Therapeutic potential of the secreted Kazal-type serine protease inhibitor SPINK4 in colitis.

Mucus injury associated with goblet cell (GC) depletion constitutes an early event in inflammatory bowel disease (IBD). Using single-cell sequencing to detect critical events in mucus dysfunction, we discover that the Kazal-type serine protease inhibitor SPINK4 is dynamically regulated in colitic intestine in parallel with disease activities. Under chemically induced colitic conditions, the grim status in Spink4-conditional knockout mice is successfully rescued by recombinant murine SPINK4. Notably, its therapeutic potential is synergistic with existing TNF-α inhibitor infliximab in colitis treatment. Mechanistically, SPINK4 promotes GC differentiation using a Kazal-like motif to modulate EGFR-Wnt/ß-catenin and -Hippo pathways. Microbiota-derived diacylated lipoprotein Pam2CSK4 triggers SPINK4 production. We also show that monitoring SPINK4 in circulation is a reliable noninvasive technique to distinguish IBD patients from healthy controls and assess disease activity. Thus, SPINK4 serves as a serologic biomarker of IBD and has therapeutic potential for colitis via intrinsic EGFR activation in intestinal homeostasis.

Monitoring and warning for ammonia nitrogen pollution of urban river based on neural network algorithms.

Ammonia nitrogen (AN) pollution frequently occurs in urban rivers with the continuous acceleration of industrialization. Monitoring AN pollution levels and tracing its complex sources often require large-scale testing, which are time-consuming and costly. Due to the lack of reliable data samples, there were few studies investigating the feasibility of water quality prediction of AN concentration with a high fluctuation and non-stationary change through data-driven models. In this study, four deep-learning models based on neural network algorithms including artificial neural network (ANN), recurrent neural network (RNN), long short-term memory (LSTM), and gated recurrent unit (GRU) were employed to predict AN concentration through some easily monitored indicators such as pH, dissolved oxygen, and conductivity, in a real AN-polluted river. The results showed that the GRU model achieved optimal prediction performance with a mean absolute error (MAE) of 0.349 and coefficient of determination (R2) of 0.792. Furthermore, it was found that data preprocessing by the VMD technique improved the prediction accuracy of the GRU model, resulting in an R2 value of 0.822. The prediction model effectively detected and warned against abnormal AN pollution (> 2 mg/L), with a Recall rate of 93.6% and Precision rate of 72.4%. This data-driven method enables reliable monitoring of AN concentration with high-frequency fluctuations and has potential applications for urban river pollution management.

Platelet-to-lymphocyte percentage ratio for assessing disease activity and predicting therapeutic outcomes in ulcerative colitis.

AIMS: Disease activity assessment and treatment outcome prediction are crucial in the patient management of ulcerative colitis (UC); yet the significance of platelet-to-lymphocyte percentage ratio (PLpR) remains unknown, which was investigated in this study. METHODS: We used data from three clinical trials: ACT 1, PURSUIT, and UNIFI. In total, 7,614 endoscopic procedures and 1,365 patients were included for assessing severity and predicting outcome, respectively. The primary outcome was endoscopic remission, defined as a Mayo endoscopic score of 0. The diagnostic capacity of PLpR was evaluated by the area under the receiver operating characteristic curve (AUC) while multivariable logistic regression was employed to assess the prognostic power of PLpR. RESULTS: PLpR showed higher AUCs than C-reactive protein in identifying endoscopic remission (P < 0.001) and improvement (P < 0.001). Besides, combining PLpR with fecal calprotectin enhanced the power to distinguish disease activity. In therapeutic outcome analyses, higher PLpR level indicated worse long-term outcomes. PLpR ≥ 1016.7 predicted a lower likelihood of endoscopic remission (OR: 0.50 [95 % CI: 0.39-0.65]; P < 0.001), endoscopic improvement (OR: 0.45 [95 % CI: 0.36-0.57]; P < 0.001), clinical remission (OR: 0.50 [95 % CI: 0.39-0.62]; P < 0.001), histologic improvement (OR: 0.50 [95 % CI: 0.31-0.79]; P = 0.004), and histologic-endoscopic mucosal improvement (OR: 0.42 [95 % CI: 0.27-0.66]; P < 0.001). Moreover, PLpR added the prognostic value to C-reactive protein, fecal calprotectin, clinical and endoscopic scores to predict long-term outcomes. CONCLUSION: PLpR could be a promising biomarker for monitoring disease activity and predicting long-term therapeutic outcomes in UC.

