The risk of rheumatoid arthritis among patients with inflammatory bowel disease: a systematic review and meta-analysis

Association between Rheumatoid Arthritis and the Incidence of IgA Nephropathy

INTRODUCTION

IgA nephropathy and rheumatoid arthritis are both common autoimmune diseases, but epidemiological data are limited on the relationship between these two diseases. We aimed to assess the association between rheumatoid arthritis and the risk of developing IgA nephropathy.

METHODS

In this study, we analyzed 4,311,393 adults using a nationwide epidemiological database in Japan. The definitions of rheumatoid arthritis and IgA nephropathy were based on ICD-10 codes. After excluding individuals with a prior history of IgA nephropathy, study participants were categorized into two groups according to the presence of rheumatoid arthritis. The primary outcome was the incidence of IgA nephropathy between January 2005 and May 2022.

RESULTS

Median (interquartile range) age was 44 (36-53) years, and 2,497,313 (58%) were men. Rheumatoid arthritis was observed in 41,828 individuals (1.0%). During a median follow-up of 1,089 (532-1,797) days, there were 2,610 and 43 incidences of IgA nephropathy in individuals without and with rheumatoid arthritis, yielding incidence rates with 95% confidence intervals of 1.74 (1.67-1.81) and 2.99 (2.22-4.04) per 10,000 person-years, respectively, indicating a higher cumulative incidence in individuals with rheumatoid arthritis (log-rank p= 0.0002). Multivariable Cox regression analysis demonstrated that comorbid rheumatoid arthritis had a higher risk for developing IgA nephropathy (Hazard ratio 1.50, 95% confidence interval 1.10-2.02). Results were consistent even when IgA nephropathy was defined as both the ICD-10 code with the confirmation of performance of kidney biopsy (Hazard ratio 1.70, 95% confidence interval 1.02-2.83).

CONCLUSION

Our analysis utilizing a largescale population-based cohort concluded that rheumatoid arthritis may increase risk of developing IgA nephropathy.

[Russian Cross-disciplinary Consensus on the diagnosis and treatment of spondyloarthritis associated with inflammatory bowel diseases]

The Russian Cross-disciplinary Consensus on the diagnositic and treatment of spondyloarthritis (SpA) in inflammatory bowel diseases (IBD) was prepared on the initiative of the Loginov Moscow Clinical Scientific Center, using the Delphic system. Its purpose was to consolidate the opinions of experts on the most actual issues of diagnosis and treatment of concomitant immuno-inflammatory diseases (SpA and IBD). An interdisciplinary approach is provided by the participation of leading gastroenterologists and rheumatologists. The working group analyzed domestic and foreign publications on the problem of curation of patients with SpA and IBD. There have been 17 statements and 2 treatment algorithms formulated. Statements 1-3 reflect the fundamental principles of management of patients with SpA and IBD. The principles of early diagnosis of SpA and IBD, including the diagnosis of complications of therapy, are described below. Eleven statements are devoted to current methods of treatment, on the basis of which 2 treatment algorithms have been developed. The statements of the Consensus were submitted to the Expert Council for consideration, edits were made, after which an online vote took place. This paper presents current recommendations for the management, diagnosis and treatment of patients with SpA and IBD.

Hospital-Treated Infections and 15-year Incidence of Musculoskeletal Disorders: A Large Population-Based Cohort Study

Background

Basic science evidence reveals interactions between the immune and bone systems. However, population studies linking infectious diseases and musculoskeletal (MSK) disorders are limited and inconsistent. We aimed to examine the risk of six main MSK disorders (osteoarthritis, rheumatoid arthritis, osteoporosis, gout, low back pain, and neck pain) following hospital-treated infections in a large cohort with long follow-up periods.

Methods

We analysed data from 502,409 UK Biobank participants. Participants free of specific MSK disorders at baseline were included in each analysis. Hospital-treated infections before baseline were identified using national inpatient data, while incident MSK outcomes were ascertained from inpatient records, primary care, and death registers. Participants with prior infections were propensity score matched (1:5) with those without. Hazard ratios (HRs) and absolute rate differences (ARDs) with 95% confidence intervals (CIs) were calculated using Cox proportional hazards models. To assess potential reverse causality due to delayed diagnosis of preexisting illness, analyses were repeated excluding MSK disorder cases that occurred within the first 5 and 10 years post-baseline.

Results

A hospital-treated infection was associated with increased risks of all six MSK disorders, with particularly strong associations for osteoporosis (HR, 1.55 [1.48-1.63]; ARD, 1.48 [95% CI 1.29-1.68] per 1000 person-years) and rheumatoid arthritis (HR, 1.53 [1.41-1.65]; ARD, 0.58 [0.46-0.71] per 1000 person-years), while other disorders showed HRs of 1.28-1.32. Bacterial and viral infections showed similar associations, with MSK infections (generally stronger risk) and other locations both linked to increased risks. Associations remained significant even for incident cases that occurred more than 10 years post-baseline.

