Artificial intelligence in inflammatory bowel disease

ABSTRACT

Inflammatory bowel disease (IBD) is a complex condition influenced by various intestinal factors. Advances in next-generation sequencing, high-throughput omics, and molecular network technologies have significantly accelerated research in this field. The emergence of artificial intelligence (AI) has further enhanced the efficient utilization and interpretation of datasets, enabling the discovery of clinically actionable insights. AI is now extensively applied in gastroenterology, where it aids in endoscopic analyses, including the diagnosis of colorectal cancer, precancerous polyps, gastrointestinal inflammatory lesions, and bleeding. Additionally, AI supports clinicians in patient stratification, predicting disease progression and treatment responses, and adjusting treatment plans in a timely manner. This approach not only reduces healthcare costs but also improves patient health and safety. This review outlines the principles of AI, the current research landscape, and future directions for its applications in IBD, with the goal of advancing targeted treatment strategies.

Mediators of Filgotinib Treatment Effects in Ulcerative Colitis: Exploring Circulating Biomarkers in the Phase 2b/3 SELECTION Study

BACKGROUND

We utilized patient samples from the large, phase 2b/3 SELECTION trial to identify circulating biomarkers of ulcerative colitis (UC) and potential early mediators of filgotinib treatment effects.

METHODS

Samples were collected at baseline and during the induction phase of the SELECTION trial. Evaluated biomarkers comprised serum and stool proteins (measured by enzyme-linked immunosorbent assay), whole-blood cell counts, and whole-blood RNA-seq-derived gene-expression factors identified via exploratory factor analysis. Biomarker levels were assessed by baseline disease severity (endoscopy/bleeding/stool and Mayo Clinic Score) and biologic status (naive vs experienced). Effects of filgotinib on biomarker levels, including week 4 biomarker changes that may mediate week 10 clinical improvements, were assessed.

RESULTS

The biomarker analysis set included 598 biologic-naive patients and 592 biologic-experienced patients. Systemic inflammatory biomarkers (C-reactive protein [CRP], interleukin-6 [IL-6], serum amyloid A [SAA], and platelet cell counts) had the strongest positive correlations with baseline UC disease severity. CRP, IL-6, SAA, and neutrophil activation biomarkers (including neutrophil gelatinase-associated lipocalin [NGAL], tumor necrosis factor ɑ, and oncostatin M [OSM]), as well as platelet, neutrophil, and monocyte cell counts were increased in biologic-experienced versus biologic-naive patients. Gene-expression-derived plasmablast and cell proliferation factors were positively correlated with disease severity; B cell, T-cell activation, and plasmacytoid dendritic cell factors were negatively correlated. Filgotinib reduced nearly all proinflammatory biomarkers correlated with baseline UC disease activity; reduced SAA, CRP, IL-6, NGAL, and OSM at week 4 were identified as mediators of improved week 10 clinical scores.

CONCLUSIONS

Filgotinib significantly impacted circulating biomarkers related to UC pathology. Several proinflammatory and neutrophil activation biomarkers may be early mediators of filgotinib treatment effects.

CLINICALTRIALS.GOV IDENTIFIER

NCT02914522.

Filamentous bacteriophage M13 induces proinflammatory responses in intestinal epithelial cells

Bacteriophages are the dominant members of the human enteric virome and can shape bacterial communities in the gut; however, our understanding of how they directly impact health and disease is limited. Previous studies have shown that specific bacteriophage populations are expanded in patients with Crohn's disease (CD) and ulcerative colitis (UC), suggesting that fluctuations in the enteric virome may contribute to intestinal inflammation. Based on these studies, we hypothesized that a high bacteriophage burden directly induces intestinal epithelial responses. We found that filamentous bacteriophages M13 and Fd induced dose-dependent IL-8 expression in the human intestinal epithelial cell line HT-29 to a greater degree than their lytic counterparts, T4 and ϕX174. We also found that M13, but not Fd, reduced bacterial internalization in HT-29 cells. This led us to investigate the mechanism underlying M13-mediated inhibition of bacterial internalization by examining the antiviral and antimicrobial responses in these cells. M13 upregulated type I and III IFN expressions and augmented short-chain fatty acid (SCFA)-mediated LL-37 expression in HT-29 cells. Taken together, our data establish that filamentous bacteriophages directly affect human intestinal epithelial cells. These results provide new insights into the complex interactions between bacteriophages and the intestinal mucosa, which may underlie disease pathogenesis.

Early detection and correction of preoperative anemia in patients undergoing colorectal surgery-a prospective study

INTRODUCTION

Preoperative anemia is an important target in preventing colorectal anastomotic leakage (CAL). However, it is not consistently detected and corrected in patients undergoing colorectal surgery. This study aimed to evaluate the impact of early detection and correction of preoperative anemia on perioperative outcomes and CAL.

METHODS

This was a prospective subanalysis of an international open-labeled trial, which implemented an enhanced care bundle to prevent CAL after elective colorectal surgeries. It introduced interventions for early detection and correction of preoperative anemia. Primary outcome was the incidence of preoperative anemia and the effect of early correction. Secondary outcomes included the impact on CAL, postoperative course, and mortality.

RESULTS

The study included 899 patients across eight European hospitals (September 2021-December 2023). Preoperative anemia was identified in 35.0% (n = 315) of participants, with 77.4% (n = 192) receiving iron therapy. Hemoglobin levels decreased in 4.2% (n = 13), remained stable in 45.8% (n = 143), and increased in 50.0% (n = 156) (p < 0.001). Perioperative hyperglycemia was more common among patients with anemia (7.8% versus 16.4%, p < 0.001). CAL occurred in 6.1% (n = 53) of patients. Anemia correction and changes in hemoglobin levels after iron treatment were not significantly associated with CAL, other complications, or mortality.

CONCLUSIONS

Early detection and correction of preoperative anemia is achievable. However, routine preoperative administration of iron alone, without concurrently optimizing other CAL risk factors, does not result in CAL prevention. Preoperative anemia indicates overall poor physiological fitness rather than being an isolated risk factor.

TRIAL NUMBER

NCT05250882 (20-01-2022).

Immune dysregulation in bipolar disorder

BACKGROUND

Bipolar disorder is a debilitating mood disorder associated with a high risk of suicide and characterized by immune dysregulation. In this study, we used a multi-faceted approach to better distinguish the pattern of dysregulation of immune profiles in individuals with BD.

METHODS

We analyzed peripheral blood mononuclear cells (bipolar disorder N = 39, control N = 30), serum cytokines (bipolar disorder N = 86, control N = 58), whole blood RNA (bipolar disorder N = 25, control N = 25), and whole blood DNA (bipolar disorder N = 104, control N = 66) to identify immune-related differences in participants diagnosed with bipolar disorder compared to controls.

RESULTS

Flow cytometry revealed a higher proportion of monocytes in participants with bipolar disorder together with a lower proportion of T helper cells. Additionally, the levels of 18 cytokines were significantly elevated, while two were reduced in participants with bipolar disorder. Most of the cytokines altered in individuals with bipolar disorder were proinflammatory. Forty-nine genes were differentially expressed in our bipolar disorder cohort and further analyses uncovered several immune-related pathways altered in these individuals. Genetic analysis indicated variants associated with inflammatory bowel disease also influences bipolar disorder risk.

DISCUSSION

Our findings indicate a significant immune component to bipolar disorder pathophysiology and genetic overlap with inflammatory bowel disease. This comprehensive study supports existing literature, whilst also highlighting novel immune targets altered in individuals with bipolar disorder. Specifically, multiple lines of evidence indicate differences in the peripheral representation of monocytes and T cells are hallmarks of bipolar disorder.

Applications of Hydrogels in Emergency Therapy

Interest in developing new, effective materials for emergency hemostasis and wound healing is steadily increasing, particularly for use in emergency, surgical, and military situations. Hydrogels, with their unique retention, swelling, and biocompatibility properties, have emerged as essential materials in emergency therapy. This review provides a comprehensive examination of recent hydrogel applications in acute medical scenarios, including hemostasis, wound management, drug delivery, soft tissue replacement, and tissue engineering. We discuss the physicochemical properties that make hydrogels suitable for rapid response situations, such as their tunable mechanical strength, adhesiveness, responsiveness to environmental stimuli, and ability to encapsulate and release therapeutic agents. Additionally, the article explores recent advancements in smart hydrogels with self-healing and antimicrobial properties, providing insights into their potential to revolutionize emergency care and increase survival rates in both civilian and military applications. Through a critical evaluation of current clinical trials and practical deployments, this review highlights both the successes and the challenges faced in integrating hydrogels into emergency medical protocols, providing a roadmap for future research and development in this dynamic field.

Dietary whey protein protects against Crohn's disease by orchestrating cross-kingdom interaction between the gut phageome and bacteriome

BACKGROUND

The gut microbiome and diet are important factors in the pathogenesis and management of Crohn's disease (CD). However, the role of the gut phageome under dietary influences is unknown.