The Effect of Radioiodine Therapy on the Prognosis of Differentiated Thyroid Cancer with Lung Metastases.

Lung metastasis substantially influences the survival of thyroid cancer (TC) patients. This study sought to investigate factors impacting the survival of differentiated thyroid cancer patients with lung metastases (DTC-LM) undergoing radioiodine therapy (RAI) after thyroid surgery. The retrospective study encompassed 609 TC patients with lung metastases. Survival outcomes-specifically, overall survival (OS) and thyroid cancer-specific survival (TCSS)-were examined through both univariate and multivariate Cox regression analyses. Radioiodine therapy (RAI)'s impact on DTC-LM patient survival was further assessed with the Kaplan-Meier survival curve. Of the 609 TC patients with lung metastases, 434 (71.3%) were found to have undergone thyroid surgery after a median follow-up of 59 months. Anaplastic thyroid cancer (ATC), stage IV, and lung metastases associated with other metastases were identified as risk factors for OS and TCSS in TCLM patients. RAI therapy significantly enhances survival in DTC-LM patients followed by primary site surgery under the age of 55, PTC patients, and those with single organ metastases at lung.

High-throughput single-cell assay for precise measurement of the intrinsic mechanical properties and shape characteristics of red blood cells.

The intrinsic physical and mechanical properties of red blood cells (RBCs), including their geometric and rheological characteristics, can undergo changes in various circulatory and metabolic diseases. However, clinical diagnosis using RBC biophysical phenotypes remains impractical due to the unique biconcave shape, remarkable deformability, and high heterogeneity within different subpopulations. Here, we combine the hydrodynamic mechanisms of fluid-cell interactions in micro circular tubes with a machine learning method to develop a relatively high-throughput microfluidic technology that can accurately measure the shear modulus of the membrane, viscosity, surface area, and volume of individual RBCs. The present method can detect the subtle changes of mechanical properties in various RBC components at continuum scales in response to different doses of cytoskeletal drugs. We also investigate the correlation between glycosylated hemoglobin and RBC mechanical properties. Our study develops a methodology that combines microfluidic technology and machine learning to explore the material properties of cells based on fluid-cell interactions. This approach holds promise in offering novel label-free single-cell-assay-based biophysical markers for RBCs, thereby enhancing the potential for more robust disease diagnosis.

Stanniocalcin-1 Promotes PARP1-Dependent Cell Death via JNK Activation in Colitis.

Stanniocalcin-1 (STC1) is upregulated by inflammation and modulates oxidative stress-induced cell death. Herein, the function of STC1 in colitis and stress-induced parthanatos, a newly identified type of programmed necrotic cell death dependent on the activation of poly-ADP ribose polymerase-1 (PARP1) is investigated. Results show that STC1 expression is markedly increased in the inflamed colonic mucosa of Crohn's disease (CD) patients and chemically-induced mice colitis models. Evaluation of parthanatos severity and pro-inflammatory cytokine expression shows that intestinal-specific Stc1 knockout (Stc1INT-KO ) mice are resistant to dextran sulfate sodium (DSS)-induced colitis and exhibit lower disease severity. STC1-overexpressing cells show an increased degree of parthanatos and proinflammatory cytokine expression, whereas STC1-knockout cells show a decreased degree of parthanatos. Co-immunoprecipitation, mass spectrometry, and proteomic analyses indicate that STC1 interacts with PARP1, which activates the JNK pathway via PARP1-JNK interactions. Moreover, inhibition of PARP1 and JNK alleviates parthanatos and inflammatory injuries triggered by STC1 overexpression. Finally, following restoration of Stc1 and Parp1 expression by adeno-associated viruses, and overexpression of Stc1 and Parp1 aggravated DSS-induced colitis in Stc1INT-KO mice. In conclusion, STC1 mediates oxidative stress-associated parthanatos and aggravates inflammation via the STC1-PARP1-JNK interactions and subsequent JNK pathway activation in CD pathogenesis.