Conclusion

Hospital-treated infections are associated with long-term MSK disorder risks, regardless of pathogen type or disorder nature (inflammatory or degenerative). Long-term monitoring and care for MSK health in patients with prior hospital-treated infections are recommended.

Gene expression analysis reveals mir-29 as a linker regulatory molecule among rheumatoid arthritis, inflammatory bowel disease, and dementia: Insights from systems biology approach

BACKGROUND

Rheumatoid arthritis (RA) is a degenerative autoimmune disease, often managed through symptomatic treatment. The co-occurrence of the reported extra-articular comorbidities such as inflammatory bowel disease (IBD), and dementia may complicate the pathology of the disease as well as the treatment strategies. Therefore, in our study, we aim to elucidate the key genes, and regulatory elements implicated in the progression and association of these diseases, thereby highlighting the linked potential therapeutic targets.

METHODOLOGY

Ten microarray datasets each for RA, and IBD, and nine datasets for dementia were obtained from Gene Expression Omnibus. We identified common differentially expressed genes (DEGs) and constructed a gene-gene interaction network. Subsequently, topology analysis for hub gene identification, cluster and functional enrichment, and regulatory network analysis were performed. The hub genes were then validated using independent microarray datasets from Gene Expression Omnibus.

RESULTS

A total of 198 common DEGs were identified from which CD44, FN1, IGF1, COL1A2, and POSTN were identified as the hub genes in our study. These hub genes were mostly enriched in significant processes and pathways like tissue development, collagen binding, cell adhesion, regulation of ERK1/2 cascade, PI3K-AKT signaling, and cell surface receptor signaling. Key transcription factors TWIST2, CEBPA, EP300, HDAC1, HDAC2, NFKB1, RELA, TWIST1, and YY1 along with the miRNA hsa-miR-29 were found to regulate the expression of the hub genes significantly. Among these regulatory molecules, miR-29 emerged as a significant linker molecule, bridging the molecular mechanisms of RA, IBD, and dementia. Validation of our hub genes demonstrated a similar expression trend in the independent datasets used for our study.

CONCLUSION

Our study underscores the significant role of miR-29 in modulating the expression of hub genes and the associated transcription factors, which are crucial in the comorbidity status of RA, dementia, and IBD. This regulatory mechanism highlights miR-29 as a key player in the pathogenesis of these comorbid diseases.

Children and Adolescents Diagnosed With Inflammatory Bowel Disease Are at Increased Risk of Developing Diseases With a Possible Autoimmune Pathogenesis

BACKGROUND

The development of diseases with a possible autoimmune pathogenesis is common in adults with inflammatory bowel disease (IBD). In early onset IBD, it may differ but the evidence is sparse. We aimed to investigate the risk and time span from IBD diagnosis to outcomes with different associated disorders with possible autoimmune pathogenesis.

METHODS

A register-based study included all Danish patients with early onset of IBD (≤18 years) between 1980 and 2021 and 50 matched references without IBD for each case. We examined the risk of type 1 and type 2 diabetes, celiac disease, thyroid disease, rheumatoid arthritis, psoriatic arthritis, and spondyloarthritis in Cox regression models.

RESULTS

In total, 6822 patients with IBD were identified, and 337 728 matched references. The median age at the time of IBD diagnosis or index date for the matched references was 16 years (25-75 percentile: 13-18 years), and the median age at the time of an outcome or at the end of follow-up was 28.1 years (25-75 percentile: 21.5-37.0 years). According to the cumulative incidence plots psoriatic arthritis, and spondyloarthritis was diagnosed approximately 10 years after the IBD onset, and the remaining outcomes later. The adjusted hazard ratio after full follow-up was 4.72 (95% CI, 3.85-5.80) for psoriatic arthritis, 5.21 (95% CI, 4.17-6.50) for spondyloarthritis, 2.77 (95% CI, 1.92-4.00) for celiac disease, 2.15 (95% CI, 1.54-3.01) for rheumatoid arthritis, 1.69 (95% CI, 1.23-2.32) and 1.64 (95% CI, 1.21-2.21) for type 1 and type 2 diabetes, respectively. For thyroid disease, it was 1.16 (95% CI, 0.97-1.40).

CONCLUSIONS

The risk estimates were significantly increased for all outcomes at the end of follow-up, except for thyroid disease, but according to the cumulative incidence plots, only psoriatic arthritis and spondyloarthritis occurred earlier in the IBD cohort than in the matched references.