OBJECTIVE

We aim to explore the effect of diet on the gut phageome-bacteriome interaction linking to CD protection.

DESIGN

We recruited CD patients and healthy subjects (n=140) and conducted a multiomics investigation, including paired ileal mucosa phageome and bacteriome profiling, dietary survey and phenome interrogation. We screened for the effect of diet on the gut phageome and bacteriome, as well as its epidemiological association with CD risks. The underlying mechanisms were explored in target phage-bacteria monocultures and cocultures in vitro and in two mouse models in vivo.

RESULTS

On dietary screening in humans, whey protein (WP) consumption was found to profoundly impact the gut phageome and bacteriome (more pronounced on the phageome) and was associated with a lower CD risk. Indeed, the WP reshaped gut phageome can causally attenuate intestinal inflammation, as shown by faecal phageome versus bacteriome transplantation from WP-consuming versus WP-non-consuming mice to recipient mice. Mechanistically, WP induced phage (a newly isolated phage AkkZT003P herein) lysis of the mucin-foraging bacterium Akkermansia muciniphila, which unleashed the symbiotic bacterium Streptococcus thermophilus to counteract intestinal inflammation.

CONCLUSION

Our study charted the importance of cross-kingdom interaction between gut phage and bacteria in mediating the dietary effect on CD protection. Importantly, we uncovered a beneficial dietary WP, a keystone phage AkkZT003P, and a probiotic S. thermophilus that can be used in CD management in the future.

Exploring therapeutic applications of PTEN, TMPRSS2:ERG fusion, and tumour molecular subtypes in prostate cancer management

Background

Prostate cancer is defined by the suppression of genes that suppress tumours and the activation of proto-oncogenes. These are the hallmarks of prostate cancer, and they have been linked to numerous genomic variations, which lead to unfavourable treatment outcomes. Prostate cancer can be categorised into various risk groups of tumour molecular subtypes grounded in the idea of genomic structural variations connected to TMPRSS2:ERG fusion and loss of PTEN. Research suggests that certain genomic alterations may be more prevalent or exhibit different patterns in prostate cancer tumours across populations. Studies have reported a higher frequency of PTEN loss and TMPRSS2:ERG fusion in prostate tumours of Black/African American men, which may contribute to the more aggressive nature of the disease in this population. Thus, therapeutically important information can be obtained from these structural variations, including correlations with poor prognosis and disease severity.

Methods

Peer-reviewed articles from 1998 to 2024 were sourced from PubMed and Google Scholar. During the review process, the following search terms were employed: "Tumour suppressor genes OR variations OR alterations OR oncogenes OR diagnostics OR ethnicity OR biomarkers OR prostate cancer genomics OR prostate cancer structural variations OR tumour and molecular subtypes OR therapeutic implications OR immunotherapy OR immunogenetics."

Results

There was a total of 13,012 results for our search query: 5,903 publications from Google Scholar with the patent and citation unchecked filer options, and 7127 articles from PubMed with the abstract, free full text, and full-text options selected. Unpublished works were not involved. Except for four articles published between 1998 and 1999, all other selected articles published in 2000 and later were considered. However, papers with irrelevant information or redundant or duplicate content were not chosen for this review. Thus, 134 met the inclusion criteria and were ultimately retained for this review.

Conclusion

This review extracted 134 relevant articles about genomic structure variations in prostate cancer. Our findings demonstrate the importance of PTEN and TMPRSS2:ERG fusion and tumour molecular subtyping in prostate cancer precision medicine.

Ileal Pouch Cancer Detected More than 30 Years after Restorative Proctocolectomy for Ulcerative Colitis

INTRODUCTION

The standard surgical treatment for ulcerative colitis (UC) is proctocolectomy with hand-sewn ileoanal pouch anastomosis (hand-sewn IPAA) or stapled ileal pouch anastomosis (stapled IPAA). The occurrence of cancer in the ileal pouch after surgery for UC is rare, and a consensus on surveillance for ileal pouch cancer has not been reached. We report a case of ileal pouch cancer diagnosed by pouchoscopy 33 years after restorative proctocolectomy with IPAA for UC.

CASE PRESENTATION

A middle-aged man presented with positive fecal occult blood. The patient had undergone restorative proctocolectomy with IPAA for UC 33 years ago. Pouchoscopy had been performed every 2-3 years in the last 10 years. In April a year ago, he tested positive for fecal occult blood, and pouchoscopy revealed an ulcerative lesion and flat elevation in the ileal pouch on the proximal side of the ileoanal anastomosis. Targeted biopsies of the ulcerative lesion revealed low-grade dysplasia (LGD). After 4 months, pouchoscopy also showed an increase in the size of the flat elevation, but targeted biopsies of this lesion also showed LGD. One year later in August, endoscopic examination for hematochezia showed a full circumferential raised lesion with a white coat and mucus draining from a fistula near the anastomosis at the same site. Pathological examination identified adenocarcinoma in the ileal mucosa. The preoperative diagnosis was ileal pouch cancer after restorative proctocolectomy with IPAA for UC, cT4bN2M0 stage IIIB (UICC-TNM, 8th), and he underwent excision of the ileal pouch body and the ileoanal anastomosis. Pathological examination showed mucinous carcinoma in the ileal mucosa with chronic inflammation. The postoperative stage was pT3N0M0 stage IIA; no postoperative chemotherapy was administered, and at 6 months postoperatively, the patient remained recurrence free.

CONCLUSION

Although ileal pouch cancer is rare, it can occur after a long period following ileal pouch surgery for UC. Endoscopic surveillance for ileal pouch cancer should be performed for early diagnosis and radical resection, especially if ileal pouch cancer occurs more than 10 years after the onset of UC.

Oral dosage forms for drug delivery to the colon: an existing gap between research and commercial applications

Oral drug administration is the preferred route for pharmaceuticals, accounting for ~90% of the global pharmaceutical market due to its convenience and cost-effectiveness. This study provides a comprehensive scientific and technological analysis of the latest advances in oral dosage forms for colon-targeted drug delivery. Utilizing scientific and patent databases, along with a bibliometric analysis and bibliographical review, we compared the oral dosage forms (technology) with the specific application of the technology (colon delivery) using four search equations. Our findings reveal a gap in the publications and inventions associated with oral dosage forms for colon release compared to oral dosage forms for general applications. While tablets and capsules were found the most used dosage forms, other platforms such as nanoparticles, microparticles, and emulsions have been also explored. Enteric coatings are the most frequently applied excipient to prevent the early drug release in the stomach with pH-triggered systems being the predominant release mechanism. In summary, this review provides a comprehensive analysis of the last advancements and high-impact resources in the development of oral dosage forms for colon-targeted drug delivery, providing insights into the technological maturity of these approaches.

Redox-Induced Stabilization of AMBRA1 by USP7 Promotes Intestinal Oxidative Stress and Colitis Through Antagonizing DUB3-Mediated NRF2 Deubiquitination

Inflammatory bowel disease (IBD) is associated with oxidative stress and redox signaling disruption. It is recently reported that proautophagic autophagy/beclin-1 regulator 1 (AMBRA1) is a positive modulator of the NF-κB pathway that promotes intestinal inflammation. However, its effect on intestinal redox state and whether AMBRA1 is regulated by oxidative stress remain unknown. In this study, it is found that AMBRA1 functions as a pro-oxidative factor that increases oxidative stress in intestinal epithelial cells (IECs) in vitro and in vivo. Mechanistically, the N-terminal F1 domain is required for AMBRA1 to competitively interact with the N-terminal domain of NRF2, thereby antagonizing the interaction between deubiquitinating protein 3 (DUB3) and NRF2, suppressing DUB3-mediated NRF2 deubiquitination, and leading to NRF2 degradation. In response to H2O2 stimulation, the interaction between AMBRA1 and ubiquitin-specific protease 7 (USP7) is enhanced, facilitating USP7 to deubiquitinate AMBRA1 at K83 and K86 and stabilize AMBRA1. Notably, the USP7 inhibitor, P5091, inhibits oxidative stress and colitis in vivo. Elevated AMBRA1 expression in inflamed colon tissues from ulcerative colitis patients is negatively correlated with decreased NRF2 protein levels. Overall, this study identifies AMBRA1 as a pro-oxidative factor in IECs and provides a redox-modulating therapeutic strategy for targeting USP7/AMBRA1 in IBD.

Immunohistochemistry Analysis in Inflammatory Bowel Disease-Should We Bring to Light Interleukin-10?