Rapidly achieving clinical remission in ulcerative colitis indicates better endoscopic and histological outcomes.

BACKGROUND: Clinical remission (CR) is the principal short-term treatment target in patients with ulcerative colitis (UC). However, whether rapidly achieving CR indicates better outcomes remains unclear. OBJECTIVES: We aimed to explore the associations between the timing of CR and therapeutic outcomes in UC. METHODS: This study included UC patients from the UNIFI trial. Week-2 CR and time to CR were the major variables of interest. Endoscopic remission (ER) at week 52 was the primary outcome. Multivariate logistic regression was performed to evaluate the association between variables and outcomes. RESULTS: Week-2 CR was associated with ER (aOR: 2.37 [95% CI: 1.28, 4.37], p = 0.006) and Histological remission (HR) (aOR: 2.87 [95% CI: 1.42, 5.72], p = 0.003) at week 52. Moreover, C-reactive protein (CRP) remission could further stratify patients without CR and predict week-52 outcomes. Patients with clinical activity + CRP remission (aOR: 0.49 [95% CI: 0.26, 0.93], p = 0.039) and clinical activity + CRP activity (aOR: 0.24 [95% CI: 0.11, 0.52], p < 0.001) had gradually decreased likelihood of achieving ER, when compared to those with CR. For time to CR, we found that the earlier to CR, the better endoscopic and histological outcomes patients would attain. Patients achieving CR at weeks 2, 4/8, 12/16 and >16 had gradually reduced proportions of ER (51.9% vs. 40.8% vs. 31.6% vs. 8.8%, p < 0.001) and HR (37.0% vs. 19.8% vs. 17.1% vs. 6.1%, p < 0.001) at week 52. Compared with week 2, achieving CR at weeks 4/8, 12/16 and >16 had 39%, 55% and 92% lower likelihoods of week-52 ER, respectively. CONCLUSIONS: Week-2 CR indicates better outcomes in UC patients receiving ustekinumab. Moreover, achieving CR more rapidly is associated with higher probability of ER and HR.

Trajectory of fecal lactoferrin for predicting prognosis in ulcerative colitis.

Objectives: To investigate the characteristics and prognostic value of fecal lactoferrin trajectories in ulcerative colitis (UC). Methods: This study used data from the UNIFI trial (ClinicalTrials.gov, NCT02407236) and included patients who received ustekinumab during induction for trajectory modeling (n = 637). Patients who received ustekinumab during maintenance therapy were used for 1-year outcome analyses (n = 403). The levels of fecal lactoferrin, fecal calprotectin, and serum C-reactive protein were measured at weeks 0, 2, 4, and 8. The trajectories of these biomarkers were developed using a latent class growth mixed model. Results: The trajectories of fecal lactoferrin, fecal calprotectin, and serum C-reactive protein were distinct, but all were associated with prior exposure to anti-tumor necrosis factor agents and vedolizumab. Furthermore, the fecal lactoferrin trajectory was the most valuable predictor of endoscopic, clinical, and histological remission. Compared to the high/moderate-rapid decrease trajectory group, the moderate-slow decrease, high-slow decrease, and high-stable groups had adjusted odds ratios (95% confidence interval) of 0.38 (0.18, 0.78; P = 0.010), 0.47 (0.23, 0.93; P = 0.032), and 0.33 (0.17, 0.63; P = 0.001), respectively, of 1-year endoscopic remission. Patients with high/moderate-rapid decrease trajectories also had the highest likelihood of achieving clinical and histological remission. Finally, we developed a patient-stratification scheme based on fecal lactoferrin trajectories and concentrations. Patients with good, moderate, and poor prognoses in the scheme had a distinct probability of achieving 1-year endoscopic remission (52.7%, 30.9%, and 12.8%, respectively). Conclusions: The trajectory of fecal lactoferrin is a valuable prognostic factor for 1-year remission in UC.