Oral Spore-Based Probiotic Supplementation Alters Post-Prandial Expression of mRNA Associated with Gastrointestinal Health

Background/Objectives: Unregulated post-prandial dietary endotoxemia may accumulate over time and underlie the development of chronic disease (e.g., leaky gut, inflammatory bowel disease, etc.), for which oral probiotic supplementation may be a prophylactic. The purpose of this study was to determine if 45 d of oral spore-based probiotic supplementation altered gastrointestinal-associated mRNA expression following a high-fat meal. Methods: A subset of apparently healthy individuals from a larger study who had dietary endotoxemia at baseline completed 45 d of supplementation with either a placebo (rice flour; n = 10) or spore-based probiotic (Megasporebiotic™; Novonesis, Kongens Lyngby, Denmark; Bacillus indicus (HU36™), Bacillus subtilis (HU58™), Bacillus coagulans (SC208™), and Bacillus licheniformis (SL-307), and Bacillus clausii (SC109™); n = 10). Venous blood was collected in Paxgene RNA tubes prior to (PRE), 3 h, and 5 h after consumption of a high-fat meal (85% of the daily fat RDA and 65% of the daily calorie needs). Total RNA was analyzed for 579 mRNAs of interest (Nanostring nCounter Sprint; Seattle, WA, USA). After normalization to housekeeping controls and calculation of differential expression relative to PRE and controlled for FDR, 15 mRNAs were determined to be significantly changed at either 3 h and/or 5 h post-prandial in the probiotic group but not in the placebo group. Results: Significant mRNA expressions were associated with gastrointestinal tract barrier function (four mRNAs: BATF3, CCR6, CXCR6, and PDCD2), gastrointestinal immunity (four mRNAs: CLEC5A, IL7, CARD9, and FCER1G), or future IBD risk (seven mRNAs: PD-L1, CSF1R, FAS, BID, FADD, GATA3, and KIR3DL). Conclusions: Collectively, the present findings may support the notion that post-prandial immune response to eating is enhanced following 45 d of probiotic supplementation.

Evaluating the significance of ECSCR in the diagnosis of ulcerative colitis and drug efficacy assessment

Background

The main challenge in diagnosing and treating ulcerative colitis (UC) has prompted this study to discover useful biomarkers and understand the underlying molecular mechanisms.

Methods

In this study, transcriptomic data from intestinal mucosal biopsies underwent Robust Rank Aggregation (RRA) analysis to identify differential genes. These genes intersected with UC key genes from Weighted Gene Co-expression Network Analysis (WGCNA). Machine learning identified UC signature genes, aiding predictive model development. Validation involved external data for diagnostic, progression, and drug efficacy assessment, along with ELISA testing of clinical serum samples.

Results

RRA integrative analysis identified 251 up-regulated and 211 down-regulated DEGs intersecting with key UC genes in WGCNA, yielding 212 key DEGs. Subsequently, five UC signature biomarkers were identified by machine learning based on the key DEGs-THY1, SLC6A14, ECSCR, FAP, and GPR109B. A logistic regression model incorporating these five genes was constructed. The AUC values for the model set and internal validation data were 0.995 and 0.959, respectively. Mechanistically, activation of the IL-17 signaling pathway, TNF signaling pathway, PI3K-Akt signaling pathway in UC was indicated by KEGG and GSVA analyses, which were positively correlated with the signature biomarkers. Additionally, the expression of the signature biomarkers was strongly correlated with various UC types and drug efficacy in different datasets. Notably, ECSCR was found to be upregulated in UC serum and exhibited a positive correlation with neutrophil levels in UC patients.

Conclusions

THY1, SLC6A14, ECSCR, FAP, and GPR109B can serve as potential biomarkers of UC and are closely related to signaling pathways associated with UC progression. The discovery of these markers provides valuable information for understanding the molecular mechanisms of UC.

Impact of Rheumatoid Arthritis on Hospitalized Inflammatory Bowel Disease Patients: Study of Demographics, Clinical Characteristics and Outcomes