Background/Objectives: Inflammatory bowel diseases (IBDs) are chronic intestinal disorders with an unpredictable course. In parallel with the advent of new biologic therapies targeting specific interleukin pathways, end-point targets have become more stringent, aiming for mucosal and even histologic healing. Methods: We conducted a prospective study assessing immunohistochemical (IHC) parameters in 46 IBD patients treated with biologic therapy. A similar IHC analysis was performed for comparison with a cohort of 10 "non-IBD" patients. Results: The highest integrated optical density (IOD) of TNF-α was observed in patients with dysplasia, abscesses, mucin depletion and basal plasmacytosis. Non-responders had higher pre- and post-treatment TNF-α expression in both UC and CD compared to responders. On the contrary, the same analysis conducted in the subpopulation treated with anti-TNF-α therapy (Infliximab and Adalimumab) did not reveal a substantial difference in TNF-α expression between responders and non-responders. High pre-treatment interleukin-10 expression was associated with biologic therapy failure, histological inflammatory activity and longer disease duration. Conclusions: Pre-treatment assessment of IL-10 might be a useful tool for identifying a high-risk subset of IBD patients and determining a more aggressive therapy and intensive monitoring strategy.

Shigella infection is facilitated by interaction of human enteric α-defensin 5 with colonic epithelial receptor P2Y11

Human enteric α-defensin 5 (HD5) is an immune system peptide that acts as an important antimicrobial factor but is also known to promote pathogen infections by enhancing adhesion of the pathogens. The mechanistic basis of these conflicting functions is unknown. Here we show that HD5 induces abundant filopodial extensions in epithelial cells that capture Shigella, a major human enteroinvasive pathogen that is able to exploit these filopodia for invasion, revealing a mechanism for HD5-augmented bacterial invasion. Using multi-omics screening and in vitro, organoid, dynamic gut-on-chip and in vivo models, we identify the HD5 receptor as P2Y11, a purinergic receptor distributed apically on the luminal surface of the human colonic epithelium. Inhibitor screening identified cAMP-PKA signalling as the main pathway mediating the cytoskeleton-regulating activity of HD5. In illuminating this mechanism of Shigella invasion, our findings raise the possibility of alternative intervention strategies against HD5-augmented infections.

Functional characterization of novel anti-DEFA5 monoclonal antibody clones 1A8 and 4F5 in inflammatory bowel disease colitis tissues

BACKGROUND

The aberrant expression of α defensin 5 (DEFA5) protein in colonic inflammatory bowel diseases (IBDs) underlies the distinct pathogenesis of Crohn's colitis (CC). It can serve as a biomarker for differentiating CC from Ulcerative colitis (UC), particularly in Indeterminate colitis (IC) cases into UC and CC. We evaluated the specificity of commercially available anti-DEFA5 antibodies, emphasizing the need to further validate their appropriateness for a given application and highlighting the necessity for novel antibodies.

METHODS

We established two mice monoclonal DEFA5 antibody clones, 1A8 and 4F5, by immunizing mice with purified recombinant protein. We validated the specificity, sensitivity, and cross-reactivity of these antibodies in recognizing both endogenous and recombinant DEFA5 protein, especially for use in Immunohistochemistry (IHC), Western blot (WB), Immunoprecipitation (IP), and enzyme-linked immunosorbent assay (ELISA).

RESULTS

Clones 1A8 and 4F5 effectively recognized the endogenous DEFA5 in active human colon tissue from patients with diverticulitis (DV), UC, CC, and IC disease samples, as well as in transiently transfected HEK293T cells expressing DEFA5 with minimal non-confounding cross reactivity.

CONCLUSIONS

The 1A8 and 4F5 clones are useful for a wide variety of immunoassays, including WB, IHC, IP/WB, and ELISA. Their specificity enhances their potential as valuable tools for research applications in IBD colitis.

Healthy microbiome-moving towards functional interpretation

BACKGROUND

Microbiome-based disease prediction has significant potential as an early, noninvasive marker of multiple health conditions linked to dysbiosis of the human gut microbiota, thanks in part to decreasing sequencing and analysis costs. Microbiome health indices and other computational tools currently proposed in the field often are based on a microbiome's species richness and are completely reliant on taxonomic classification. A resurgent interest in a metabolism-centric, ecological approach has led to an increased understanding of microbiome metabolic and phenotypic complexity, revealing substantial restrictions of taxonomy-reliant approaches.

FINDINGS

In this study, we introduce a new metagenomic health index developed as an answer to recent developments in microbiome definitions, in an effort to distinguish between healthy and unhealthy microbiomes, here in focus, inflammatory bowel disease (IBD). The novelty of our approach is a shift from a traditional Linnean phylogenetic classification toward a more holistic consideration of the metabolic functional potential underlining ecological interactions between species. Based on well-explored data cohorts, we compare our method and its performance with the most comprehensive indices to date, the taxonomy-based Gut Microbiome Health Index (GMHI), and the high-dimensional principal component analysis (hiPCA) methods, as well as to the standard taxon- and function-based Shannon entropy scoring. After demonstrating better performance on the initially targeted IBD cohorts, in comparison with other methods, we retrain our index on an additional 27 datasets obtained from different clinical conditions and validate our index's ability to distinguish between healthy and disease states using a variety of complementary benchmarking approaches. Finally, we demonstrate its superiority over the GMHI and the hiPCA on a longitudinal COVID-19 cohort and highlight the distinct robustness of our method to sequencing depth.

CONCLUSIONS

Overall, we emphasize the potential of this metagenomic approach and advocate a shift toward functional approaches to better understand and assess microbiome health as well as provide directions for future index enhancements. Our method, q2-predict-dysbiosis (Q2PD), is freely available (https://github.com/Kizielins/q2-predict-dysbiosis).

Pregnancy in Inflammatory Bowel Disease: Data from a Real-World Cohort in Germany

Background: Inflammatory bowel disease (IBD) frequently manifests at a young age, during the peak fertility years. Understanding the risks of negative pregnancy outcomes associated with IBD is crucial for effective pregnancy management and support. Additionally, it is essential to provide patients with the necessary knowledge to make informed choices and foster their confidence in navigating pregnancy while maintaining effective disease management. Although IBD frequently appears during the peak fertility years, knowledge about managing pregnancy in the context of IBD remains limited and often inaccurate among both physicians and patients. Our study aims to assess the complications occurring during pregnancy in patients with IBD, considering the level of disease activity, and to evaluate the standard of care provided to patients with chronic inflammatory conditions through a cohort analysis. Methods: Patients with IBD who had children were included in this single-center mixed-method (retrospective and prospective) study. Clinical data, disease progression, course of pregnancy, and complications were examined in women. Outcomes for children of men with IBD were also analyzed. To supplement the data, a survey addressing various pregnancy-related topics, including all patients from the university outpatient clinic for IBD, was conducted over a period of six months. Results: A total of 410 patients were screened retrospectively between 2010 and 2021. In total, 134 patients who had children were included in the study: 51.4% (n = 69) had Crohn's disease, 44% (n = 59) had ulcerative colitis, and 4.6% (n = 6) had unclassified inflammatory bowel disease. Of the women, 85% (n = 34) were in remission for at least three months before pregnancy, 14.6% (n = 6) experienced an acute flare-up during pregnancy, and 10.3% (n = 4) and 7.7% (n = 3) had active disease at the time of delivery and during breastfeeding, respectively. Patients with IBD who were in remission before pregnancy did not experience a higher risk of pregnancy complications (no cases of pre-eclampsia or placental abruption were reported in this group). However, the rates of gestational diabetes and fever during pregnancy were 10% for those in remission, compared to 25% for those with active disease. Conclusions: Patients with IBD in remission did not present an increased risk of pregnancy complications. However, our survey indicates that those with active disease at conception were more likely to experience complications such as gestational diabetes and fever. These findings underscore the importance of adequate patient education regarding the safety of various IBD medications during pregnancy in order to avoid pregnancy-related complications.

Pathologist-level diagnosis of ulcerative colitis inflammatory activity level using an automated histological grading method

BACKGROUND AND AIMS

Inflammatory bowel disease (IBD) is a global disease that is evolving with increasing incidence. However, there are few works on computationally assisted diagnosis of IBD based on pathological images. Therefore, based on the UK and Chinese IBD diagnostic guidelines, our study established an artificial intelligence-assisted diagnostic system for histologic grading of inflammatory activity in ulcerative colitis (UC).

METHODS

We proposed an efficient deep-learning (DL) method for grading inflammatory activity in whole-slide images (WSIs) of UC pathology. Our model was constructed using 603 UC WSIs from Nanjing Drum Tower Hospital for model train set and internal test set. We collected 212 UC WSIs from Zhujiang Hospital as an external test set. Initially, the pre-trained ResNet50 model on the ImageNet dataset was employed to extract image patch features from UC patients. Subsequently, a multi-instance learning (MIL) approach with embedded self-attention was utilized to aggregate tissue image patch features, representing the entire WSI. Finally, the model was trained based on the aggregated features and WSI annotations provided by senior gastrointestinal pathologists to predict the level of inflammatory activity in UC WSIs.

