD risk.

Farnesol ameliorates DSS-induced IBD by regulating inflammatory cytokines, repairing the intestinal barrier, reversing the gut microbiota imbalance, and influencing fecal metabolome in C57BL/6 mice

The incidence of inflammatory bowel disease (IBD) is rising globally, increasing interest in food ingredients for its prevention and control. This study evaluated the effect of farnesol (FAR), a key component of pomelo flower volatile oil, on dextran sodium sulfate (DSS)-induced colitis in C57BL/6 mice. FAR significantly alleviated DSS-induced colitis and secondary liver injury, as shown by improved body weight, DAI, colon length, and pathology, as well as liver function and blood lipid indices. The mechanism involves FAR-mediated regulation of inflammatory cytokines, increased expression of tight junction protein genes, and decreased expression of lipid metabolism-related proteins. FAR also enhanced gut microbiota diversity, balancing harmful and probiotic bacteria. Fecal metabolome analysis indicated FAR's role in reversing metabolic disturbances related to inflammation and liver lipid metabolism. These findings support developing functional foods for IBD treatment using pomelo flower volatile oil.

Polygenic risk score for ulcerative colitis predicts immune checkpoint inhibitor-mediated colitis

Immune checkpoint inhibitor-mediated colitis (IMC) is a common adverse event of treatment with immune checkpoint inhibitors (ICI). We hypothesize that genetic susceptibility to Crohn's disease (CD) and ulcerative colitis (UC) predisposes to IMC. In this study, we first develop a polygenic risk scores for CD (PRSCD) and UC (PRSUC) in cancer-free individuals and then test these PRSs on IMC in a cohort of 1316 patients with ICI-treated non-small cell lung cancer and perform a replication in 873 ICI-treated pan-cancer patients. In a meta-analysis, the PRSUC predicts all-grade IMC (ORmeta=1.35 per standard deviation [SD], 95% CI = 1.12-1.64, P = 2×10-03) and severe IMC (ORmeta=1.49 per SD, 95% CI = 1.18-1.88, P = 9×10-04). PRSCD is not associated with IMC. Furthermore, PRSUC predicts severe IMC among patients treated with combination ICIs (ORmeta=2.20 per SD, 95% CI = 1.07-4.53, P = 0.03). Overall, PRSUC can identify patients receiving ICI at risk of developing IMC and may be useful to monitor patients and improve patient outcomes.

A family with ulcerative colitis maps to 7p21.1 and comprises a region with regulatory activity for the aryl hydrocarbon receptor gene

We have mapped a locus on chromosome 7p22.3-7p15.3 spanning a 22.4 Mb region for ulcerative colitis (UC) by whole genome linkage analyses of a large Danish family. The family represent three generations with UC segregating as an autosomal dominant trait with variable expressivity. The whole-genome scan resulted in a logarithm of odds score (LOD score) of Z = 3.31, and a whole genome sequencing (WGS) of two affected excluded disease-causing mutations in the protein coding genes. Two rare heterozygote variants, rs182281985:G>A and rs541426369:G>A, both with low allele frequencies (MAF A:0.0001, gnomAD ver3.1.2), were found in clusters of ChiP-seq transcription factors binding sites close to the AHR (aryl hydrocarbon receptor) gene and the UC associated SNP rs1077773:G>A. Testing the two SNPs in a promoter reporter assay for regulatory activity revealed that rs182281985:G>A influenced the AHR promoter. These results suggest a regulatory region that include rs182281985:G>A close to the UC GWAS SNP rs1077773:G>A and further demonstrate evidence that the AHR gene on the 7p-tel region is a candidate susceptible gene for UC.

The Association between Total Protein, Animal Protein, and Animal Protein Sources with Risk of Inflammatory Bowel Diseases: A Systematic Review and Meta-Analysis of Cohort Studies

We aimed to conduct this dose-dependent meta-analysis to examine the relation between total protein, animal protein, and its sources with inflammatory bowel disease (IBD). We searched databases, comprising PubMed/Medline, Web of Science (ISI), Embase, and Google Scholar, for the published studies up to 28 March 2023. Prospective cohort study designs that investigated associations between dietary intake of various animal protein sources and with risk of IBD in the general population were identified. Eleven prospective cohort studies with 4,302,554 participants and 8067 cases were considered eligible. Findings indicated that higher intake of dairy was significantly associated with a lower risk of IBD (relative risk [RR]: 0.81; 95% confidence interval [CI]: 0.72, 0.90), Crohn disease (RR: 0.69; 95% CI: 0.56, 0.86), and ulcerative colitis (RR: 0.84; 95% CI: 0.75, 0.94). There was no association between different sources of animal protein and the risk of IBD. The dose-response analysis suggested that each 100 g/d increment in dietary total meat consumption was associated with a 38% greater risk of IBD. Moreover, a positive linear association was found between total meat intake and risk of IBD (Pnonlinearity = 0.522, Pdose-response = 0.005). Overall, among the dietary sources of protein, the risk of IBD increased only with increasing total meat intake, and the consumption of protein from dairy products was found to be a protective factor against the IBD risk. This trial was registered at PROSPERO as CRD42023397719.

Interplay of broccoli/broccoli sprout bioactives with gut microbiota in reducing inflammation in inflammatory bowel diseases

Inflammatory Bowel Diseases (IBD) are chronic, reoccurring, and debilitating conditions characterized by inflammation in the gastrointestinal tract, some of which can lead to more systemic complications and can include autoimmune dysfunction, a change in the taxonomic and functional structure of microbial communities in the gut, and complicated burdens in a person's daily life. Like many diseases based in chronic inflammation, research on IBD has pointed towards a multifactorial origin involving factors of the person's lifestyle, immune system, associated microbial communities, and environmental conditions. Treatment currently exists only as palliative care, and seeks to disrupt the feedback loop of symptoms by reducing inflammation and allowing as much of a return to homeostasis as possible. Various anti-inflammatory options have been explored, and this review focuses on the use of diet as an alternative means of improving gut health. Specifically, we highlight the connection between the role of sulforaphane from cruciferous vegetables in regulating inflammation and in modifying microbial communities, and to break down the role they play in IBD.

Gut microbiota-derived metabolite trimethylamine N-oxide and biomarkers of inflammation are linked to endothelial and coronary microvascular function in patients with inflammatory bowel disease

BACKGROUND

Inflammatory bowel disease (IBD), which is an umbrella term used for ulcerative colitis (UC) and Crohn's disease (CD), is associated with an increased risk for atherosclerotic cardiovascular disease (CVD). We aimed to investigate the association of local and systemic biomarkers of inflammation and gut microbiota-derived metabolite trimethylamine N-oxide (TMAO) with endothelial and coronary microvascular dysfunction in IBD.

METHODS

A total of 56 patients with IBD (20 with UC and 36 with CD) and 34 age and gender matched controls were included. For all participants, samples were collected to analyze faecal calprotectin, and TMAO concentrations. Ultrasound-based examinations were done to measure flow-mediated vasodilatation (FMD) and coronary flow velocity reserve (CFVR).