Background Inflammatory bowel disease (IBD), comprising ulcerative colitis and Crohn's disease gives rise to chronic intestinal inflammation. Rheumatoid arthritis (RA) is a chronic autoimmune disorder characterized by joint and systemic inflammation. IBD is often linked with various autoimmune diseases, with RA being one of the most common. The coexistence of IBD and RA results in an increased inflammatory state, significantly compromising quality of life. Understanding the epidemiological and clinical characteristics of IBD patients with RA is essential for optimizing their management and improving outcomes. Methodology This retrospective observational study utilized data from the National Inpatient Sample (NIS) database from 2016 to 2020. Patients aged 18 years and older with a primary discharge diagnosis of IBD were included. This population was subdivided into two groups based on the presence and absence of RA. The primary objective was to compare outcomes between hospitalized IBD patients with and without RA. Key outcomes assessed included mortality rates, hospital length of stay (LOS), and total hospital charges. Secondary outcomes included the prevalence of comorbidities and IBD-related complications. Results From 2016 to 2020, a total of 455,655 hospitalized IBD patients were identified, among whom 10,590 (2.32%) had an underlying diagnosis of RA. Patients with both IBD and RA were significantly older than those without RA (mean age 52.21 vs. 45.72 years, p < 0.001) and had a higher proportion of females (72.51% vs. 53.27%, p < 0.01). RA patients exhibited a greater risk of cardiovascular risk factors compared to non-RA patients, including diabetes [adjusted odd ratio (aOR ) 1.12 (1.09-1.16)], hypertension [aOR 1.19 (1.07-1.33)], hyperlipidemia [aOR 1.61 (1.60-1.63)], chronic kidney disease stage 1-4 [aOR 1.35 (1.29-1.41)], coronary artery disease [aOR 1.67 (1.65-1.69)], and heart failure [aOR 1.45 (1.43-1.48)]. However, there were no significant differences in the rates of IBD-related complications or in-hospital mortality between the two groups. The mean hospital LOS was 5.15 days for RA patients and 4.95 days for non-RA patients (p = 0.08), with similar total hospital charges ($48,442.7 vs. $48,720.3, p = 0.88). Conclusion This study shows hospitalized IBD patients with and without RA have similar hospitalization outcomes, however, patients with RA have a higher cardiovascular risk. The findings emphasize the importance of integrated, multidisciplinary management approaches for these patients, addressing not only their gastrointestinal and rheumatologic conditions but also their associated comorbidities.

Identification of shared disease marker genes and underlying mechanisms between rheumatoid arthritis and Crohn disease through bioinformatics analysis

As chronic autoimmune inflammatory diseases, rheumatoid arthritis (RA) and Crohn disease (CD) are closely associated and display a significant positive correlation. However, the underlying mechanisms and disease markers responsible for their cooccurrence remain unknown and have not been systematically studied. Therefore, this study aimed to identify key molecules and pathways commonly involved in both RA and CD through bioinformatic analysis of public sequencing databases. Datasets for RA and CD were downloaded from the GEO database. Overlapping genes were identified using weighted gene co-expression network analysis and differential analysis crossover, and enrichment analysis was conducted for these genes. Protein-protein interaction networks were then constructed using these overlapping genes to identify hub genes. Expression validation and receiver operating characteristic curve validation were performed for these hub genes using different datasets. Additionally, the immune cell correlation, single-cell expression cluster, and the immune cell expression cluster of the core gene were analyzed. Furthermore, upstream shared microRNAs (miRNA) were predicted and a miRNA-gene network was constructed. Finally, drug candidates were analyzed and predicted. These core genes were found to be positively correlated with multiple immune cells that are infiltrated by the disease. Analysis of gene expression clusters revealed that these genes were mostly associated with inflammatory and immune responses. The miRNA-genes network analysis suggested that hsa-miR-31-5p may play an important role in the common mechanism of RA and CD. Finally, tamibarotene, retinoic acid, and benzo[a]pyrene were identified as potential treatment options for patients with both RA and CD. This bioinformatics study has identified ITGB2, LCP2, and PLEK as key diagnostic genes in patients with both RA and CD. The study has further confirmed that inflammation and immune response play a central role in the development of both RA and CD. Interestingly, the study has highlighted hsa-miR-31-5p as a potential key player in the common mechanism of both diseases, representing a new direction in research and a potential therapeutic target. These shared genes, potential mechanisms, and regulatory networks offer new opportunities for further research and may provide hope for future treatment of patients with both RA and CD.

Identification of therapeutic targets and medicines for comorbid Crohn's disease and rheumatoid arthritis: A comprehensive analysis

Objective

The incidence of Crohn's disease (CD) and rheumatoid arthritis (RA) co-morbidity, as well as the number of individuals affected, is on the rise due to their shared molecular and cellular factors. This study aimed to identify potential therapeutic targets and medicines for comorbid CD and RA.

Methods

We integrated single-cell RNA sequencing, Mendelian randomization, and colocalization analysis results from public databases to analyse immune cell subgroups in CD and RA patients and identify candidate therapeutic targets. We further screened potential medicines for the identified candidate targets using the Comparative Toxicogenomics Database (CTD) and molecular docking and molecular dynamics simulations.

Results

The proportion of CD8 effector memory T cells (Tem) was consistently elevated in the peripheral blood mononuclear cells (PBMCs) of both CD and RA patients. MYBL1 had a causal effect on the onset of both CD (OR = 1.23; 95 % CI, 1.05-1.45; P = 0.046) and RA (OR = 1.45; 95 % CI, 1.14-1.85; P = 0.04). Four potential therapeutic molecules were retrieved from the CTD database, among which tretinoin (docking score: -6.3 kcal/mol) showed the best potential.