RESULTS

In the task of distinguishing the presence or absence of inflammatory activity, the Area Under Curve (AUC) value in the internal test set is 0.863 (95% confidence interval [CI] 0.829, 0.898), with a sensitivity of 0.913 (95% [CI] 0.866, 0.961), and specificity of 0.816 (95% [CI] 0.771, 0.861). The AUC in the external test set is 0.947 (95% confidence interval [CI] 0.939, 0.955), with a sensitivity of 0.889 (905% [CI] 0.837, 0.940), and specificity of 0.858 (95% [CI] 0.777, 0.939). For distinguishing different levels of inflammatory activity in UC, the average Macro-AUC in the internal test set and the external test set are 0.827 (95% [CI] 0.803, 0.850) and 0.908 (95% [CI] 0.882, 0.935). the average Micro-AUC in the internal test set and the external test set are 0.816 (95% [CI] 0.792, 0.840) and 0.898 (95% [CI] 0.869, 0.926).

CONCLUSIONS

Comparative analysis with diagnoses made by pathologists at different expertise levels revealed that the algorithm reached a proficiency comparable to the pathologist with 5 years of experience. Furthermore, our algorithm performed superior to other MIL algorithms.

Optimization of a green tea seed oil-loaded double-layer emulsion and its preventive effects on dextran sulfate sodium-induced colitis in mice

Green tea seed oil (GTSO; Camellia sinensis) is rich in bioactive compounds and has great potential for preventing intestinal inflammation. Conversely, high-fat diets have been shown to promote or aggravate gastrointestinal inflammation, and the bioactive ingredients of GTSO face difficulty passing through the gastrointestinal tract while remaining intact. This study employed whey protein isolate (WPI) and sodium carboxymethyl cellulose (CMC-Na) to prepare a GTSO-loaded double-layer emulsion. The optimal parameters were as follows: WPI (2% w/w) and 35% oil phase for the primary emulsion preparation, CMC-Na (0.8% w/w) for the final emulsion, and 450 W of ultrasonic power for homogenization. No significant changes in particle size or coalescence in the emulsions were observed after 30 days of storage at 4°C. In addition, in a simulated gastrointestinal digestion system, more than 60% of the encapsulated GTSO was able to remain intact while passing through the gastric and small intestinal environment. In mice with dextran sulfate sodium-induced colitis, pretreatment with the GTSO emulsion significantly prevented the further development of colitis, whereas an empty-carrier-plus-free-GTSO treatment had no such protective effects and even tended to aggravate the disease. The results of the present study suggest that encapsulated GTSO is a reliable alternative approach for colitis prevention. PRACTICAL APPLICATION: The green tea seed oil-loaded double-layer emulsion demonstrates good storage stability when kept at 4°C, exhibits excellent slow-release performance, and achieves superior outcomes in the prevention of colitis. Our current study provides a reliable alternative approach for the prevention of colitis.

Effectiveness and safety outcomes after long-term (54 weeks) vedolizumab therapy for Crohn's disease: a prospective, real-world observational study including patient-reported outcomes (POLONEZ II)

BACKGROUND

The Crohn's Disease (CD) Activity Index (CDAI), Inflammatory Bowel Disease (IBD) Questionnaire (IBDQ), and IBD-Fatigue (IBD-F) scale are useful patient-reported outcome (PRO) tools for assessing the treatment benefits of vedolizumab (VDZ) beyond clinical trial endpoints in patients with CD.

OBJECTIVES

To assess clinical response, clinical remission, steroid-free remission, changes from baseline for PROs, and safety in a real-world cohort of patients with moderate-to-severe active CD treated with VDZ.

DESIGN

POLONEZ II was a multicenter, observational, prospective study across 10 Polish centers from April 2020 to October 2023 for 54 weeks in patients with CD eligible for reimbursed VDZ.

METHODS

Primary endpoints at week 54 (W54) were clinical response (⩾70-point reduction in CDAI and >25% reduction vs baseline), remission (CDAI score ⩽150), and steroid-free remission. Other outcomes were changes in PROs (CDAI score and health-related quality of life) and safety. Kaplan-Meier survival analyses were performed.

RESULTS

Of 98 patients with CD, the mean age was 35.2 years, 57.1% were male, and 72.4% had an ileocolonic disease. At W54 (n = 98), 63.3% of patients achieved clinical response, 48.0% remission, and 36.0% steroid-free remission. The durability of clinical response, remission, and steroid-free remission (W14-W54) were 68.9%, 62.9%, and 57.1%, respectively. By W54, a significant reduction in the PROs, such as the total CDAI score (p < 0.001), stool frequency (p < 0.001), abdominal pain score (p < 0.001), IBDQ (p < 0.001), IBD-F (p < 0.05), and fatigue impact on daily activities (p < 0.001), was observed. During VDZ treatment, arthralgia (23.7%-8.7%) and anemia (22.6%-15.9%) decreased between baseline and W54. Non-serious adverse events (SAEs; 12.2%), SAEs (7.1%), and VDZ-related rash (1.0%) were reported. Mean CD-related hospitalization duration decreased from baseline (10.2 days) to the end of the study (5.3 days).

CONCLUSION

POLONEZ II demonstrated long-term real-world benefits of VDZ toward effectiveness, safety, and improved PROs and patients' quality of life.

TRIAL REGISTRATION

ENCePP (EUPAS32716).

The resolvin D2 and omega-3 polyunsaturated fatty acid as a new possible therapeutic approach for inflammatory bowel diseases

Inflammatory bowel diseases (IBD) are idiopathic disorders characterized by chronic gastrointestinal inflammation. Given conventional therapies' adverse effects and clinical failures, novel approaches are being investigated. Recent studies have highlighted the role of specialized pro-resolving lipid mediators (SPMs) in the active resolution of chronic inflammation. In this regard, omega-3 fatty acid-derived Resolvin D2 (RvD2) appears to play a protective role in the pathophysiology of IBD. Therefore, we characterized the RvD2 pathway and its receptor expression in the intestinal mucosa of experimental colitis induced by dextran sulfate sodium. We also evaluated the preventive impact of an omega-3-enriched diet and the therapeutic efficacy of RvD2 compared with anti-TNF-α treatment. We found an increase in TNFα and IL22 expression and decreased levels of enzymes involved in RvD2 biosynthesis, such as PLA2, 15-LOX, 5-LOX, and its receptor GPR18 in experimental colitis. Omega-3 supplementation reduced the Disease Activity Index (DAI), weight loss, colonic shortening, and inflammation. These results and the increased IL-10 transcriptional levels after RvD2 treatment suggest that this mediator attenuated experimental colitis. These results enhance our understanding of the molecular mechanisms involved in the exacerbated inflammatory response present in experimental colitis and suggest that RvD2 and its omega-3 precursor offer a promising therapeutic approach for IBD.

Improving Differentiation of Crohn's Disease and Ulcerative Colitis Proteomes through Protein-Wide Association Study Feature Selection in Machine Learning

Background and Aims

Diagnostic differentiation between Crohn's disease (CD) and ulcerative colitis (UC) is crucial for timely and suitable therapeutic measures. The current gold standard for differentiating between CD and UC involves endoscopy and histology, which are invasive and costly. We aimed to identify blood plasma proteomic signatures using a Protein-Wide Association Study (PWAS) approach to differentiate CD from UC and evaluate the efficacy of these signatures as features in machine learning (ML) classifiers.

Methods

Among participants (n=1,106; nCD=636; nUC=470) of the Study of a Prospective Adult Research Cohort with IBD (SPARC), plasma protein (n=2,920) levels were estimated using Olink proteomics. A PWAS with Bonferroni correction for multiple testing was used to identify proteins associated with disease states after controlling for age, sex, and disease severity. ML classifiers examined the diagnostic utility of these models. Feature importance was determined via SHapley Additive exPlanations (SHAP) analysis.

Results

Thirteen proteins which were significantly differentially abundant in CD vs UC (all |β|s > 0.22, all adjusted p values < 8.42E-06). Random forest models of proteins differentiated between CD and UC with models trained only on PWAS identified proteins (Average ROC-AUC 0.73) outperforming models trained of the full proteome (Average ROC-AUC 0.62). SHAP analysis revealed that Granzyme B, insulin-like peptide 5 (INSL5), and interleukin-12 subunit beta (IL-12B) were the most important features.

Conclusions

Our findings demonstrate that PWAS-based feature selection approaches are a powerful method to identify features in complex, noisy datasets. Importantly, we have identified novel peptide based biomarkers such as INSL5, that can be potentially used to complement existing strategies to differentiate between CD and UC.

Nasopharyngeal carcinoma-associated inflammatory cytokines: ongoing biomarkers

Nasopharyngeal carcinoma (NPC) is a neoplasm related to inflammation; the expression of cytokines, such as CCL3, CCL4, CCL20, IL-1α, IL-1β, IL-6, IL-8, and IL-10, among others, is presumed to be associated with NPC occurrence and development. Therefore, the circulating levels of these cytokines may be potential biomarkers for assessing tumor aggressiveness, exploring cellular interactions, and monitoring tumor therapeutic responses. Numerous scholars have comprehensively explored the putative mechanisms through which these inflammatory factors affect NPC progression and therapeutic responses. Moreover, investigations have focused on elucidating the correlation between the systemic levels of these cytokines and the incidence and prognosis of NPC. This comprehensive review aims to delineate the advancements in research concerning the relationship between inflammatory factors and NPC while considering their prospective roles as novel prognostic and predictive biomarkers in the context of NPC.