Current insights on the roles of gut microbiota in inflammatory bowel disease-associated extra-intestinal manifestations: pathophysiology and therapeutic targets.

Inflammatory bowel disease (IBD) is a chronic, recurrent inflammatory disease of the gastrointestinal tract. In addition to digestive symptoms, patients with IBD may also develop extra-intestinal manifestations (EIMs), the etiology of which remains undefined. The gut microbiota has been reported to exert a critical role in the pathogenesis of IBD, with a similar pattern of gut dysbiosis observed between patients with IBD and those with EIMs. Therefore, it is hypothesized that the gut microbiota is also involved in the pathogenesis of EIMs. The potential mechanisms are presented in this review, including: 1) impaired gut barrier: dysbiosis induces pore formation in the intestinal epithelium, and activates pattern recognition receptors to promote local inflammation; 2) microbial translocation: intestinal pathogens, antigens, and toxins translocate via the impaired gut barrier into extra-intestinal sites; 3) molecular mimicry: certain microbial antigens share similar epitopes with self-antigens, inducing inflammatory responses targeting extra-intestinal tissues; 4) microbiota-related metabolites: dysbiosis results in the dysregulation of microbiota-related metabolites, which could modulate the differentiation of lymphocytes and cytokine production; 5) immunocytes and cytokines: immunocytes are over-activated and pro-inflammatory cytokines are excessively released. Additionally, we summarize microbiota-related therapies, including probiotics, prebiotics, postbiotics, antibiotics, and fecal microbiota transplantation, to promote better clinical management of IBD-associated EIMs.

Decreased TMIGD1 aggravates colitis and intestinal barrier dysfunction via the BANF1-NF-κB pathway in Crohn's disease.

BACKGROUND: Disrupted intestinal epithelial barrier is one of the major causes of Crohn's disease (CD). Novel molecular targets for intestinal epithelial barrier are essential to treatment of CD. Transmembrane and immunoglobulin domain-containing protein 1 (TMIGD1) is an adhesion molecule that regulates cell adhesion, migration, and enterocyte differentiation. However, the function and mechanism of TMIGD1 in CD and intestinal epithelial barrier has rarely been studied. Furthermore, the association between TMIGD1 and the clinical features of CD remains unclear. METHODS: Transcriptome analysis on colonic mucosa from CD patients and healthy individuals were performed to identify dysregulated genes. Multi-omics integration of the 1000IBD cohort including genomics, transcriptomics of intestinal biopsies, and serum proteomics identified the association between genes and characteristics of CD. Inflammation was assessed by cytokine production in cell lines, organoids and intestinal-specific Tmigd1 knockout (Tmigd1INT-KO) mice. Epithelial barrier integrity was evaluated by trans-epithelium electrical resistance (TEER), paracellular permeability, and apical junction complex (AJC) expression. Co-immunoprecipitation, GST pull-down assays, mass spectrometry, proteomics, and transcriptome analysis were used to explore downstream mechanisms. RESULTS: Multi-omics integration suggested that TMIGD1 was negatively associated with inflammatory characteristics of CD. TMIGD1 was downregulated in inflamed intestinal mucosa of patients with CD and mice colitis models. Tmigd1INT-KO mice were more susceptible to chemically induced colitis. In epithelial cell lines and colonic organoids, TMIGD1 knockdown caused impaired intestinal barrier integrity evidenced by increased paracellular permeability and reduced TEER and AJC expression. TMIGD1 knockdown in intestinal epithelial cells also induced pro-inflammatory cytokine production. Mechanistically, TMIGD1 directly interacted with cytoplasmic BAF nuclear assembly factor 1 (BANF1) to inhibit NF-κB activation. Exogenous expression of TMIGD1 and BANF1 restored intestinal barrier function and inhibited inflammation in vitro and in vivo. TMIGD1 expression predicted response to anti-TNF treatment in patients with CD. CONCLUSIONS: Our study demonstrated that TMIGD1 maintained intestinal barrier integrity and inactivated inflammation, and was therefore a potential therapeutic target for CD.

Protocadherin 20 maintains intestinal barrier function to protect against Crohn's disease by targeting ATF6.