Conclusion

Our comprehensive analysis suggests that CD8 Tem cells are a key cell group in comorbid RA and CD and that MYBL1 has a causal effect. Tretinoin was identified as a potential targeted therapeutic drug, which is of great clinical research value.

Fisetin modulates the gut microbiota alongside biomarkers of senescence and inflammation in a DSS-induced murine model of colitis

Colitis, a subtype of inflammatory bowel disease (IBD), is a multifactorial disorder characterized by chronic inflammation of the colon. Among various experimental models used in the study of IBD, the chemical colitogenic dextran sulfate sodium (DSS) is most commonly employed to induce colitis in vivo. In the search for new therapeutic strategies, Fisetin, a flavonoid found in many fruits and vegetables, has recently garnered attention for its senolytic properties. Female mice were administered 2.5% DSS in sterile drinking water and were subsequently treated with Fisetin or vehicle by oral gavage. DSS significantly upregulated beta-galactosidase activity in colonic proteins, while Fisetin remarkably inhibited its activity to baseline levels. Particularly, qPCR revealed that the senescence and inflammation markers Vimentin and Ptgs2 were elevated by DSS exposure with Fisetin treatment inhibiting the expression of p53, Bcl2, Cxcl1, and Mcp1, indicating that the treatment reduced senescent cell burden in the DSS targeted intestine. Alongside, senescence and inflammation associated miRNAs miR-149-5p, miR-96-5p, miR-34a-5p, and miR-30e-5p were significantly inhibited by DSS exposure and restored by Fisetin treatment, revealing novel targets for the treatment of IBDs. Metagenomics was implemented to assess impacts on the microbiota, with DSS increasing the prevalence of bacteria in the phyla Bacteroidetes. Meanwhile, Fisetin restored gut health through increased abundance of Akkermansia muciniphila, which is negatively correlated with senescence and inflammation. Our study suggests that Fisetin mitigates DSS-induced colitis by targeting senescence and inflammation and restoring beneficial bacteria in the gut indicating its potential as a therapeutic intervention for IBDs.

Sishen Pill and its active phytochemicals in treating inflammatory bowel disease and colon cancer: an overview

The incidence of inflammatory bowel disease (IBD) and the associated risk of colon cancer are increasing globally. Traditional Chinese medicine (TCM) treatment has unique advantages. The Sishen Pill, a common Chinese patented drug used to treat abdominal pain and diarrhea, consists mainly of Psoraleae Fructus, Myristicae Semen, Euodiae Fructus, and Schisandra Chinensis. Modern research has confirmed that Sishen Pill and its active secondary metabolites, such as psoralen, myristicin, evodiamine, and schisandrin, can improve intestinal inflammation and exert antitumor pharmacological effects. Common mechanisms in treating IBD and colon cancer mainly include regulating inflammation-related signaling pathways such as nuclear factor-kappa B, mitogen-activated protein kinase, phosphatidylinositol 3-kinase, NOD-like receptor heat protein domain-related protein 3, and wingless-type MMTV integration site family; NF-E2-related factor 2 and hypoxia-inducible factor 1α to inhibit oxidative stress; mitochondrial autophagy and endoplasmic reticulum stress; intestinal immune cell differentiation and function through the Janus kinase/signal transducer and activator of transcription pathway; and improving the gut microbiota and intestinal barrier. Overall, existing evidence suggests the potential of the Sishen pill to improve IBD and suppress inflammation-to-cancer transformation. However, large-scale randomized controlled clinical studies and research on the safety of these clinical applications are urgently required.

The effect of anti-TNF drugs on the intestinal microbiota in patients with spondyloarthritis, rheumatoid arthritis, and inflammatory bowel diseases

Spondyloarthritis (SpA), rheumatoid arthritis (RA), and inflammatory bowel diseases (IBD) are chronic inflammatory autoimmune diseases that are associated with alterations in the composition of the intestinal microbiota (i.e., dysbiosis). For SpA and RA, a gut-joint-enthesis axis is hypothesized and recent data suggests that dysbiosis may contribute directly to initiating and perpetuating joint and spine inflammation. Biologic drugs targeting tumor necrosis factor (TNF) are effective in treating these diseases and have been shown to partially restore the disrupted microbiome. Hence, drugs that affect both the intestinal and joint components of these diseases, such as anti-TNF drugs, may act on the intestinal microbiome. However, despite the remarkable efficacy of anti-TNF-α treatments, non-responders are frequent, and predictors of patient outcomes have not been identified. In this narrative review, we summarize recent research on the downstream effects of anti-TNF drugs on the intestinal microbiota in SpA, RA, and IBD. We also discuss whether these changes could have a role as predictive biomarkers of anti-TNF response.