Evaluating the predictive effect of vitamin D on clinical outcomes of infliximab-treated Crohn's disease patients in western China

The aim was to evaluate predictors of clinical outcomes in infliximab (IFX)-treated Crohn's disease (CD) patients in western China and provide evidence for future treatment optimization. Our retrospective study included CD patients at Chongqing General Hospital from July 2022 to July 2023. Clinical data of CD patients at baseline and the endpoint (the seventh IFX treatment, 38 weeks) were collected. Baseline variables of IFX-treated patients with regard to clinical remission [Crohn's Disease Activity Index (CDAI) < 150] at endpoint were assessed, and the correlation of serum vitamin D (Vit-D) levels before initiating IFX therapy and CDAI at week 38 was analyzed. Sixty patients with IFX-treated CD were included. The Vit-D-deficient rate was 51.7% at baseline, 81.7% of patients achieved clinical remission, and 66.7% achieved endoscopic remission at week 38 of IFX treatment. Vit-D level at baseline was an independent predictors of clinical remission after IFX treatment (P < 0.05). Receiver operating characteristic curve analysis showed that when Vit-D concentration was 15.81 ng/ml, the area under the curve was 0.711 (95% CI 0.523-0.899, P = 0.03). The sensitivity and specificity were 81.6% and 63.6%, respectively. Vit-D level in the normal BMI, non-smoking, immunosuppressant-treated subgroup had independent predictive value for CDAI at endpoint (P < 0.05). Baseline Vit-D level predicted clinical remission in CD patients after IFX treatment, especially in those with normal body mass index, who do not smoke, and who take IFX in combination with immunosuppressants.

The role of Nrf2 in immune cells and inflammatory autoimmune diseases: a comprehensive review

INTRODUCTION

Nrf2 regulates mild stress, chronic inflammation, and metabolic changes by regulating different immune cells via downstream signaling. Collection of information about the role of Nrf2 in inflammatory autoimmune diseases will better understand the therapeutic potential of targeting Nrf2 in these diseases.

AREAS COVERED

In this review, we comprehensively discussed biological function of Nrf2 in different immune cells, including Nrf2 preventing oxidative tissue injury, affecting apoptosis of immune cells and inflammatory cytokine production. Moreover, we discussed the role of Nrf2 in the development of inflammatory autoimmune diseases.

EXPERT OPINION

Nrf2 binds to downstream signaling molecules and then provides durable protection against different cellular and organ stress. It has emerged as an important target for inflammatory autoimmune diseases. Development of Nrf2 modulator drugs needs to consider factors such as target specificity, short/long term safety, disease indication identification, and the extent of variation in Nrf2 activity. We carefully discussed the dual role of Nrf2 in some diseases, which helps to better target Nrf2 in the future.

Anti-DEFA5 Monoclonal Antibody Clones 1A8 and 4F5 Immunoreactive Bioassay for Diagnosing Inflammatory Bowel Disease

Background

Robust evidence suggests that the aberrant expression of α defensin 5 protein (DEFA5) in colon inflammatory bowel diseases (IBDs) underlies the distinct pathogenesis of Crohn's colitis, can be exploited as a reliable diagnostic biomarker to differential diagnosis of Crohn's colitis (CC) from Ulcerative colitis (UC) in otherwise indeterminate colitis (IC). We evaluated the specificity of the commercially available anti-DEFA5 antibodies and showed further validation of their appropriateness for a given application is required.

Methods

We established two mouse monoclonal DEFA5 antibody clones 1A8 and 4F5 by immunizing the mice with purified recombinant protein and validated the specificity, selectivity and cross reactivity in recognizing the endogenous and recombinant DEFA5 protein, especially for Immunohistochemistry, Western blot, Immunoprecipitation, or enzyme-linked immunosorbent assay.

Results

Clones 1A8 and 4F5 recognized effectively the endogenous DEFA5 in active human diverticulitis (DV), UC, CC or IC disease samples, including transiently transfected HEK293T cells expressing DEFA5 with high degree of specificity and minimal non-confounding cross reactivity.

Conclusions

1A8 and 4F5 clones are worth studying in larger IBD cohorts to fully address whether DEFA5 expression may be used as a diagnostic biomarker to discrimination of the diagnosis of UC from CC or IC into authentic CC or UC or a colitis with different pathological characteristics.

Exploring Fecal Microbiota Transplantation for Modulating Inflammation in Parkinson's Disease: A Review of Inflammatory Markers and Potential Effects

Parkinson's disease (PD) is a complex neurodegenerative disorder characterized by numerous motor and non-motor symptoms. Recent data highlight a potential interplay between the gut microbiota and the pathophysiology of PD. The degeneration of dopaminergic neurons in PD leads to motor symptoms (tremor, rigidity, and bradykinesia), with antecedent gastrointestinal manifestations, most notably constipation. Consequently, the gut emerges as a plausible modulator in the neurodegenerative progression of PD. Key molecular changes in PD are discussed in the context of the gut-brain axis. Evidence suggests that the alterations in the gut microbiota composition may contribute to gastroenteric inflammation and influence PD symptoms. Disturbances in the levels of inflammatory markers, including tumor necrosis factor-α (TNF α), interleukin -1β (IL-1β), and interleukin-6 (IL-6), have been observed in PD patients. These implicate the involvement of systemic inflammation in disease pathology. Fecal microbiota transplantation emerges as a potential therapeutic strategy for PD. It may mitigate inflammation by restoring gut homeostasis. Preclinical studies in animal models and initial clinical trials have shown promising results. Overall, understanding the interplay between inflammation, the gut microbiota, and PD pathology provides valuable insights into potential therapeutic interventions. This review presents recent data about the bidirectional communication between the gut microbiome and the brain in PD, specifically focusing on the involvement of inflammatory biomarkers.

Blood metabolites mediate the causal relationship between circulating CX3CL1 levels and prostate cancer: A 2-step Mendelian randomization study

Chemokines influence the progression of prostate cancer (PCa) through multiple mechanisms. However, the effect of C-X3-C chemokine ligand 1 (CX3CL1) on PCa risk remains controversial. Our study aimed to investigate whether circulating CX3CL1 is causally associated with PCa and to identify metabolites that have mediating effects using the 2-step bidirectional Mendelian randomization (MR) analysis process. Inverse variance weighting (IVW) results were used as the primary observations, while additional sensitivity analyses were conducted. For each standard deviation increase exhibited by the circulating CX3CL1 levels, the risk of PCa was reduced by 0.4% (IVW: OR = 0.996, [95% CI = 0.994-0.998], P < .001), and blood alliin levels increased by 19% (IVW: OR = 1.185, [95% CI = 1.01-1.54], P = .003). For each standard deviation increase in the blood alliin levels, the risk of PCa was reduced by 0.1% (IVW: OR = 0.999, [95% CI = 0.997-0.999], P = .03). Therefore, the protective effect of circulating CX3CL1 on PCa may be mediated by blood alliin levels (mediated proportion = 6.7%). The results supported the notion that high levels of circulating CX3CL1 indicate a lower PCa risk and the idea that the food-derived antioxidant alliin may mediate this association. We emphasize that the use of CX3CL1 as a protective factor against PCa may provide new strategies for PCa prevention and care in the future.

Early diagnosis and treatment of perianal Crohn's disease in a 1-year-old infant: Case report and review of literature

Inflammatory bowel disease is rare in infants and it includes perianal Crohn's disease, which is inflammation at or near the anus. An early diagnosis is essential to prevent the complications that may affect the development and growth of the child.

Correction: Linking bacterial enterotoxins and alpha defensin 5 expansion in the Crohn's colitis: A new insight into the etiopathogenetic and differentiation triggers driving colonic inflammatory bowel disease

[This corrects the article DOI: 10.1371/journal.pone.0246393.].

Exploring Predictive Biomarkers of Relapse in Ulcerative Colitis: A Proteomics Approach

INTRODUCTION AND AIMS

Risk stratification of subjects with a history of inflammatory bowel disease (IBD) into those likely to relapse and those who will remain quiescent continues to be a significant challenge. The aim of this study was to investigate whether certain proteomic signature profiles or biomarkers during remission are associated with future disease relapse in patients with ulcerative colitis (UC).

METHODS

Endoscopic rectal samples from patients with UC in clinical, endoscopic, and histological remission at index endoscopy were collected, as well as samplers from normal control individuals. The patients were stratified to early relapsers (ERs) if they developed clinical signs of UC flare within 6 months of index endoscopy or nonrelapsers (NRs) if there was no relapse after 36 months of follow-up. The pooled rectal samples from ERs, NRs, and control individuals were subjected to nano-liquid chromatography and tandem mass spectrometry as per standard iTRAQ (isobaric tags for relative and absolute quantitation) workflow methodology. Selected proteomics-yielded candidates were subjected to orthogonal validation via immunoblotting, in a biomarker discovery exercise.