RESULTS

Patients with IBD had lower CFVR (2.07 (1.82-2.40)) and FMD (8.7 ± 3.7) as compared to controls (2.30 (2.07-2.74), p = 0.005 and 11.9 ± 6.8, p = 0.03). In patients with IBD, TMAO concentration (r = -0.30, p = 0.03), C-reactive protein (r = -0.29, p = 0.03) and WBC count (r = -0.37, p = 0.006) had a significant negative correlation with CFVR, and TMAO (β = -0.27, 95 % CI: -0.23 to -0.02) and WBC count (β = -0.31, 95 % CI: -0.56 to -0.06) were significant predictors of CFVR after multivariate adjustment. None of the biomarkers of inflammation or TMAO showed significant correlations with FMD. In patients with UC, TMAO showed a significant correlation with both CFVR (r = -0.55, p = 0.01) and FMD (r = -0.60, p = 0.005) while only WBC count had a statistically significant correlation with CFVR (r = -0.49, p = 0.004) in patients with CD.

CONCLUSIONS

Gut microbiota-derived metabolite TMAO and biomarkers of systemic inflammation are associated with measures of endothelial/coronary microvascular dysfunction in patients with IBD.

Association Between Inflammatory Bowel Disease and Both Psoriasis and Psoriatic Arthritis: A Bidirectional 2-Sample Mendelian Randomization Study

Importance

Psoriasis, psoriatic arthritis, and inflammatory bowel disease, ie, Crohn disease and ulcerative colitis, are chronic systemic immune-mediated disorders affecting an increasing proportion of adults and children worldwide. Observational studies have suggested an association between inflammatory bowel disease and psoriasis and vice versa. So far, however, it remains unclear whether and in which direction causal relationships exist.

Objective

To investigate the association between inflammatory bowel disease, particularly Crohn disease and ulcerative colitis, and psoriasis or psoriatic arthritis.

Design, Setting, and Participants

A bidirectional 2-sample mendelian randomization study was conducted using summary statistics from genome-wide association studies including up to 463 372 European individuals. Total and direct effects were derived performing an iterative radial and robust inverse-variance weighted method within the univariable and multivariable mendelian randomization setting, respectively. Causal estimates were verified using a validation inflammatory bowel disease sample, a series of pleiotropy-robust mendelian randomization methods, and sensitivity analyses based on a PhenoScanner search in conjunction with network analysis. Data analysis was performed from April to May 2022.

Main Outcomes and Measures

Inflammatory bowel disease, Crohn disease, ulcerative colitis, psoriasis, and psoriatic arthritis were used as both exposures and outcomes.

Results

The European samples included 12 882 cases of inflammatory bowel disease and 5621 cases of psoriasis. The proportion of women ranged between 48% and 56%. Genetically predicted inflammatory bowel disease was associated with higher risk of psoriasis (pooled odds ratio [OR], 1.10; 95% CI, 1.05-1.15; P < .001) and psoriatic arthritis (pooled OR, 1.10; 95% CI, 1.04-1.18; P = .003). In contrast with ulcerative colitis, the Crohn disease subentity was associated with psoriasis (OR, 1.16; 95% CI, 1.12-1.20; P < .001) and psoriatic arthritis (OR, 1.13; 95% CI, 1.06-1.20; P < .001). Regarding the reverse directions, no notable associations could be found.

Conclusions and Relevance

Findings of this mendelian randomization study support a causal effect between inflammatory bowel disease and psoriasis as well as psoriatic arthritis, but not vice versa. It seems that especially Crohn disease and not ulcerative colitis is responsible for the causal effect of inflammatory bowel disease on both psoriasis outcomes. These findings have implications for the management of inflammatory bowel disease and psoriasis in clinical practice.

A systematic review and functional bioinformatics analysis of genes associated with Crohn's disease identify more than 120 related genes

BACKGROUND

Crohn's disease is one of the two categories of inflammatory bowel diseases that affect the gastrointestinal tract. The heritability estimate has been reported to be 0.75. Several genes linked to Crohn's disease risk have been identified using a plethora of strategies such as linkage-based studies, candidate gene association studies, and lately through genome-wide association studies (GWAS). Nevertheless, to our knowledge, a compendium of all the genes that have been associated with CD is lacking.

METHODS

We conducted functional analyses of a gene set generated from a systematic review where genes potentially related to CD found in the literature were analyzed and classified depending on the genetic evidence reported and putative biological function. For this, we retrieved and analyzed 2496 abstracts comprising 1067 human genes plus 22 publications regarding 133 genes from GWAS Catalog. Then, each gene was curated and categorized according to the type of evidence associated with Crohn's disease.

RESULTS

We identified 126 genes associated with Crohn's disease risk by specific experiments. Additionally, 71 genes were recognized associated through GWAS alone, 18 to treatment response, 41 to disease complications, and 81 to related diseases. Bioinformatic analysis of the 126 genes supports their importance in Crohn's disease and highlights genes associated with specific aspects such as symptoms, drugs, and comorbidities. Importantly, most genes were not included in commercial genetic panels suggesting that Crohn's disease is genetically underdiagnosed.

CONCLUSIONS

We identified a total of 126 genes from PubMed and 71 from GWAS that showed evidence of association to diagnosis, 18 to treatment response, and 41 to disease complications in Crohn's disease. This prioritized gene catalog can be explored at http://victortrevino.bioinformatics.mx/CrohnDisease .

Association between intestinal microbiome and inflammatory bowel disease: insights from bibliometric analysis

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Intestinal microbiota has been increasingly studied in the field of IBD over the last 20 years.

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The gut microbiome, metabolites, and their corresponding host signaling pathways are highly associated with IBD.

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Probiotics may relieve IBD as a complementary therapy.

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The pathogenesis and treatment strategies of IBD need to be further studied.

The gut microbiome is highly linked to inflammatory bowel disease (IBD). A total of 3890 publications related to the two terms from 2000 to 2020 were extracted from the Web of Science Core Collection to study the association from a bibliometric perspective. Publications on this topic have grown rapidly since 2008. The United States and Harvard University are the country and institution with the largest number of publications, respectively. Inflammatory Bowel Diseases is the most productive journal with 211 published articles. The most influential journal in this field is Gut with 13,359 citations. The co-citation analysis of references showed that the IBD-related topics with the highest focus are “gut microbiota,” “metagenomics,” “bacterial community,” “fecal microbiota transplantation,” “probiotics,” and “colitis-associated colorectal cancer.” Keyword cluster and keyword burst analyses showed that “gut microbiota,” “metagenomics,” and “fecal microbiota transplantation” are currently the most researched topics in the field of IBD. The literature in this field is mainly distributed between alterations of the intestinal microbiota, microbial metabolites, and related host signaling pathways. Probiotic treatment also frequently appears in literature. This bibliometric analysis can guide future research and promote the development of the field of gut microbiome and IBD.

Differential prevalence of pathobionts and host gene polymorphisms in chronic inflammatory intestinal diseases: Crohn's disease and intestinal tuberculosis

BACKGROUND AND OBJECTIVES

Crohn's disease (CD) and Intestinal tuberculosis (ITB) are chronic inflammatory ulcero-constrictive intestinal diseases with similar phenotype. Although both are disease models of chronic inflammation and their clinical presentations, imaging, histological and endoscopic findings are very similar, yet their etiologies are diverse. Hence, we aimed to look at differences in the prevalence of pathobionts like adherent-invasive Escherichia coli (AIEC), Listeria monocytogenes, Campylobacter jejuni and Yersinia enterocolitica in CD and ITB as well as their associations with host-associated genetic polymorphisms in genes majorly involved in pathways of microbial handling and immune responses.

METHODS

The study cohort included 142 subjects (69 patients with CD, 32 with ITB and 41 controls). RT- PCR amplification was used to detect the presence of AIEC, L. monocytogenes, C. jejuni, and Y. enterocolitica DNA in colonic mucosal biopsies. Additionally, we tested three SNPs in IRGM (rs13361189, rs10065172, and rs4958847), one SNP in ATG16L1 (rs2241880) and one SNP in TNFRSF1A (rs4149570) by real-time PCR with SYBR green from peripheral blood samples in this cohort.