Psychiatric disorders in paediatric-onset immune-mediated inflammatory diseases: a nationwide Danish study

OBJECTIVES

To investigate the frequency of psychiatric disorders before and after onset of paediatric-onset immune-mediated inflammatory diseases (pIMID).

STUDY DESIGN

In a nationwide study from 1996 to 2018, we investigated psychiatric disorders in patients with paediatric-onset inflammatory bowel diseases, autoimmune liver diseases and rheumatic diseases, using Danish national healthcare and population registers. Each case was matched with up to 10 controls from the background population. The cumulative incidence for psychiatric disorders prior to pIMID onset in patients was compared with controls. Cox proportional regression was used to estimate adjusted HRs (aHR) with a 95% CI between cases and controls after the index date.

RESULTS

We included 11 208 cases (57% female) and 98 387 controls. The median age at disease onset was 12.5 years (IQR 8-15) and follow-up time 9.8 years (IQR 5-15). We found an association between psychiatric disorders before index date and a diagnosis of subsequent pIMID (OR 1.3, 95% CI 1.2 to 1.4). Notably, after index date, cases also had an increased risk (aHR 1.6, 95% CI 1.5 to 1.7) of psychiatric disorders compared with controls. This risk was increased for all groups of psychiatric disorders. Female patients had an increased risk of suicide attempt after index date (aHR 1.4, 95% CI 1.1 to 1.8).

CONCLUSION

Patients with pIMID are at increased risk for a broad spectrum of psychiatric disorders both before and after onset of pIMID. The results support the need for awareness of psychiatric morbidity in this young patient group and the need for coordinated healthcare for those with comorbid states.

Noncoding RNAs improve the predictive power of network medicine

Network medicine has improved the mechanistic understanding of disease, offering quantitative insights into disease mechanisms, comorbidities, and novel diagnostic tools and therapeutic treatments. Yet, most network-based approaches rely on a comprehensive map of protein-protein interactions (PPI), ignoring interactions mediated by noncoding RNAs (ncRNAs). Here, we systematically combine experimentally confirmed binding interactions mediated by ncRNA with PPI, constructing a comprehensive network of all physical interactions in the human cell. We find that the inclusion of ncRNA expands the number of genes in the interactome by 46% and the number of interactions by 107%, significantly enhancing our ability to identify disease modules. Indeed, we find that 132 diseases lacked a statistically significant disease module in the protein-based interactome but have a statistically significant disease module after inclusion of ncRNA-mediated interactions, making these diseases accessible to the tools of network medicine. We show that the inclusion of ncRNAs helps unveil disease-disease relationships that were not detectable before and expands our ability to predict comorbidity patterns between diseases. Taken together, we find that including noncoding interactions improves both the breath and the predictive accuracy of network medicine.

Microscopic colitis and risk of incident rheumatoid arthritis: A nationwide population-based matched cohort study

BACKGROUND

Microscopic colitis (MC) has been linked to several autoimmune conditions. Results from previous studies on the association with rheumatoid arthritis (RA) have been inconsistent.

AIM

To assess the risk of future RA in MC.

METHODS

We conducted a nationwide matched cohort study in Sweden of 8179 patients with biopsy-verified MC (diagnosed in 2007-2017), 36,400 matched reference individuals and 8202 siblings without MC, with follow-up until 2021. Information on MC was obtained from all of Sweden's regional pathology registers (n = 28) through the ESPRESSO cohort. Data on incident RA were collected from the National Patient Register. Using Cox regression, we calculated adjusted hazard ratios (aHRs) and 95% confidence intervals (CIs).

RESULTS

During a median follow-up of 9.1 years (interquartile range = 6.7-11.7), 73 MC patients and 183 reference individuals from the general population were diagnosed with RA (99 vs. 55 events per 100,000 person-years), equivalent to one extra case of RA in 226 patients with MC followed for 10 years. These rates corresponded to an aHR of 1.83 (95% CI = 1.39-2.41). The aHR was highest during the first year of follow-up (2.31 [95% CI = 1.08-4.97]) and remained significantly elevated up to 5 years after MC diagnosis (aHR 2.16; 95% CI = 1.42-3.30). Compared to siblings, without MC, the aHR was 2.04 (95% CI = 1.18-3.56).

CONCLUSION

Patients with MC are at a nearly two-fold risk of developing RA compared to the general population. Knowledge of this increased risk may expedite evaluation for RA in patients with MC presenting with joint symptoms and/or arthralgia, thus preventing delay until RA diagnosis.

Identifying shared genetic loci and common risk genes of rheumatoid arthritis associated with three autoimmune diseases based on large-scale cross-trait genome-wide association studies

Introduction

Substantial links between autoimmune diseases have been shown by an increasing number of studies, and one hypothesis for this comorbidity is that there is a common genetic cause.