RESULTS

Sixty-one patients were included, of whom 8 had clinical relapse within 6 months from the index endoscopy, and 43 patients had no clinical symptoms of relapse within the 36-month follow-up period. Ten patients who had clinical signs of relapse between 6 and 36 months were excluded. Seventeen control individuals were also included. Soluble proteomics analyses between ERs, NRs, and control individuals revealed a series of upregulated and downregulated proteins. Following orthogonal validation, upregulated TRX (P = .001) and IGHA1 (P = .001) were observed in ERs relative to NRs.

CONCLUSIONS

Several novel candidate tissue biomarkers have been identified in this study, which could discriminate patients with UC at risk of early relapse from those in long-term sustained remission. Our findings may pave the way for pre-emptive UC disease monitoring and therapeutic decision making.

A systematic review and meta-regression on international trends in the incidence of ulcerative colitis in children and adolescents associated with socioeconomic and geographic factors

The incidence of ulcerative colitis (UC) among children and adolescents is rising globally, albeit with notable discrepancies across countries. This systematic review and meta-analysis aims to provide a comprehensive overview of the incidence rates of pediatric UC in various countries and explore potential influencing factors. A systematic literature search was conducted in PubMed and EMBASE (via OVID) for studies published between January 1, 1970, and December 31, 2019. Additionally, a manual search was performed to identify relevant systematic reviews. Meta-analyses and meta-regressions were employed to determine the overall incidence rate and examine potential factors that may influence it. A total of 66 studies were included in the qualitative analysis, while 65 studies were included in the meta-analysis and 50 studies were meta-regression. The study reports a rising incidence of pediatric UC in several countries but significant differences across geographic regions, with no discernible global temporal trend. In addition, our meta-regression analysis showed that geographic location and socioeconomic factors significantly influenced the incidence of UC.

CONCLUSION

Our findings indicate a rising incidence of pediatric UC in numerous countries since 1970, but with significant geographical variation, potentially presenting challenges for respective healthcare systems. We have identified geographic and socioeconomic factors that contribute to the observed heterogeneity in incidence rates. These findings provide a foundation for future research and health policies, aiming to tackle the growing burden of UC among children and adolescents.

WHAT IS KNOWN

• The incidence of ulcerative colitis in childhood and adolescence appears to be increasing worldwide and varies internationally. • Environmental and lifestyle factors are suspected as potential causes.

WHAT IS NEW

• Our results highlight that the heterogeneity in incidence rates can be attributed to geographic and socio-economic factors.

Cirsimaritin Alleviates Dextran Sodium Sulfate-Induced Acute Colitis in Experimental Animals: A Therapeutic Approach for Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) is a chronic disease that affects the entire digestive tract. IBD can be classified as ulcerative colitis or Crohn's disease. The key symptoms of IBD include the emergence of abscesses or pustules, pronounced abdominal discomfort, diarrhea, fistulas, and intestinal narrowing, all of which can greatly affect a patient's daily well-being. Several factors, including bacterial infections, immune response irregularities, and changes in the intestinal milieu, can contribute to the onset of IBD. The aim of this study was investigating the role of cirsimaritin in reducing the severity of colitis in animal model. To induce colitis in laboratory Swiss albino mice, a 4% dextran sulfate sodium (DSS) concoction was provided in their hydration source for a duration of six days. Before the onset of colitis, mice were treated with cirsimaritin (10 mg/kg) once daily to evaluate its potential treatment effects against DSS-induced inflammation. The results showed that 10 mg/kg of cirsimaritin decreased colitis severity (P<0.05). Moreover, cirsimaritin successfully reversed the detrimental effects induced by DSS, including weight reduction, colon truncation, tissue-related damage, increased levels of inflammatory cells in the affected region, and secretion of proinflammatory cytokines. Our findings suggest that cirsimaritin can effectively alleviate acute colitis triggered by DSS.

Identification of cell differentiation trajectory-related gene signature to reveal the prognostic significance and immune landscape in prostate cancer based on multiomics analysis

Background

In the context of prostate cancer (PCa), the occurrence of biochemical recurrence (BCR) stands out as a pivotal factor significantly impacting prognosis, potentially leading to metastasis and mortality. However, the early detection of BCR poses a substantial challenge for PCa patients. There is an urgent need to pinpoint hub genes that can serve as predictive indicators for BCR in PCa patients.

Methods

Our primary goal was to identify cell differentiation trajectory-related gene signature in PCa patients by pseudo-time trajectory analysis. We further explored the functional enrichment of overlapped marker genes and probed clinically relevant modules and BCR-related genes using Weighted Gene Co-expression Network Analysis (WGCNA) in PCa patients. Key genes predicting recurrence-free survival were meticulously identified through univariate and multivariate Cox regression analyses. Subsequently, these genes were utilized to construct a prognostic gene signature, the expression, predictive efficacy, putative functions, and immunological landscape of which were thoroughly validated. Additionally, we employed immunohistochemistry (IHC) and a western blotting assay to quantify the expression of PYCR1 in clinical samples.

Results

Our single-cell RNA (scRNA) sequencing analysis unveiled three subgroups characterized by distinct differentiation trajectories, and the marker genes associated with these groups were extracted from PCa patients. These marker genes successfully classified the PCa sample into two molecular subtypes, demonstrating a robust correlation with clinical characteristics and recurrence-free survival. Through WGCNA and Lasso analysis, we identified four hub genes (KLK3, CD38, FASN, and PYCR1) to construct a risk profile of prognostic genes linked to BCR. Notably, the high-risk patient group exhibited elevated levels of B cell naive, Macrophage M0, and Macrophage M2 infiltration, while the low-risk group displayed higher levels of T cells CD4 memory activated and monocyte infiltration. Furthermore, IHC and western blotting assays confirmed the heightened expression of PYCR1 in PCa tissues.

Conclusion

This study leveraged the differentiation trajectory and genetic variability of the microenvironment to uncover crucial prognostic genes associated with BCR in PCa patients. These findings present novel perspectives for tailoring treatment strategies for PCa patients on an individualized basis.

Sex-specific colonic mitochondrial dysfunction in the indomethacin-induced rat model of inflammatory bowel disease

Introduction: Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract and encompasses Crohn's Disease and Ulcerative Colitis. Women appear to have more severe and recurring symptoms of IBD compared to men, most likely due to hormonal fluctuations. Studies have shown that mitochondrial dysfunction plays a role in the development of inflammation and there is evidence of colon mitochondrial alterations in IBD models and patients. In this study we have identified the presence of sex-specific colon mitochondrial dysfunction in a rat model of IBD. Methods: Eight-week-old male and female rats were treated with indomethacin to induce IBD and mitoTEMPO was administered daily either after or before induction of IBD and until euthanasia. Colons were collected for histology and mitochondrial experiments. Intact mitochondrial respiration, reactive oxygen species (mtROS), the activities of the individual electron transport complexes and the activities of the antioxidant enzymes were measured to assess mitochondrial function. Results: IBD male rats showed a decrease in citrate synthase activity, cardiolipin levels, catalase activity and an increase in mtROS production. IBD females show a decrease in intact colon mitochondrial respiration, colon mitochondria respiratory control ratio (RCR), complex I activity, complex IV activity, and an increase in mtROS. Interestingly, control females showed a significantly higher rate of complex I and II-driven intact mitochondrial respiration, MCFA oxidation, complex II activity, complex III activity, and complex IV activity compared to control males. The use of a mitochondrial-targeted therapy, mitoTEMPO, improved the disease and colon mitochondrial function in female IBD rats. However, in the males there was no observed improvement, likely due to the decrease in catalase activity. Conclusion: Our study provides a better understanding of the role mitochondria in the development of IBD and highlights sex differences in colon mitochondrial function. It also opens an avenue for the development of strategies to re-establish normal mitochondrial function that could provide more options for preventive and therapeutic interventions for IBD.

Correlation of Socioeconomic and Environmental Factors With Incidence of Crohn Disease in Children and Adolescents: Systematic Review and Meta-Regression

BACKGROUND

The worldwide incidence of Crohn disease (CD) in childhood and adolescence has an increasing trend, with significant differences between different geographic regions and individual countries. This includes an increase in the incidence of CD in countries and geographic regions where CD was not previously prevalent. In response to the increasing incidence, the pediatric care landscape is facing growing challenges.

OBJECTIVE

This systematic review and meta-analysis were undertaken to comprehensively delineate the incidence rates of CD in pediatric populations across different countries and to explore potential influencing factors.

METHODS

We performed a systematic review of PubMed and Embase (via Ovid) for studies from January 1, 1970, to December 31, 2019. In addition, a manual search was performed in relevant and previously published reviews. The results were evaluated quantitatively. For this purpose, random effects meta-analyses and meta-regressions were performed to investigate the overall incidence rate and possible factors influencing the incidence.