RESULTS

In patients with CD, AIEC was most frequently present (16/ 69, 23.19%) followed by L. monocytogenes (14/69, 20.29%), C. jejuni (9/69, 13.04%), and Y. enterocolitica (7/69, 10.14%). Among them, L. monocytogenes and Y. enterocolitica were significantly associated with CD (p = 0.02). In addition, we identified all the three SNPs in IRGM (rs13361189, rs10065172, and rs4958847), one SNP in ATG16L1 (rs2241880) and TNFRSF1A (rs4149570) with a significant difference in frequency in patients with CD compared with ITB and controls (p<0.05).

CONCLUSION

Higher prevalence of host gene polymorphisms, as well as the presence of pathobionts, was seen in the colonic mucosa of patients with CD as compared to ITB, although both are disease models of chronic inflammation.

Periodontal and dental health in inflammatory bowel diseases: a systematic review

Introduction: An increased risk of dental caries and periodontal diseases has been reported for inflammatory bowel disease (IBD) patients and are challenging conditions to manage.Areas covered: The authors searched international databases to find all studies assessing dental/periodontal outcomes in patients with IBD and other immune-mediated inflammatory disease (IMID), as well as the association between IMID medications and dental/periodontal status.Expert opinion: IBD are associated with a higher risk of both periodontitis and caries. Some evidence from rheumatoid arthritis suggests that periodontitis may be associated with a lower response to anti-TNF. There is no reliable evidence that IBD patients may be at greater risk of complications during routine dental care. On the basis of current data, guidelines can be proposed for the dental management focusing on the detection and eradication of infectious foci prior to the implementation of immunosuppressants/biologics and modified dental treatment protocol for invasive dental procedures that includes antibiotic prophylaxis.

Copy number variation: Characteristics, evolutionary and pathological aspects

Copy number variants (CNVs) were the subject of extensive research in the past years. They are common features of the human genome that play an important role in evolution, contribute to population diversity, development of certain diseases, and influence host–microbiome interactions. CNVs have found application in the molecular diagnosis of many diseases and in non-invasive prenatal care, but their full potential is only emerging. CNVs are expected to have a tremendous impact on screening, diagnosis, prognosis, and monitoring of several disorders, including cancer and cardiovascular disease. Here, we comprehensively review basic definitions of the term CNV, outline mechanisms and factors involved in CNV formation, and discuss their evolutionary and pathological aspects. We suggest a need for better defined distinguishing criteria and boundaries between known types of CNVs.

Ingestion of Porphyromonas gingivalis exacerbates colitis via intestinal epithelial barrier disruption in mice

OBJECTIVE

This study aimed to evaluate the effects of ingested periodontal pathogens on experimental colitis in mice and to elucidate its underlying mechanisms.

BACKGROUND

Inflammatory bowel disease (IBD) is defined as a chronic intestinal inflammation that results in damage to the gastrointestinal tract. Epidemiological studies have shown an association between IBD and periodontitis. Although a large number of ingested oral bacteria reach gastrointestinal tract constantly, the effect of ingested periodontal pathogens on intestinal inflammation is still unknown.

METHODS

Experimental colitis was induced by inclusion of dextran sodium sulfate solution in drinking water of the mice. Major periodontal pathogens (Porphyromonas gingivalis, Prevotella intermedia, and Fusobacterium nucleatum) were administered orally every day during the experiment. The severity of colitis between the groups was compared. In vitro studies of the intestinal epithelial cell line were conducted to explore the molecular mechanisms by which periodontal pathogens affect the development of colitis.

RESULTS

The oral administration of P. gingivalis significantly increased the severity of colitis when compared to other pathogens in the DSS-induced colitis model. The ingested P. gingivalis disrupted the colonic epithelial barrier by decreasing the expression of tight junction proteins in vivo. In vitro permeability assays using the intestinal epithelial cell line suggested the P. gingivalis-specific epithelial barrier disruption. The possible involvement of gingipains in the exacerbation of colitis was implied by using P. gingivalis lacking gingipains.

CONCLUSION

Porphyromonas gingivalis exacerbates gastrointestinal inflammation by directly interacting with the intestinal epithelial barrier in a susceptible host.

Coumarin Derivatives in Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) is a non-communicable disease characterized by a chronic inflammatory process of the gut and categorized into Crohn’s disease and ulcerative colitis, both currently without definitive pharmacological treatment and cure. The unclear etiology of IBD is a limiting factor for the development of new drugs and explains the high frequency of refractory patients to current drugs, which are also related to various adverse effects, mainly after long-term use. Dissatisfaction with current therapies has promoted an increased interest in new pharmacological approaches using natural products. Coumarins comprise a large class of natural phenolic compounds found in fungi, bacteria, and plants. Coumarin and its derivatives have been reported as antioxidant and anti-inflammatory compounds, potentially useful as complementary therapy of the IBD. These compounds produce protective effects in intestinal inflammation through different mechanisms and signaling pathways, mainly modulating immune and inflammatory responses, and protecting against oxidative stress, a central factor for IBD development. In this review, we described the main coumarin derivatives reported as intestinal anti-inflammatory products and its available pharmacodynamic data that support the protective effects of these products in the acute and subchronic phase of intestinal inflammation.

Meta-analysis of protein intake on the effect of Crohn's disease and ulcerative colitis

BACKGROUND AND PURPOSE

published studies have assessed the effect of protein intake on Crohn's disease (CD) and ulcerative colitis (UC). However, the results were inconsistent. To provide a more precise estimation, a meta-analysis was performed to evaluate the association of protein intake in Crohn's disease and ulcerative colitis.

METHODS

the PubMed, Chinese National Knowledge Infrastructure databases (CNKI), and Wanfang databases were searched to identify relevant studies. The summarized results of the relative risk (RR) with the corresponding 95 % confidence intervals (CI) were calculated using a random effects model.

RESULTS

the final analysis included a total of nine articles. Nine studies reported on protein intake for the risk of UC and five studies reported on protein intake for the risk of CD. Overall, based on current studies, no significant association was found between protein intake and the risk of UC (RR = 1.13, 95 % CI = 0.82-1.55) or CD (RR = 1.18, 95 % CI = 0.51-2.74). A significant change was not found in the stratified analysis by study design and geographic location.

CONCLUSIONS

in conclusion, the present meta-analysis suggested that dietary protein intake did not show a significant effect on the risk of UC or CD.

Toward a porcine in vivo model to analyze the pathogenesis of TLR5-dependent enteropathies

Non-communicable diseases, such as the metabolic syndrome and inflammatory bowel disease, constitute serious public health threats in developed countries. Besides environmental factors, genetic predispositions contribute to the onset and progression of the disease. State-of-the-art mouse models recently highlight the involvement of Toll-like receptor 5 (TLR5)-driven microbiota composition in the development of metabolic disorders. Here, we discuss the causes and consequences of an altered enteric microbiota and provide information on a similar mechanism in another species, the pig. We show for the first time that a single nucleotide polymorphism in the porcine TLR5 gene conferring impaired functionality is associated with changes in the intestinal microbiota in adult sows and neonatal piglets. Changes in the developing adaptive cellular immune response support the concept of TLR5-driven changes of the microbe-host interplay also in the pig. Together, these findings suggest that pigs with impaired TLR-functionality might represent a model for TLR5-driven diseases in humans.