Methods

In this paper, a large-scale cross-trait Genome-wide Association Studies (GWAS) was conducted to investigate the genetic overlap among rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease and type 1 diabetes.

Results and discussion

Through the local genetic correlation analysis, 2 regions with locally significant genetic associations between rheumatoid arthritis and multiple sclerosis, and 4 regions with locally significant genetic associations between rheumatoid arthritis and type 1 diabetes were discovered. By cross-trait meta-analysis, 58 independent loci associated with rheumatoid arthritis and multiple sclerosis, 86 independent loci associated with rheumatoid arthritis and inflammatory bowel disease, and 107 independent loci associated with rheumatoid arthritis and type 1 diabetes were identified with genome-wide significance. In addition, 82 common risk genes were found through genetic identification. Based on gene set enrichment analysis, it was found that shared genes are enriched in exposed dermal system, calf, musculoskeletal, subcutaneous fat, thyroid and other tissues, and are also significantly enriched in 35 biological pathways. To verify the association between diseases, Mendelian randomized analysis was performed, which shows possible causal associations between rheumatoid arthritis and multiple sclerosis, and between rheumatoid arthritis and type 1 diabetes. The common genetic structure of rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease and type 1 diabetes was explored by these studies, and it is believed that this important discovery will lead to new ideas for clinical treatment.

Contrasting Autoimmune Comorbidities in Microscopic Colitis and Inflammatory Bowel Diseases

BACKGROUND

Inflammatory bowel diseases (Crohn's disease and ulcerative colitis) and microscopic colitis (lymphocytic and collagenous colitis) are immune-mediated diseases of the gastrointestinal tract, with distinct pathophysiology.

OBJECTIVE

We sought to compare the prevalence of autoimmune diseases between microscopic colitis (MC) and inflammatory bowel diseases (IBDs) in our patient cohorts in their medical history.

METHODS

We collected data from 611 patients (508 with IBD, 103 with MC). We recorded cases of other autoimmune diseases. The screened documentation was written in the period between 2008 and 2022. We sought to determine whether colonic involvement had an impact on the prevalence of autoimmune diseases.

RESULTS

Ulcerative colitis patients and patients with colonic-predominant Crohn's disease had a greater propensity for autoimmune conditions across the disease course than patients with ileal-predominant Crohn's disease. Gluten-related disorders were more common in Crohn's disease than in ulcerative colitis, and slightly more common than in microscopic colitis. In ulcerative colitis, 10 patients had non-differentiated collagenosis registered, which can later develop into a definite autoimmune disease.

CONCLUSIONS

Predominantly colonic involvement can be a predisposing factor for developing additional autoimmune disorders in IBD. Ulcerative colitis patients may have laboratory markers of autoimmunity, without fulfilling the diagnostic criteria for definitive autoimmune disorders (non-differentiated collagenosis).

Research hotspot and trend analysis in the diagnosis of inflammatory bowel disease: A machine learning bibliometric analysis from 2012 to 2021

Aims

This study aimed to conduct a bibliometric analysis of the relevant literature on the diagnosis of inflammatory bowel disease (IBD), and show its current status, hot spots, and development trends.

Methods

The literature on IBD diagnosis was acquired from the Science Citation Index Expanded of the Web of Science Core Collection. Co-occurrence and cooperation relationship analysis of authors, institutions, countries, journals, references, and keywords in the literature were carried out through CiteSpace software and the Online Analysis platform of Literature Metrology. At the same time, the relevant knowledge maps were drawn, and the keywords cluster analysis and emergence analysis were performed.

Results

14,742 related articles were included, showing that the number of articles in this field has increased in recent years. The results showed that PEYRIN-BIROULET L from the University Hospital of Nancy-Brabois was the author with the most cumulative number of articles. The institution with the most articles was Mayo Clin, and the United States was far ahead in the article output and had a dominant role. Keywords analysis showed that there was a total of 818 keywords, which were mainly focused on the research of related diseases caused or coexisted by IBD, such as colorectal cancer and autoimmune diseases, and the diagnosis and treatment methods of IBD. Emerging analysis showed that future research hotspots and trends might be the treatment of IBD and precision medicine.

Conclusion

This research was the first bibliometric analysis of publications in the field of IBD diagnosis using visualization software and data information mining, and obtained the current status, hotspots, and development of this field. The future research hotspot might be the precision medicine of IBD, and the mechanism needed to be explored in depth to provide a theoretical basis for its clinical application.