BACKGROUND: Intestinal barrier dysfunction plays a central role in the pathological onset of Crohn's disease. We identify the cadherin superfamily member protocadherin 20 (PCDH20) as a crucial factor in Crohn's disease. Here we describe the function of PCDH20 and its mechanisms in gut homeostasis, barrier integrity, and Crohn's disease development. RESULTS: PCDH20 mRNA and protein expression is significantly downregulated in the colonic epithelium of Crohn's disease patients and mice with induced colitis compared with controls. In mice, intestinal-specific Pcdh20 knockout causes defects in enterocyte proliferation and differentiation, while causing morphological abnormalities. Specifically, the deletion disrupts barrier integrity by unzipping adherens junctions via ß-catenin regulation and p120-catenin phosphorylation, thus aggravating colitis in DSS- and TNBS-induced colitis mouse models. Furthermore, we identify activating transcription factor 6 (ATF6), a key chaperone of endoplasmic reticulum stress, as a functional downstream effector of PCDH20. By administering a selective ATF6 activator, the impairment of intestinal barrier integrity and dysregulation of CHOP/ß-catenin/p-p120-catenin pathway was reversed in Pcdh20-ablated mice with colitis and PCDH20-deficient colonic cell lines. CONCLUSIONS: PCDH20 is an essential factor in maintaining intestinal epithelial homeostasis and barrier integrity. Specifically, PCDH20 helps to protect against colitis by tightening adherens junctions through the ATF6/CHOP/ß-catenin/p-p120-catenin axis.

Prognostic models for predicting postoperative recurrence in Crohn's disease: a systematic review and critical appraisal.

Background and Aims: Prophylaxis of postoperative recurrence is an intractable problem for clinicians and patients with Crohn's disease. Prognostic models are effective tools for patient stratification and personalised management. This systematic review aimed to provide an overview and critically appraise the existing models for predicting postoperative recurrence of Crohn's disease. Methods: Systematic retrieval was performed using PubMed and Web of Science in January 2022. Original articles on prognostic models for predicting postoperative recurrence of Crohn's disease were included in the analysis. The risk of bias was assessed using the Prediction Model Risk of Bias Assessment (PROBAST) tool. This study was registered with the International Prospective Register of Systematic Reviews (PROSPERO; number CRD42022311737). Results: In total, 1948 articles were screened, of which 15 were ultimately considered. Twelve studies developed 15 new prognostic models for Crohn's disease and the other three validated the performance of three existing models. Seven models utilised regression algorithms, six utilised scoring indices, and five utilised machine learning. The area under the receiver operating characteristic curve of the models ranged from 0.51 to 0.97. Six models showed good discrimination, with an area under the receiver operating characteristic curve of >0.80. All models were determined to have a high risk of bias in modelling or analysis, while they were at low risk of applicability concerns. Conclusions: Prognostic models have great potential for facilitating the assessment of postoperative recurrence risk in patients with Crohn's disease. Existing prognostic models require further validation regarding their reliability and applicability. Systematic review registration: https://www.crd.york.ac.uk/PROSPERO/, identifier CRD42022311737.

Recent developments on BMPs and their antagonists in inflammatory bowel diseases.

Inflammatory bowel diseases (IBDs), including ulcerative colitis, and Crohn's disease, are intestinal disorders characterized by chronic relapsing inflammation. A large proportion of patients with IBD will progress to develop colitis-associated colorectal cancer due to the chronic intestinal inflammation. Biologic agents that target tumour necrosis factor-α, integrin α4ß7, and interleukin (IL)12/23p40 have been more successful than conventional therapies in treating IBD. However, drug intolerance and loss of response are serious drawbacks of current biologics, necessitating the development of novel drugs that target specific pathways in IBD pathogenesis. One promising group of candidate molecules are bone morphogenetic proteins (BMPs), members of the TGF-ß family involved in regulating morphogenesis, homeostasis, stemness, and inflammatory responses in the gastrointestinal tract. Also worth examining are BMP antagonists, major regulators of these proteins. Evidence has shown that BMPs (especially BMP4/6/7) and BMP antagonists (especially Gremlin1 and follistatin-like protein 1) play essential roles in IBD pathogenesis. In this review, we provide an updated overview on the involvement of BMPs and BMP antagonists in IBD pathogenesis and in regulating the fate of intestinal stem cells. We also described the expression patterns of BMPs and BMP antagonists along the intestinal crypt-villus axis. Lastly, we synthesized available research on negative regulators of BMP signalling. This review summarizes recent developments on BMPs and BMP antagonists in IBD pathogenesis, which provides novel insights into future therapeutic strategies.