Regulation of IL12B Expression in Human Macrophages by TALEN-mediated Epigenome Editing

Although the exact etiology of inflammatory bowel disease (IBD) remains unclear, exaggerated immune response in genetically predisposed individuals has been reported. Th1 and Th17 cells mediate IBD development. Macrophages produce IL-12 and IL-23 that share p40 subunit encoded by IL12B gene as heteromer partner to drive Th1 and Th17 differentiation. The available animal and human data strongly support the pathogenic role of IL-12/IL-23 in IBD development and suggest that blocking p40 might be the potential strategy for IBD treatment. Furthermore, aberrant alteration of some cytokines expression via epigenetic mechanisms is involved in pathogenesis of IBD. In this study, we analyzed core promoter region of IL12B gene and investigated whether IL12B expression could be regulated through targeted epigenetic modification with gene editing technology. Transcription activator-like effectors (TALEs) are widely used in the field of genome editing and can specifically target DNA sequence in the host genome. We synthesized the TALE DNA-binding domains that target the promoter of human IL12B gene and fused it with the functional catalytic domains of epigenetic enzymes. Transient expression of these engineered enzymes demonstrated that the TALE-DNMT3A targeted the selected IL12B promoter region, induced loci-specific DNA methylation, and down-regulated IL-12B expression in various human cell lines. Collectively, our data suggested that epigenetic editing of IL12B through methylating DNA on its promoter might be developed as a potential therapeutic strategy for IBD treatment.

HLA-A alleles including HLA-A29 affect the composition of the gut microbiome: a potential clue to the pathogenesis of birdshot retinochoroidopathy

Birdshot retinochoroidopathy occurs exclusively in individuals who are HLA-A29 positive. The mechanism to account for this association is unknown. The gut microbiome has been causally implicated in many immune-mediated diseases. We hypothesized that HLA-A29 would affect the composition of the gut microbiome, leading to a dysbiosis and immune-mediated eye disease. Fecal and intestinal biopsy samples were obtained from 107 healthy individuals from Portland, Oregon environs, 10 of whom were HLA-A29 positive, undergoing routine colonoscopy. Bacterial profiling was achieved via 16S rRNA metabarcoding. Publicly available whole meta-genome sequencing data from the Human Microbiome Project (HMP), consisting of 298 healthy controls mostly of US origin, were also interrogated. PERMANOVA and sparse partial least squares discriminant analysis (sPLSDA) demonstrated that subjects who were HLA-A29 positive differed in bacterial species composition (beta diversity) compared to HLA-A29 negative subjects in both the Portland (p = 0.019) and HMP cohorts (p = 0.0002). The Portland and HMP cohorts evidenced different subsets of bacterial species associated with HLA-A29 status, likely due to differences in the metagenomic techniques employed. The functional composition of the HMP cohort did not differ overall (p = 0.14) between HLA-A29 positive and negative subjects, although some distinct pathways such as heparan sulfate biosynthesis showed differences. As we and others have shown for various HLA alleles, the HLA allotype impacts the composition of the microbiome. We hypothesize that HLA-A29 may predispose chorioretinitis via an altered gut microbiome.

Identification of Disease-associated Traits and Clonotypes in the T Cell Receptor Repertoire of Monozygotic Twins Affected by Inflammatory Bowel Diseases

BACKGROUND AND AIMS

Intestinal inflammation in inflammatory bowel diseases [IBD] is thought to be T cell mediated and therefore dependent on the interaction between the T cell receptor [TCR] and human leukocyte antigen [HLA] proteins expressed on antigen presenting cells. The collection of all TCRs in one individual, known as the TCR repertoire, is characterised by enormous diversity and inter-individual variability. It was shown that healthy monozygotic [MZ] twins are more similar in their TCR repertoire than unrelated individuals. Therefore MZ twins, concordant or discordant for IBD, may be useful to identify disease-related and non-genetic factors in the TCR repertoire which could potentially be used as disease biomarkers.

METHODS

Employing unique molecular barcoding that can distinguish between polymerase chain reaction [PCR] artefacts and true sequence variation, we performed deep TCRα and TCRβ repertoire profiling of the peripheral blood of 28 MZ twin pairs from Denmark and Germany, 24 of whom were discordant and four concordant for IBD.

RESULTS

We observed disease- and smoking-associated traits such as sharing, diversity and abundance of specific clonotypes in the TCR repertoire of IBD patients, and particularly in patients with active disease, compared with their healthy twins.

CONCLUSIONS

Our findings identified TCR repertoire features specific for smokers and IBD patients, particularly when signs of disease activity were present. These findings are a first step towards the application of TCR repertoire analyses as a valuable tool to characterise inflammatory bowel diseases and to identify potential biomarkers and true disease causes.

Pilot study of cytokine changes evaluation after fecal microbiota transplantation in patients with ulcerative colitis

AIMS

To evaluate the changes of serum cytokines levels after fecal microbiota transplantation (FMT) in patients with active ulcerative colitis (UC) and the correlation with UC disease activity.

METHODS

Patients with active UC who meet the inclusion and exclusion criteria were recruited, and received FMT from a single donor for three times with an interval of 2-3 months. Serum samples were collected before every FMT. Clinical responses to FMT were assessed according to the criteria of Mayo score. 41 serum cytokines, C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) were quantitatively detected. Changes in serum cytokines levels after FMT and their correlation with CRP, ESR and Mayo scores were investigated.

RESULTS

16 active UC patients were enrolled, and 14(87.5%) patients achieved clinical response to FMT. Compared with those before FMT, serum concentrations of IL-1Ra, IL-6, IP-10 and ENA-78 decreased significantly after the second FMT (P < 0.05), and serum concentrations of MEC, VCAM-1 and G-CSF decreased significantly after both the first and second FMT (P < 0.05). Serum levels of IL-6, IL-1Ra and VCAM-1 were all significantly positively correlated with CRP and ESR. Serum level of IP-10 was significantly positively correlated with CRP, ESR and Mayo score. Serum level of G-CSF was significantly positively correlated with Mayo score.

CONCLUSIONS

FMT may play a therapeutic role partly through modulating the host immune response. IL-6, IL-1Ra, IP-10, VCAM-1 and G-CSF may be biomarkers to evaluate the effect of FMT on UC.

Inflammatory bowel disease - one entity with many molecular faces

Inflammatory bowel disease (IBD) is a heterogenous group of chronic inflammations in the gastrointestinal tract, which traditionally consists of two types: Crohn’s disease and ulcerative colitis. They differ when it comes to clinical, endoscopic, and histopathological changes. The exact aetiology of IBD has not been fully comprehended, but what is known so far is that the aetiopathogenesis of the disease is compound. Many articles have been written on the cellular/molecular background of IBD. Based on various molecular pathways, new forms of the disease have been discovered, including very early-onset IBD (VEO-IBD) or IBD coexisting with primary sclerosing cholangitis. The aim of this article is to present the molecular mechanisms leading to IBD, focusing on new forms of this disorder.

Active matrix metalloproteinase-8 and periodontal bacteria-interlink between periodontitis and inflammatory bowel disease?

BACKGROUND

The aim of this study was the investigation of concentration and prevalence of selected periodontal pathogenic bacteria and concentration of active matrix metalloproteinase-8 (aMMP-8) within a group of patients with inflammatory bowel diseases (IBD) and to compare the results with a group of healthy control subjects (HC).