RESULTS

A qualitative synthesis of 74 studies was performed, with 72 studies included in the meta-analyses and 52 in the meta-regressions. The results of our meta-analysis showed significant heterogeneity between the individual studies, which cannot be explained by a sample effect alone. Our findings showed geographical differences in incidence rates, which increased with increasing distance from the equator, although no global temporal trend was apparent. The meta-regression analysis also identified geographic location, UV index, and Human Development Index as significant moderators associated with CD incidence.

CONCLUSIONS

Our results suggest that pediatric CD incidence has increased in many countries since 1970 but varies widely with geographic location, which may pose challenges to the respective health care systems. We identified geographic, environmental, and socioeconomic factors that contribute to the observed heterogeneity in incidence rates. These results can serve as a basis for future research. To this end, implementations of internationally standardized and interoperable registries combined with the dissemination of health data through federated networks based on a common data model, such as the Observational Medical Outcomes Partnership, would be beneficial. This would deepen the understanding of CD and promote evidence-based approaches to preventive and interventional strategies as well as inform public health policies aimed at addressing the increasing burden of CD in children and adolescents.

TRIAL REGISTRATION

PROSPERO International prospective register of systematic reviews CRD42020168644; https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=168644.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

RR2-10.1136/bmjopen-2020-037669.

Discerning Endoscopic Severity of Inflammatory Bowel Disease by Scoping the Peripheral Blood Transcriptome

Background and Aims

Ulcerative colitis (UC) and Crohn's disease (CD) are chronic inflammatory bowel diseases (IBDs) with an incompletely understood etiology and pathogenesis. Identification of suitable drug targets and assessment of disease severity are crucial for optimal management.

Methods

Using RNA sequencing, we investigated differential gene expression in peripheral blood samples from IBD patients and non-inflamed controls, analyzed pathway enrichment, and identified genes whose expression correlated with endoscopic disease severity.

Results

Neutrophil degranulation emerged as the most significant pathway across all IBD sample types. Signaling by interleukins was prominent in patients with active intestinal inflammation but also enriched in CD and UC patients without intestinal inflammation. Nevertheless, genes correlated to endoscopic disease severity implicated the primary cilium in CD patients and translation and focal adhesion in UC patients. Moreover, several of these genes were located in genome-wide associated loci linked to IBD, cholesterol levels, blood cell counts, and levels of markers assessing liver and kidney function. These genes also suggested connections to intestinal epithelial barrier dysfunction, contemporary IBD drug treatment, and new actionable drug targets. A large number of genes associated with endoscopic disease severity corresponded to noncoding RNAs.

Conclusion

This study revealed biological pathways associated with IBD disease state and endoscopic disease severity, thus providing insights into the underlying mechanisms of IBD pathogenesis as well as identifying potential biomarkers and therapies. Peripheral blood might constitute a suitable noninvasive diagnostic sample type, in which gene expression profiles might serve as indicators of ongoing mucosal inflammation, and thus guide personalized treatment decisions.

A leaky gut dysregulates gene networks in the brain associated with immune activation, oxidative stress, and myelination in a mouse model of colitis

The gut and brain are increasingly linked in human disease, with neuropsychiatric conditions classically attributed to the brain showing an involvement of the intestine and inflammatory bowel diseases (IBDs) displaying an ever-expanding list of neurological comorbidities. To identify molecular systems that underpin this gut-brain connection and thus discover therapeutic targets, experimental models of gut dysfunction must be evaluated for brain effects. In the present study, we examine disturbances along the gut-brain axis in a widely used murine model of colitis, the dextran sodium sulfate (DSS) model, using high-throughput transcriptomics and an unbiased network analysis strategy coupled with standard biochemical outcome measures to achieve a comprehensive approach to identify key disease processes in both colon and brain. We examine the reproducibility of colitis induction with this model and its resulting genetic programs during different phases of disease, finding that DSS-induced colitis is largely reproducible with a few site-specific molecular features. We focus on the circulating immune system as the intermediary between the gut and brain, which exhibits an activation of pro-inflammatory innate immunity during colitis. Our unbiased transcriptomics analysis provides supporting evidence for immune activation in the brain during colitis, suggests that myelination may be a process vulnerable to increased intestinal permeability, and identifies a possible role for oxidative stress and brain oxygenation. Overall, we provide a comprehensive evaluation of multiple systems in a prevalent experimental model of intestinal permeability, which will inform future studies using this model and others, assist in the identification of druggable targets in the gut-brain axis, and contribute to our understanding of the concomitance of intestinal and neuropsychiatric dysfunction.

Impact of insomnia upon inflammatory digestive diseases and biomarkers: a two-sample mendelian randomization research on Europeans

BACKGROUND

A number of observational studies indicate that insomnia is linked to inflammatory digestive diseases (IDDs). However, the definite relationship between insomnia and IDDs remains unclear.

METHODS

We obtained the publicly available data from genome-wide association studies (GWAS) to conduct two-sample Mendelian randomization (MR) for association assessment. Five MR analysis methods were used to calculate the odds ratio (OR) and effect estimate, and the heterogeneity and pleiotropy tests were performed to evaluate the robustness of the variable instruments (IVs).

RESULTS

One exposure and twenty outcome datasets based on European populations were included in this study. Using the inverse variance weighted method, we found insomnia was closely correlated with esophageal ulcer (OR = 1.011, 95%CI = 1.004-1.017, p = 0.001) and abdominal pain (effect estimate = 1.016, 95%CI = 1.005-1.026, p = 0.003). Suggestive evidence of a positively association was observed between insomnia and duodenal ulcer (OR = 1.006, 95%CI = 1.002-1.011, p = 0.009), gastric ulcer (OR = 1.008, 95%CI = 1.001-1.014, p = 0.013), rectal polyp (OR = 1.005, 95%CI = 1.000-1.010, p = 0.034), haemorrhoidal disease (OR = 1.242, 95%CI = 1.004-1.535, p = 0.045) and monocyte percentage (effect estimate = 1.151, 95%CI = 1.028-1.288, p = 0.014). No correlations were observed among other IDDs, phenotypes and biomarkers.

CONCLUSIONS

Our MR study assessed the relationship between insomnia and IDDs/phenotypes/biomarkers in depth and revealed potential associations between insomnia and ulcers of the esophagus and abdominal pain.

Altered metabolome and microbiome features provide clues in predicting recurrence of ulcerative colitis

PURPOSE

Many studies have shown that the imbalance of the intestinal flora and metabolite can lead to the development of ulcerative colitis (UC), but their role in recurrent-UC is still unclear. We studied the intestinal flora and metabolites associated with recurrent-UC to elucidate the mechanism and biomarkers of recurrent-UC.

METHODS

Ulcerative colitis (UC) models in active, remission, and recurrence stages were established, and the abundance of intestinal flora was determined by 16 S rRNA sequencing. The changes in the metabolites present in feces and serum were analyzed by UPLC-MS/MS.

RESULTS

We identified 24 metabolites in feces and serum, which might be used as diagnostic and predictive biomarkers of recurrent-UC. The dominant flora of recurrent-UC included Romboutsia, UCG-005, etc. The results of a network analysis found that long-chain fatty acids and phenylalanine were strongly correlated with Firmicutes and Proteobacteria, which indicated that the recurrence of UC might be closely related to metabolites and microorganisms.

CONCLUSION

The changes in intestinal microbiota and metabolites are closely related to the development of UC. Microbiota is an important inducer of UC, which can regulate metabolites through the 'microorganism-gut-metabolite' axis. It may provide a new method for the prediction and treatment of UC.

Global evolving patterns and cross-country inequalities of inflammatory bowel disease burden from 1990 to 2019: a worldwide report

AIMS

Inflammatory bowel disease (IBD) is a global disease. We aim to summarize the latest epidemiological patterns of IBD at the national, regional and global levels to give well-deserved attention and outline facilitating measures to reduce the disease burden.

METHODS

We collected the incidence, prevalence, mortality and disability-adjusted life years (DALYs) of IBD in 204 countries and territories from 1990 to 2019 using data from the Global Burden of Disease Study 2019. We further calculated the estimated annual percentage change (EAPC) to qualify the temporal trends of IBD burden by sex, age and region over the past 30 years.

RESULTS

Globally, a total of 404.55 thousand incident cases, 4898.56 thousand prevalent cases, 41.00 thousand deaths and 1622.50 thousand DALYs of IBD were estimated in 2019. The age-standardized DALYs decreased from 27.2 in 1990 to 20.15 per 100,000 people in 2019, with an EAPC of -1.04. The high socio-demographic index regions presented pronounced age-standardized rates (ASRs) consistently over the last 30 years. The high-income North America had the highest ASRs in 2019, followed by Western Europe and Australasia. No gender difference was observed after being stratified by sex.

CONCLUSIONS

The accumulated IBD patients are expected to increase in the future due to the increased rate of IBD in developing countries, and social aging in developed countries. Understanding the changes in epidemiological patterns helps to provide evidence to mitigate the rising burden of IBD.