Fecal lactoferrin early predicts long-term outcomes in ulcerative colitis: A post-hoc analysis of the UNIFI and PURSUIT trials.

BACKGROUND: Fecal lactoferrin (FL) is associated with disease activity and relapse in ulcerative colitis. However, whether FL could early predict long-term outcomes in ulcerative colitis is poorly understood. METHODS: This post-hoc analysis included participants who received biologics and had available data of FL concentration at week 4 from the UNIFI and PURSUIT trials (n = 1063). Therapeutic outcomes, including clinical remission, endoscopic improvement and remission, and histological improvement and remission, were evaluated at the end of maintenance therapy. The incidence of colectomy was observed from week 0 to maximum week 228 in the PURSUIT trial (n = 667). Multivariate logistic and Cox proportional-hazard regression were conducted to evaluate the associations between FL and therapeutic outcomes and colectomy, respectively. RESULTS: A high FL level at week 4 was associated with poor long-term clinical, endoscopic and histologic outcomes. FL >84.5 µg/mL predicted a low likelihood of clinical (OR [95% CI]: 0.43 [0.32, 0.57]; p < 0.001), endoscopic (OR [95% CI]: 0.40 [0.29, 0.56]; p < 0.001), and histological (OR [95% CI]: 0.27 [0.14, 0.53]; p < 0.001) remission. Moreover, week-4 FL could add prognostic value to fecal calprotectin and clinical and endoscopic scores for informing long-term therapeutic outcomes. For the risk of colectomy, patients with week-4 FL <20.1 and ≥20.1 µg/mL had an incidence rate of 1.10% and 6.39%, respectively. Patients with FL ≥20.1 µg/mL had a 995% higher risk of colectomy (HR [95% CI], 10.95 [1.45, 82.74]). CONCLUSION: FL could be a promising prognostic biomarker for long-term therapeutic outcomes and risk of colectomy in patient of ulcerative colitis.

A Novel Nomogram Combining Mucus Barrier Index for Predicting Treatment Failures in Ulcerative Colitis.

Background: Treatment failures (TFs) generally exist in the course of ulcerative colitis (UC), while early reliable predictors of TFs are still lacking. We aimed to generate nomograms for the prediction of TFs. Methods: In this retrospective case-control study, the endpoint was the occurrence of TFs, which included medically associated treatment failures and surgery-associated treatment failures (colectomy). Clinical features and mucus integrity evident by goblet cells (GCs) number, expression levels of MUC2 and SLC26A3 were enrolled in the univariate analysis. Nomogram performance was evaluated by discrimination and calibration. Results: We identified 256 UC patients at our center from January 2010 to June 2022. Fourteen variables for TFs and 9 for colectomy were identified by univariate analysis. Five baseline indices were incorporated into the nomogram for the prediction of TFs: area of GCs, age at diagnosis, disease duration, hemoglobin, and Mayo score. The model was presented with decent discrimination (C index of 0.822) and well calibration. In addition, the colectomy predictive nomogram was built using MUC2 intensity, age at onset, and Mayo score with a good discrimination (C index of 0.92). Conclusion: Nomograms based on comprehensive factors including mucus barrier function were developed to predict TFs in UC patients with great discrimination, which may serve as practical tools aiming to identify high-risk subgroups warrant timely intervention.

Serum amyloid protein A in inflammatory bowel disease: from bench to bedside.