METHODS

Fifty-nine IBD patients with Crohn`s disease (CD, n = 30) or ulcerative colitis (UC, n = 29) and 59 HC were included in this cross-sectional study. Based on periodontal probing depth (PD) and clinical attachment level (CAL), periodontitis was classified as healthy/mild, moderate, or severe. aMMP-8 was analyzed from gingival crevicular fluid using enzyme linked immunosorbent assay. Eleven selected periodontal pathogenic bacteria were analyzed in subgingival plaque samples using polymerase chain reaction.

RESULTS

IBD patients showed higher CAL (P < 0.01), more severe periodontitis (P = 0.04), gingival bleeding (P < 0.01) and aMMP-8 concentration (P < 0.01) than HC. Only in CD, increasing severity of periodontitis was associated with an increase in aMMP-8 concentration (P = 0.02). The prevalences of Eubacterium nodatum and Eikenella corrodens were significantly lower in IBD compared to HC (P = 0.01). Additionally, the prevalence of Eikenella corrodens was significantly higher in CD compared to the UC group (P = 0.04). Further statistically significant differences in selected bacteria between IBD and HC or CD and UC groups could not be found (P > 0.05).

CONCLUSIONS

The results reveal changes in host immune response of IBD patients in terms of aMMP-8. Only in CD increasing aMMP-8 was associated with severity of periodontal disease. The role of periodontal pathogenic bacteria in the interrelationship between IBD and periodontitis remains unclear.

Mannose-binding lectin (MBL) in adult patients with inflammatory bowel disease

Inflammatory bowel disease (IBD) refers to disorders associated with progressive inflammatory processes in the gastrointestinal system. IBD consists of two major forms, Crohn's disease (CD), and ulcerative colitis (UC). IBD became a global disease in the 21^st century. Its pathogenesis is still not fully understood. Mannose-binding lectin (MBL) is a pattern-recognising molecule, involved in anti-microbial and anti-cancer immunity. It is able to opsonize microorganisms and abnormal host cells, and to initiate complement activation. The aim of this study was to investigate possible involvement of MBL in inflammatory bowel disease in adults. Forty persons diagnosed with CD and 28 with ulcerative colitis were recruited. The control group consisted of 136 healthy persons. Single nucleotide polymorphisms of the MBL2 gene (localised to both promoter and exon 1) were determined as were serum MBL concentrations. The exon 1 variant alleles and MBL deficiency-associated genotypes were more frequent among patients compared with controls, although this difference was not statistically significant. No differences of MBL levels were found between the major groups. However in MBL2 A/A homozygous IBD patients, the median was significantly higher than in corresponding healthy subjects. That was particularly evident in the case of active Crohn's disease (1493 ng/ml vs. 800 ng/ml, p = 0.021). It may suggest that MBL and MBL-dependent complement activation contributes to excessive inflammation and its adverse effects in the course of CD. It cannot also be excluded that high MBL activity constitutes in some cases part of a multifactorial network conducing to development of CD.

Association of Psoriasis With Inflammatory Bowel Disease: A Systematic Review and Meta-analysis

Importance

Patients with psoriasis may experience comorbidities involving cardiovascular diseases, chronic kidney disease, uveitis, psychiatric disturbances, and metabolic syndrome. However, the association between psoriasis and inflammatory bowel disease (IBD) has been largely unclear.

Objective

To investigate the association of psoriasis with IBD.

Data Sources

For this systematic review and meta-analysis, MEDLINE, Embase, and the Cochrane Central Register of Controlled Trials were searched for relevant studies from inception to January 17, 2018.

Study Selection

Case-control, cross-sectional, or cohort studies that examined either the odds or risk of IBD in patients with psoriasis were included. No geographic or language limitations were used in the search.

Data Extraction and Synthesis

The PRISMA and MOOSE guidelines were followed for data extraction. The Newcastle-Ottawa Scale was used to evaluate the risk of bias of included studies. Crohn disease and ulcerative colitis were analyzed separately and random-effects model meta-analysis was conducted. A subgroup analysis was performed on psoriatic arthritis.

Main Outcomes and Measures

The risk and odds of IBD, Crohn disease, and ulcerative colitis in patients with psoriasis.

Results

A total of 5 case-control or cross-sectional studies and 4 cohort studies with 7 794 087 study participants were included. Significant associations were found between psoriasis and Crohn disease (odds ratio, 1.70; 95% CI, 1.20-2.40) and between psoriasis and ulcerative colitis (odds ratio, 1.75; 95% CI, 1.49-2.05). Patients with psoriasis had an increased risk of Crohn disease (risk ratio, 2.53; 95% CI, 1.65-3.89) and ulcerative colitis (risk ratio, 1.71; 95% CI, 1.55-1.89).

Conclusions and Relevance

These findings suggest that psoriasis is significantly associated with IBD. Gastroenterology consultation may be indicated when patients with psoriasis present with bowel symptoms.

Association of Hidradenitis Suppurativa With Inflammatory Bowel Disease: A Systematic Review and Meta-analysis

Importance

Hidradenitis suppurativa (HS) and inflammatory bowel disease (IBD) are inflammatory diseases that share common genetic susceptibility and immunologic features. However, the link between HS and IBD has been largely unclear.

Objective

To conduct a meta-analysis to investigate the association between HS and IBD.

Data Sources

A search of the MEDLINE, Cochrane Central Register of Controlled Trials, and Embase databases yielded 397 relevant studies from inception to June 10, 2018. Two additional studies were supplied by one of the investigators.

Study Selection

Case-control, cross-sectional, or cohort studies that examined the odds or risk of IBD in patients with HS were included. No geographic or language limitations were imposed.

Data Extraction and Synthesis

The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed. The Newcastle-Ottawa Scale was used to assess the risk of bias of included studies. Crohn disease and ulcerative colitis were analyzed separately, and a random-effects model meta-analysis was conducted.

Main Outcomes and Measures

The odds ratios (ORs) and hazard ratios (HRs) of IBD, Crohn disease, and ulcerative colitis in association with HS.

Results

Five case-control studies, 2 cross-sectional studies, and 1 cohort study with a total of 93 601 unique participants were included. The meta-analysis of case-control and cross-sectional studies showed significant associations of HS with Crohn disease (pooled OR, 2.12; 95% CI, 1.46-3.08) and ulcerative colitis (pooled OR, 1.51; 95% CI, 1.25-1.82). Two case-control studies found significant association of HS with IBD (ORs, 2.16 [95% CI, 1.40-3.34] and 10.00 [95% CI, 1.94-51.50]). One cohort study found an increased risk of IBD in patients with HS (HR, 5.6; 95% CI not reported; P < .002).

Conclusions and Relevance

The evidence to date supports an association of HS with IBD. These results suggest that consultation with gastroenterologists should be sought when patients with HS present with recurrent abdominal pain, chronic diarrhea, bloody stool, and body weight loss.