Matrix Metalloproteinases: From Molecular Mechanisms to Physiology, Pathophysiology, and Pharmacology

The first matrix metalloproteinase (MMP) was discovered in 1962 from the tail of a tadpole by its ability to degrade collagen. As their name suggests, matrix metalloproteinases are proteases capable of remodeling the extracellular matrix. More recently, MMPs have been demonstrated to play numerous additional biologic roles in cell signaling, immune regulation, and transcriptional control, all of which are unrelated to the degradation of the extracellular matrix. In this review, we will present milestones and major discoveries of MMP research, including various clinical trials for the use of MMP inhibitors. We will discuss the reasons behind the failures of most MMP inhibitors for the treatment of cancer and inflammatory diseases. There are still misconceptions about the pathophysiological roles of MMPs and the best strategies to inhibit their detrimental functions. This review aims to discuss MMPs in preclinical models and human pathologies. We will discuss new biochemical tools to track their proteolytic activity in vivo and ex vivo, in addition to future pharmacological alternatives to inhibit their detrimental functions in diseases. SIGNIFICANCE STATEMENT: Matrix metalloproteinases (MMPs) have been implicated in most inflammatory, autoimmune, cancers, and pathogen-mediated diseases. Initially overlooked, MMP contributions can be both beneficial and detrimental in disease progression and resolution. Thousands of MMP substrates have been suggested, and a few hundred have been validated. After more than 60 years of MMP research, there remain intriguing enigmas to solve regarding their biological functions in diseases.

Validation of algorithms for selecting rheumatoid arthritis patients in the Tuscan healthcare administrative databases

Validation of algorithms for selecting patients from healthcare administrative databases (HAD) is recommended. This PATHFINDER study section is aimed at testing algorithms to select rheumatoid arthritis (RA) patients from Tuscan HAD (THAD) and assessing RA diagnosis time interval between the medical chart date and that of THAD. A population was extracted from THAD. The information of the medical charts at the Rheumatology Unit of Pisa University Hospital represented the reference. We included first ever users of biologic disease modifying anti-rheumatic drugs (bDMARDs) between 2014 and 2016 (index date) with at least a specialist visit at the Rheumatology Unit of the Pisa University Hospital recorded from 2013 to the index date. Out of these, we tested four index tests (algorithms): (1) RA according to hospital discharge records or emergency department admissions (ICD-9 code, 714*); (2) RA according to exemption code from co-payment (006); (3) RA according to hospital discharge records or emergency department admissions AND RA according to exemption code from co-payment; (4) RA according to hospital discharge records or emergency department admissions OR RA according to exemption code from co-payment. We estimated sensitivity, specificity, positive and negative predicted values (PPV and NPV) with 95% confidence interval (95% CI) and the RA diagnosis median time interval (interquartile range, IQR). Two sensitivity analyses were performed. Among 277 reference patients, 103 had RA. The fourth algorithm identified 96 true RA patients, PPV 0.78 (95% CI 0.70-0.85), sensitivity 0.93 (95% CI 0.86-0.97), specificity 0.84 (95% CI 0.78-0.90), and NPV 0.95 (95% CI 0.91-0.98). The sensitivity analyses confirmed performance. The time measured between the actual RA diagnosis date recorded in medical charts and that assumed in THAD was 2.2 years (IQR 0.5-8.4). In conclusion, this validation showed the fourth algorithm as the best. The time interval elapsed between the actual RA diagnosis date in medical charts and that extrapolated from THAD has to be considered in the design of future studies.

Microbial-derived indoles inhibit neutrophil myeloperoxidase to diminish bystander tissue damage

During episodes of acute inflammation, polymorphonuclear leukocytes (PMNs) are actively recruited to sites of inflammation or injury where they provide anti-microbial and wound-healing functions. One enzyme crucial for fulfilling these functions is myeloperoxidase (MPO), which generates hypochlorous acid from Cl^- and hydrogen peroxide. The potential exists, however, that uncontrolled the extracellular generation of hypochlorous acid by MPO can cause bystander tissue damage and inhibit the healing response. Previous work suggests that the microbiota-derived tryptophan metabolites 1H-indole and related molecules ("indoles") are protective during intestinal inflammation, although their precise mechanism of action is unclear. In the present work, we serendipitously discovered that indoles are potent and selective inhibitors of MPO. Using both primary human PMNs and recombinant human MPO in a cell-free system, we revealed that indoles inhibit MPO at physiologic concentrations. Particularly, indoles block the chlorinating activity of MPO, a reliable marker for MPO-associated tissue damage, as measured by coulometric-coupled HPLC. Further, we observed direct interaction between indoles and MPO using the established biochemical techniques microscale thermophoresis and STD-NMR. Utilizing a murine colitis model, we demonstrate that indoles inhibit bystander tissue damage, reflected in decreased colon 3-chlorotyrosine and pro-inflammatory chemokine expression in vivo. Taken together, these results identify microbiota-derived indoles that acts as endogenous immunomodulatory compounds through their actions on MPO, suggesting a symbiotic association between the gut microbiota and host innate immune system. Such findings offer exciting new targets for future pharmacological intervention.