Understanding exosomes: Part 1-Characterization, quantification and isolation techniques

Exosomes are the smallest subset of extracellular signaling vesicles secreted by most cells with a diameter in the range of 30-150 nm. Their use has gained great momentum recently due to their ability to be utilized as diagnostic tools with a vast array of therapeutic applications. Over 5000 publications are currently being published yearly on this topic, and this number is only expected to dramatically increase as novel therapeutic strategies continue to be investigated. This review article first focuses on understanding exosomes, including their cellular origin, biogenesis, function, and characterization. Thereafter, overviews of the quantification methods and isolation techniques are given with discussion over their potential use as novel therapeutics in regenerative medicine.

Uphill battle: Innovation of thiopurine therapy in global inflammatory bowel disease care

Inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract that encompasses two major conditions: Crohn's disease (CD) and ulcerative colitis (UC). Historically, IBD has been primarily reported in western countries, but over the past decades, its prevalence is rapidly increasing, especially in lower and middle-income countries (LMICs) such as India and China and also in Sub-Saharan Africa. The prevalence of IBD in LMICs has been the subject of growing concern due to the impact of access to public healthcare and the burden it places on healthcare resources. The classical thiopurines face significant challenges due to cessation of therapy in approximately half of patients within one year due to side effects or ineffectiveness. In this article, we highlight innovating thiopurine treatment for IBD patients in downregulating side effects and improving efficacy.

Lnc-ing RNA to intestinal homeostasis and inflammation

Long noncoding RNAs (lncRNAs) play important roles in numerous biological processes, including the immune system. Initial research in this area focused on cell-based studies, but recent advances underscore the profound significance of lncRNAs at the organismal level, providing invaluable insights into their roles in inflammatory diseases. In this rapidly evolving field, lncRNAs have been described with pivotal roles in the intestinal tract where they regulate intestinal homeostasis and inflammation by influencing processes such as immune cell development, inflammatory signaling pathways, epithelial barrier function, and cellular metabolism. Understanding the regulation and function of lncRNAs in this tissue may position lncRNAs not only as potential disease biomarkers but also as promising targets for therapeutic intervention in inflammatory bowel disease and related diseases.

Serum and Urine Metabolomic Profiling of Newly Diagnosed Treatment-Naïve Inflammatory Bowel Disease Patients

BACKGROUND AND AIMS

Inflammatory bowel disease (IBD) is a prevalent chronic noncurable disease associated with profound metabolic changes. The discovery of novel molecular indicators for unraveling IBD etiopathogenesis and the diagnosis and prognosis of IBD is therefore pivotal. We sought to determine the distinctive metabolic signatures from the different IBD subgroups before treatment initiation.

METHODS

Serum and urine samples from newly diagnosed treatment-naïve IBD patients and age and sex-matched healthy control (HC) individuals were investigated using proton nuclear magnetic resonance spectroscopy. Metabolic differences were identified based on univariate and multivariate statistical analyses.

RESULTS

A total of 137 Crohn's disease patients, 202 ulcerative colitis patients, and 338 HC individuals were included. In the IBD cohort, several distinguishable metabolites were detected within each subgroup comparison. Most of the differences revealed alterations in energy and amino acid metabolism in IBD patients, with an increased demand of the body for energy mainly through the ketone bodies. As compared with HC individuals, differences in metabolites were more marked and numerous in Crohn's disease than in ulcerative colitis patients, and in serum than in urine. In addition, clustering analysis revealed 3 distinct patient profiles with notable differences among them based on the analysis of their clinical, anthropometric, and metabolomic variables. However, relevant phenotypical differences were not found among these 3 clusters.

CONCLUSIONS

This study highlights the molecular alterations present within the different subgroups of newly diagnosed treatment-naïve IBD patients. The metabolomic profile of these patients may provide further understanding of pathogenic mechanisms of IBD subgroups. Serum metabotype seemed to be especially sensitive to the onset of IBD.

The Incidence of Pouch Neoplasia Following Ileal Pouch-Anal Anastomosis in Patients With Inflammatory Bowel Disease

BACKGROUND

Ileal pouch-anal anastomosis (IPAA) is the standard restorative procedure following proctocolectomy in patients with inflammatory bowel disease (IBD) who require colectomy. However, removal of the diseased colon does not eliminate the risk of pouch neoplasia. We aimed to assess the incidence of pouch neoplasia in IBD patients following IPAA.

METHODS

All patients at a large tertiary center with International Classification of Diseases-Ninth Revision/International Classification of Diseases-Tenth Revision codes for IBD who underwent IPAA and had subsequent pouchoscopy were identified using a clinical notes search from January 1981 to February 2020. Relevant demographic, clinical, endoscopic, and histologic data were abstracted.

RESULTS

In total, 1319 patients were included (43.9% women). Most had ulcerative colitis (95.2%). Out of 1319 patients, 10 (0.8%) developed neoplasia following IPAA. Neoplasia of the pouch was seen in 4 cases with neoplasia of the cuff or rectum seen in 5 cases. One patient had neoplasia of the prepouch, pouch, and cuff. Types of neoplasia included low-grade dysplasia (n = 7), high-grade dysplasia (n = 1), colorectal cancer (n = 1), and mucosa-associated lymphoid tissue lymphoma (n = 1). Presence of extensive colitis, primary sclerosing cholangitis, backwash ileitis, and rectal dysplasia at the time of IPAA were significantly associated with increased risk of pouch neoplasia.

CONCLUSIONS

The incidence of pouch neoplasia in IBD patients who have undergone IPAA is relatively low. Extensive colitis, primary sclerosing cholangitis, and backwash ileitis prior to IPAA and rectal dysplasia at the time of IPAA raise the risk of pouch neoplasia significantly. A limited surveillance program might be appropriate for patients with IPAA even with a history of colorectal neoplasia.

Awareness of inflammatory bowel disease among the general population of Al-Baha region, Saudi Arabia

Inflammatory bowel disease (IBD) is a chronic gastrointestinal disorder that encompasses Crohn's disease (CD) and ulcerative colitis (UC). IBD can be debilitating and has severe effects on the quality of life of the affected individuals. However, despite the increasing frequency of IBD around the world, the general population lacks knowledge and comprehension of this illness. The aim of this study was to determine the level of knowledge and awareness of IBD among the general population in Al-Baha region, Saudi Arabia. We carried out a cross-sectional study using an online self-administered validated questionnaire. The questionnaire included demographic questions, as well as questions regarding knowledge and awareness of IBD. The study included 473 participants selected by convenience random sampling with equal chance of selection. Approximately 61% of the participants had never heard about IBD, and for those who did, social media was the most common source of information (40.6%). Also, the majority of participants had limited knowledge about the different types of IBD (74%), their symptoms, and long-term effects. Women had a significantly higher level of adequate knowledge (12.1%) compared to men (4.8%) (P = 0.011). The study demonstrated a substantial lack of understanding and awareness of IBD among the general population in Al-Baha region, notably regarding the different types of IBD, their symptoms, and their long-term effects. The study underscores the need for further educational initiatives and resources to raise public knowledge and comprehension of IBD globally.

Cancer in the Anal Transition Zone and Ileoanal Pouch following Surgery for Ulcerative Colitis

Restorative proctocolectomy with ileal pouch-anal anastomosis remains the gold standard treatment for patients with ulcerative colitis who desire restoration of intestinal continuity. Despite a significant cancer risk reduction after surgical removal of the colon and rectum, dysplasia and cancers of the ileal pouch or anal transition zone still occur and are a risk even if an anal canal mucosectomy is performed. Surgical care and maintenance after ileoanal anastomosis must include consideration of malignant potential along with other commonly monitored variables such as bowel function and quality of life. Cancers and dysplasia of the ileal pouch are rare but sometimes difficult-to-manage sequelae of pouch surgery.

Two-component system RstAB promotes the pathogenicity of adherent-invasive Escherichia coli in response to acidic conditions within macrophages

Adherent-invasive Escherichia coli (AIEC) strain LF82, isolated from patients with Crohn's disease, invades gut epithelial cells, and replicates in macrophages contributing to chronic inflammation. In this study, we found that RstAB contributing to the colonization of LF82 in a mouse model of chronic colitis by promoting bacterial replication in macrophages. By comparing the transcriptomes of rstAB mutant- and wild-type when infected macrophages, 83 significant differentially expressed genes in LF82 were identified. And we identified two possible RstA target genes (csgD and asr) among the differentially expressed genes. The electrophoretic mobility shift assay and quantitative real-time PCR confirmed that RstA binds to the promoters of csgD and asr and activates their expression. csgD deletion attenuated LF82 intracellular biofilm formation, and asr deletion reduced acid tolerance compared with the wild-type. Acidic pH was shown by quantitative real-time PCR to be the signal sensed by RstAB to activate the expression of csgD and asr. We uncovered a signal transduction pathway whereby LF82, in response to the acidic environment within macrophages, activates transcription of the csgD to promote biofilm formation, and activates transcription of the asr to promote acid tolerance, promoting its replication within macrophages and colonization of the intestine. This finding deepens our understanding of the LF82 replication regulation mechanism in macrophages and offers new perspectives for further studies on AIEC virulence mechanisms.