Swedish Inflammatory Bowel Disease Register (SWIBREG) - a nationwide quality register

Background: Inflammatory bowel disease (IBD) is a chronic, inflammatory relapsing disease with increasing incidence. IBD research and long-term follow-up of patients have, however, been hampered by lack of detailed data on disease phenotype, patient-reported outcome measures, Physician Global Assessment, disease activity, and hospital-administered drugs. Aim: To review the Swedish IBD quality register (SWIBREG). Methods: Review of SWIBREG including questionnaire data from users and patients. Results: SWIBREG was launched in 2005, and as of April 2019, contains 46,400 patients with IBD (Crohn's disease: n = 15,705, ulcerative colitis: n = 21,540, IBD unclassified and other colitis (including e.g., microscopic colitis): n = 9155). Of these IBD patients, 7778 had been diagnosed in childhood (16.8%). Earlier research has shown that combining SWIBREG and the Swedish National Patient Register (NPR) yields a positive predictive value of 100% (95%CI = 95-100%) for having a diagnosis of IBD. Moreover, out of all patients in the NPR with a diagnosis of IBD plus either IBD-related surgery or immunomodulatory/biological treatment during the past 18 months, SWIBREG covers 59.0%. SWIBREG records not only information on conventional therapies but also on biological treatment, surgery, smoking, disease activity, patient-reported outcome measures (PROMs), and patient-experienced measures (PREMs). Data are presented through a graphical decision support system. Conclusion: SWIBREG benefits patients with IBD, and offers an ideal opportunity for healthcare personnel and researchers to examine disease phenotype and activity, PROMs/PREMs, and hospital-administered drugs in patients with IBD.

Big data in IBD: a look into the future

Big data methodologies, made possible with the increasing generation and availability of digital data and enhanced analytical capabilities, have produced new insights to improve outcomes in many disciplines. Application of big data in the health-care sector is in its early stages, although the potential for leveraging underutilized data to gain a better understanding of disease and improve quality of care is enormous. Owing to the intrinsic characteristics of inflammatory bowel disease (IBD) and the management dilemmas that it imposes, the implementation of big data research strategies not only can complement current research efforts but also could represent the only way to disentangle the complexity of the disease. In this Review, we explore important potential applications of big data in IBD research, including predictive models of disease course and response to therapy, characterization of disease heterogeneity, drug safety and development, precision medicine and cost-effectiveness of care. We also discuss the strengths and limitations of potential data sources that big data analytics could draw from in the field of IBD, including electronic health records, clinical trial data, e-health applications and genomic, transcriptomic, proteomic, metabolomic and microbiomic data.

I_MDS: an inflammatory bowel disease molecular activity score to classify patients with differing disease-driving pathways and therapeutic response to anti-TNF treatment

Crohn’s disease and ulcerative colitis are driven by both common and distinct underlying mechanisms of pathobiology. Both diseases, exhibit heterogeneity underscored by the variable clinical responses to therapeutic interventions.

We aimed to identify disease-driving pathways and classify individuals into subpopulations that differ in their pathobiology and response to treatment.

We applied hierarchical clustering of enrichment scores derived from gene set variation analysis of signatures representative of various immunological processes and activated cell types, to a colonic biopsy dataset that included healthy volunteers, Crohn’s disease and ulcerative colitis patients. Patient stratification at baseline or after anti-TNF treatment in clinical responders and non-responders was queried. Signatures with significantly different enrichment scores were identified using a general linear model. Comparisons to healthy controls were made at baseline in all participants and then separately in responders and non-responders. Fifty-nine percent of the signatures were commonly enriched in both conditions at baseline, supporting the notion of a disease continuum within ulcerative colitis and Crohn’s disease. Signatures included T cells, macrophages, neutrophil activation and poly:IC signatures, representing acute inflammation and a complex mix of potential disease-driving biology. Collectively, identification of significantly enriched signatures allowed establishment of an inflammatory bowel disease molecular activity score which uses biopsy transcriptomics as a surrogate marker to accurately track disease severity. This score separated diseased from healthy samples, enabled discrimination of clinical responders and non-responders at baseline with 100% specificity and 78.8% sensitivity, and was validated in an independent data set that showed comparable classification. Comparing responders and non-responders separately at baseline to controls, 43% and 70% of signatures were enriched, respectively, suggesting greater molecular dysregulation in TNF non-responders at baseline. This methodological approach could facilitate better targeted design of clinical studies to test therapeutics, concentrating on patient subsets sharing similar underlying pathobiology, therefore increasing the likelihood of clinical response.

Patients exhibiting similar phenotypical characteristics, diagnosed with the same disease, exhibit variable response to therapeutics. This is a major health care issue, due to the increased patient suffering and the socioeconomical burden that occurs. Crohn’s disease and ulcerative colitis constitute good examples of inflammatory conditions, with sufferers responding differentially to existent therapeutics. Here, we identified disease-driving pathways and classified individuals into subpopulations that differ in their pathobiology and response to treatment. We utilized gene set variation analysis and transcriptomic data from inflammatory bowel disease sufferers to stratify patients at baseline or after anti-TNF treatment in clinical responders and non-responders. We explored gene signatures obtained from the literature, relevant to immune processes, which were significantly enriched in disease compared to healthy controls, as well as before and after treatment. Using these signatures, we established an inflammatory bowel disease molecular activity score, which allowed us to separate clinical responders and non-responders at baseline with high specificity and sensitivity. We validated the proposed approach in an independent data set, demonstrating comparable classification. This methodological approach may lead to better targeted design of clinical studies, allowing the selection of patient sharing similar underlying pathobiology, thus increasing the likelihood of clinical response to treatment.

Innate Lymphoid Cells: Diversity, Plasticity, and Unique Functions in Immunity

Type 1, 2, and 3 innate lymphoid cells (ILCs) have emerged as tissue-resident innate correlates of T helper 1 (Th1), Th2, and Th17 cells. Recent studies suggest that ILCs are more diverse than originally proposed; this might reflect truly distinct lineages or adaptation of ILCs to disparate tissue microenvironments, known as plasticity. Given that ILCs strikingly resemble T cells, are they redundant? While the regulation, timing, and magnitude of ILC and primary T cell responses differ, tissue-resident memory T cells may render ILCs redundant during secondary responses. The unique impact of ILCs in immunity is probably embodied in the extensive array of surface and intracellular receptors that endow these cells with the ability to distinguish between normal and pathogenic components, interact with other cells, and calibrate their cytokine secretion accordingly. Here I review recent advances in elucidating the diversity of ILCs and discuss their unique and redundant functions.

A Phase 1, Multiple-Dose Study of Vedolizumab in Japanese Patients With Ulcerative Colitis

Although previous studies have shown that patients with ulcerative colitis may benefit from treatment with vedolizumab, a humanized monoclonal antibody targeting the α₄β₇ integrin heterodimer, no data exist in Japanese populations. The aim of this phase 1, open‐label, multicenter study was to assess the pharmacokinetics, pharmacodynamics, efficacy, and safety of vedolizumab in Japanese patients with ulcerative colitis. Adult patients with confirmed ulcerative colitis received either 150 mg (step 1) or 300 mg (step 2) of intravenous (IV) vedolizumab on days 1, 15, and 43 of the study protocol. Pharmacokinetic, pharmacodynamic, safety, and efficacy parameters were all assessed through study end (day 239). Nine patients were enrolled in this study (150 mg, n = 3; 300 mg, n = 6). Patients who received vedolizumab IV 300 mg had approximately twice the drug exposure of those receiving vedolizumab IV 150 mg (day 1 AUC_day14 744 vs 408 μg·d/mL) and a longer‐lasting maximal saturation of α₄β₇ integrin (155 vs 99 days). The number of treatment‐emergent adverse events, all of which were mild or moderate in intensity, was similar between the 150‐mg (15 events) and 300‐mg (20 events) groups. The 2 patients (150 mg group) not in clinical remission by partial Mayo score at the start of the study met the criteria for clinical remission on days 15 and 155 of the study, respectively. In conclusion, in Japanese patients with ulcerative colitis, vedolizumab showed similar pharmacokinetic and pharmacodynamic results to those seen in non‐Japanese patients. Vedolizumab was well tolerated and demonstrated clinical activity consistent with previous studies.

AIEC infection triggers modification of gut microbiota composition in genetically predisposed mice, contributing to intestinal inflammation

A high prevalence of adherent-invasive E. coli (AIEC) in the intestinal mucosa of Crohn's disease patients has been shown. AIEC colonize the intestine and induce inflammation in genetically predisposed mouse models including CEABAC10 transgenic (Tg) mice expressing human CEACAM6-receptor for AIEC and eif2ak4-/- mice exhibiting autophagy defect in response to AIEC infection. Here, we aimed at investigating whether gut microbiota modification contributes to AIEC-induced intestinal inflammation in these mouse models. For this, eif2ak4+/+ and eif2ak4-/- mice or CEABAC10 Tg mice invalidated for Eif2ak4 gene (Tg/eif2ak4-/-) or not (Tg/eif2ak4+/+) were infected with the AIEC reference strain LF82 or the non-pathogenic E. coli K12 MG1655 strain. In all mouse groups, LF82 colonized the gut better and longer than MG1655. No difference in fecal microbiota composition was observed in eif2ak4+/+ and eif2ak4-/- mice before infection and at day 1 and 4 post-infection. LF82-infected eif2ak4-/- mice exhibited altered fecal microbiota composition at day 14 and 21 post-infection and increased fecal lipocalin-2 level at day 21 post-infection compared to other groups, indicating that intestinal inflammation developed after microbiota modification. Similar results were obtained for LF82-infected Tg/eif2ak4-/- mice. These results suggest that in genetically predisposed hosts, AIEC colonization might induce chronic intestinal inflammation by altering the gut microbiota composition.

The Interaction of the Gut Microbiota with the Mucus Barrier in Health and Disease in Human

Glycoproteins are major players in the mucus protective barrier in the gastrointestinal and other mucosal surfaces. In particular the mucus glycoproteins, or mucins, are responsible for the protective gel barrier. They are characterized by their high carbohydrate content, present in their variable number, tandem repeat domains. Throughout evolution the mucins have been maintained as integral components of the mucosal barrier, emphasizing their essential biological status. The glycosylation of the mucins is achieved through a series of biosynthetic pathways processes, which generate the wide range of glycans found in these molecules. Thus mucins are decorated with molecules having information in the form of a glycocode. The enteric microbiota interacts with the mucosal mucus barrier in a variety of ways in order to fulfill its many normal processes. How bacteria read the glycocode and link to normal and pathological processes is outlined in the review.

Smoking is associated with risk for developing inflammatory bowel disease including late onset ulcerative colitis: a prospective study

OBJECTIVES

Life style factors have been associated with inflammatory bowel disease (IBD) but there is a lack of data on the exposure of life styles factors before the onset of IBD. Our aim was to study the association between lifestyle factors and the development of IBD in a prospective setting.

MATERIALS AND METHODS

We performed a case control study of 72 patients who later developed ulcerative colitis (UC), 26 patients who developed Crohn's disease (CD) and 427 healthy controls from the Västerbotten intervention project matched for gender, age, year of health survey and area of residence. At recruitment, participants completed validated lifestyle questionnaires including data on alcohol intake. Information from this was used to assess the connection between lifestyle factors and later developing IBD.

RESULTS

For CD and UC, the median age at diagnosis was 53 and 52 years and median time of survey was 4 and 6 years before diagnosis, respectively. Multivariate odds ratio (OR) showed an association between never smoking and not developing IBD, including both UC and CD, OR (95% CI) 0.341 (0.136-0.853) and 0.473 (0.259-0.864), respectively. Marital status, educational level, alcohol consumption, reported physical activity and use of moist smokeless tobacco (snus) did not differ between patients and controls.

CONCLUSIONS

Smoking proves to be a risk factor for both CD and UC in this prospective case-control study. No association was seen for snus users, implying a non-nicotine pathogenic mechanism from combusted tobacco.

Genetic polymorphism in ATG16L1 gene is associated with adalimumab use in inflammatory bowel disease

Background

The role of single nucleotide polymorphisms (SNPs) associated with inflammatory bowel disease (IBD) is gaining interest. With the advent of novel therapies, personalized treatment in IBD is a future goal. We wondered whether IBD-associated SNPs are able to predict response to anti-TNFα treatment.

Methods

Data on treatment use and primary response, loss of response and side effects to anti-TNFα treatments were retrieved for 570 IBD patients. rs13361189 (IRGM), rs10210302 (ATG16L1), rs2066844, rs2066845, rs2066847 (NOD2), rs35873774 (XBP1), rs11175593 (LRRK2), rs11465804 (IL23R), rs2301436 (CCR6), rs744166 (STAT3) and rs4821544 (NCF4) SNP status were determined.

Results

No associations were found between genetic variants of the LRRK2, CCR6, IL23R and NCF4 genes and response to anti-TNFα. For NOD2 and XBP1 associations were found, however, these associations were not strong enough to survive multiple testing corrections. Strikingly, patients carrying the ATG16L1 T300A variant were more likely to be treated with adalimumab, even after correction for disease phenotype, disease behavior and age (p = 0.004, OR 2.8, CI 1.6–5.0).

Conclusions

Genetic polymorphisms in the known IBD-associated gene ATG16L1 correlate with requirement of treatment, suggesting a different IBD disease phenotype in these patients. Further investigation will need to elucidate the implications of these findings and identify the underlying disease characteristics.

Electronic supplementary material

The online version of this article (10.1186/s12967-017-1355-9) contains supplementary material, which is available to authorized users.

Race/Ethnicity-Specific Disparities in the Severity of Disease at Presentation in Adults with Ulcerative Colitis: A Cross-Sectional Study

BACKGROUND

While ulcerative colitis (UC) is well studied in Caucasian populations, less data are available on UC patients of racial/ethnic minorities, including variations in disease severity at presentation.

AIM

To evaluate race/ethnicity-specific disparities in UC disease presentation among an ethnically diverse underserved population.

METHODS

We performed a cross-sectional study of all consecutive UC adults among a large ethnically diverse safety-net hospital from July 2014 to May 2016 to compare race/ethnicity-specific disparities in severity of disease at presentation. Severity was evaluated using the clinician-based simple clinical colitis activity index (SCCAI) and the Mayo score at time of presentation. Multivariate ordered logistic regression models were used to evaluate associations with SCCAI and Mayo scores.

RESULTS

Among 98 UC patients (56.1% male, mean age 40.1 (SD 14.2), 32.0% were African-American, 26.7% Hispanic, 16.0% Asian, and 20.0% Caucasian. Mean Mayo score was 6.6 and mean SCCAI score was 6.5. When stratified by race/ethnicity, SCCAI scores were significantly higher in non-Caucasians compared to Caucasians (7.0 vs 4.6, p = 0.03) and in Asians compared to Caucasians (8.0 vs 4.6, p = 0.02). There was a trend toward higher mean SCCAI in Hispanics compared to Caucasians (6.9 vs 4.6, p = 0.07). Mayo scores at presentation demonstrated similar trends. On multivariate logistic regression, Asians (OR 5.26, 95% CI 1.24-22.42) and Hispanics (OR 3.74; 95% CI 1.02-13.66) had more severe disease at presentation than Caucasians based on SCCAI.

CONCLUSIONS

Among a diverse underserved cohort of UC patients, racial/ethnic minority patients with UC, specifically Asians and Hispanics, had more severe disease at presentation compared to Caucasians. The differences may reflect disparities in timely access to specialty care and treatment and deserves greater attention and research.

TSPO PET Imaging: From Microglial Activation to Peripheral Sterile Inflammatory Diseases?

Peripheral sterile inflammatory diseases (PSIDs) are a heterogeneous group of disorders that gathers several chronic insults involving the cardiovascular, respiratory, gastrointestinal, or musculoskeletal system and wherein inflammation is the cornerstone of the pathophysiology. In PSID, timely characterization and localization of inflammatory foci are crucial for an adequate care for patients. In brain diseases, in vivo positron emission tomography (PET) exploration of inflammation has matured over the last 20 years, through the development of radiopharmaceuticals targeting the translocator protein-18 kDa (TSPO) as molecular biomarkers of activated microglia. Recently, TSPO has been introduced as a possible molecular target for PSIDs PET imaging, making this protein a potential biomarker to address disease heterogeneity, to assist in patient stratification, and to contribute to predicting treatment response. In this review, we summarized the major research advances recently made in the field of TSPO PET imaging in PSIDs. Promising preliminary results have been reported in bowel, cardiovascular, and rheumatic inflammatory diseases, consolidated by preclinical studies. Limitations of TSPO PET imaging in PSIDs, regarding both its large expression in healthy peripheral tissues, unlike in central nervous system, and the production of peripheral radiolabeled metabolites, are also discussed, regarding their possible consequences on TSPO PET signal's quantification.

Resolution of inflammation in inflammatory bowel disease

Treatment of inflammatory bowel disease at present mainly targets mediators of inflammation to stop or suppress pro-inflammatory processes. Typical examples are steroids, suppression of T cells by thioguanine nucleotides, or antibodies against cytokines such as tumour necrosis factor, interleukin 12, or interleukin 23. In addition to suppression of inflammation, development of therapeutic strategies that support resolution of inflammation or that actively resolve inflammation might be desirable. Resolution of inflammation is now seen as an active process involving specific mediators (eg, lipid mediators or specific cytokines) that is mandatory to restore organ function and completely shut down inflammation. The molecular pathways involved in resolution of inflammation have been investigated in recent years and could be adopted in treatment strategies for inflammatory bowel disease. Among these approaches are anti-integrin strategies and means to produce or locally increase restitution or resolution factors, such as restoration of the activity of transforming growth factor-β by anti-SMAD7 antisense oligonucleotides. The potential role of inflammation-resolving lipid mediators (eg, resolvins), however, still warrants further study and clinical development. This Review focuses on the specific role of active resolution of inflammation in inflammatory bowel disease pathophysiology. Potential therapeutic targets based on these pathways are also discussed.

MiR-126 impairs the intestinal barrier function via inhibiting S1PR2 mediated activation of PI3K/AKT signaling pathway

BACKGROUND

Aberrant expression of miRNAs was a critical element in the pathogenesis of inflammatory bowel disease (IBD). This study aimed to explore the involvement and mechanism of miR-126 in IBD.

METHODS

In this study, the endogenous expressions of miR-126, S1PR2 and S1P in the pathological tissues of patients with IBD were detected using qRT-PCR and western blot assay, respectively. The luciferase reporter gene assay was performed to confirm the targeting regulatory relation between miR-126 and S1PR2. The transendothelial electrical resistance assay was used to measured the value of TEER.

RESULTS

The expressions of miR-126, S1PR2 and S1P in the pathological tissues of IBD patients were significantly higher than that of the control group. Moreover, miR-126 overexpression contributed to intestinal mucosal barrier dysfunction in vitro. S1PR2 was a direct target of miR-126, and S1PR2 expression was negatively regulated by miR-126 in Caco-2 cells. However, S1PR2 activated by S1P had the protection effect for the integrity and permeability of intestinal mucosal barrier via a PI3K/Akt dependent mechanism. MiR-126 silencing possessed obvious protective effects on the intestinal barrier function, but these effects could be reversed by JTE-013 or LY294002.

CONCLUSION

MiR-126 down-regulated S1PR2 and then prevented the activation of PI3K/AKT signaling pathway, which ultimately could damage intestinal mucosal barrier function.

Opportunities and challenges of whole-genome and -exome sequencing

Recent advances in the development of sequencing technologies provide researchers with unprecedented possibilities for genetic analyses. In this review, we will discuss the history of genetic studies and the progress driven by next-generation sequencing (NGS), using complex inflammatory bowel diseases as an example. We focus on the opportunities, but also challenges that researchers are facing when working with NGS data to unravel the genetic causes underlying diseases.

Antioxidant Supplements and Gastrointestinal Diseases: A Critical Appraisal

The gastrointestinal tract digests and absorbs dietary nutrients, protects the body against physical and chemical damage from contents in its lumen, provides immunity against external antigens, and keeps an optimum environment for the gut microbiota. These functions cannot be performed normally in several diseases of which the following are discussed here: irritable bowel syndrome and inflammatory bowel disease, which includes Crohn's disease and ulcerative colitis. Because these diseases are associated with oxidative stress, a host of antioxidant supplements are used for maintenance and recovery of the gut functions. However, the benefits of these supplements have not been established. The available 80 human trials were rated for levels of confidence and for benefits of the antioxidant supplements. For Crohn's disease, the supplements for which clear benefits occurred in at least 2 studies were allopurinol, Boswellia serrata (frankincense or shallaki), Artemesia species (wormwood), Tripterygium wilfordii (léi gōng téng), and omega-3 fatty acids. Similar beneficial supplements for ulcerative colitis were allopurinol, Matricaria chamomilla (chamomile), Curcuma longa (curcumin in turmeric), and omega-3 fatty acids. There was also a clear benefit for ulcerative colitis in 2 studies where a multiherbal Chinese medicine preparation and an Ayurvedic medicine preparation were used. For irritable bowel syndrome, there was only a marginal benefit of some of the antioxidant supplements. Thus, some antioxidant supplements may be beneficial at certain stages of specific diseases. This is consistent with the current concept that antioxidants act by inhibiting oxidative stress pathways in a tissue- and environment-specific manner and not by simply acting as scavengers.

Genetic architecture differences between pediatric and adult-onset inflammatory bowel diseases in the Polish population

Most inflammatory bowel diseases (IBDs) are classic complex disorders represented by common alleles. Here we aimed to define the genetic architecture of pediatric and adult-onset IBDs for the Polish population. A total of 1495 patients were recruited, including 761 patients with Crohn’s disease (CD; 424 pediatric), 734 patients with ulcerative colitis (UC; 390 pediatric), and 934 healthy controls. Allelotyping employed a pooled-DNA genome-wide association study (GWAS) and was validated by individual genotyping. Whole exome sequencing (WES) was performed on 44 IBD patients diagnosed before 6 years of age, 45 patients diagnosed after 40 years of age, and 18 healthy controls. Altogether, out of 88 selected SNPs, 31 SNPs were replicated for association with IBD. A novel BRD2 (rs1049526) association reached significance of P = 5.2 × 10⁻¹¹ and odds ratio (OR) = 2.43. Twenty SNPs were shared between pediatric and adult patients; 1 and 7 were unique to adult-onset and pediatric-onset IBD, respectively. WES identified numerous rare and potentially deleterious variants in IBD-associated or innate immunity-associated genes. Deleterious alleles in both groups were over-represented among rare variants in affected children. Our GWAS revealed differences in the polygenic architecture of pediatric- and adult-onset IBD. A significant accumulation of rare and deleterious variants in affected children suggests a contribution by yet unexplained genetic components.