Inflammatory bowel diseases (IBD) is featured by gastrointestinal inflammation and a disease course with alternating recurrence and remission. The global burden caused by IBD has significantly boosted in recent years, necessitating treatment optimization. Serum amyloid A (SAA) is a class of 104 amino acid conservative acute-phase proteins, which is essential in immune-mediated inflammatory processes, like IBD. The SAA monomeric structure is composed of four α-helical regions and a C-terminal amorphous tail. Its disordered structure enables multiple bindings to different ligands and permits multiple functions. It has been proven that SAA has dual roles in the inflammatory process. SAA stimulates the pro-inflammatory cytokine expression and promotes the pathogenic differentiation of TH17 cells. In addition, SAA can remove toxic lipids produced during inflammatory responses and membrane debris from dead cells, redirect HDL, and recycle cholesterol for tissue repair. In IBD, SAA acts on gut epithelium barriers, induces T-cell differentiation, and promotes phagocytosis of Gram-negative bacteria. Owing to the tight connection between SAA and IBD, several clinical studies have taken SAA for a biomarker for diagnosis, assessing disease activity, and predicting prognosis in IBD. Furthermore, 5-MER peptide, a drug specifically targeting SAA, has shown anti-inflammatory effects in some SAA-dependent animal models, providing novel insights into the therapeutic targets of IBD.

Oxidative stress gene expression, DNA methylation, and gut microbiota interaction trigger Crohn's disease: a multi-omics Mendelian randomization study.

BACKGROUND: Oxidative stress (OS) is a key pathophysiological mechanism in Crohn's disease (CD). OS-related genes can be affected by environmental factors, intestinal inflammation, gut microbiota, and epigenetic changes. However, the role of OS as a potential CD etiological factor or triggering factor is unknown, as differentially expressed OS genes in CD can be either a cause or a subsequent change of intestinal inflammation. Herein, we used a multi-omics summary data-based Mendelian randomization (SMR) approach to identify putative causal effects and underlying mechanisms of OS genes in CD. METHODS: OS-related genes were extracted from the GeneCards database. Intestinal transcriptome datasets were collected from the Gene Expression Omnibus (GEO) database and meta-analyzed to identify differentially expressed genes (DEGs) related to OS in CD. Integration analyses of the largest CD genome-wide association study (GWAS) summaries with expression quantitative trait loci (eQTLs) and DNA methylation QTLs (mQTLs) from the blood were performed using SMR methods to prioritize putative blood OS genes and their regulatory elements associated with CD risk. Up-to-date intestinal eQTLs and fecal microbial QTLs (mbQTLs) were integrated to uncover potential interactions between host OS gene expression and gut microbiota through SMR and colocalization analysis. Two additional Mendelian randomization (MR) methods were used as sensitivity analyses. Putative results were validated in an independent multi-omics cohort from the First Affiliated Hospital of Sun Yat-sen University (FAH-SYS). RESULTS: A meta-analysis from six datasets identified 438 OS-related DEGs enriched in intestinal enterocytes in CD from 817 OS-related genes. Five genes from blood tissue were prioritized as candidate CD-causal genes using three-step SMR methods: BAD, SHC1, STAT3, MUC1, and GPX3. Furthermore, SMR analysis also identified five putative intestinal genes, three of which were involved in gene-microbiota interactions through colocalization analysis: MUC1, CD40, and PRKAB1. Validation results showed that 88.79% of DEGs were replicated in the FAH-SYS cohort. Associations between pairs of MUC1-Bacillus aciditolerans and PRKAB1-Escherichia coli in the FAH-SYS cohort were consistent with eQTL-mbQTL colocalization. CONCLUSIONS: This multi-omics integration study highlighted that OS genes causal to CD are regulated by DNA methylation and host-microbiota interactions. This provides evidence for future targeted functional research aimed at developing suitable therapeutic interventions and disease prevention.

Dietary palmitoleic acid reprograms gut microbiota and improves biological therapy against colitis.

Magnitude and diversity of gut microbiota and metabolic systems are critical in shaping human health and diseases, but it remains largely unclear how complex metabolites may selectively regulate gut microbiota and determine health and diseases. Here, we show that failures or compromised effects of anti-TNF-α therapy in inflammatory bowel diseases (IBD) patients were correlated with intestinal dysbacteriosis with more pro-inflammatory bacteria, extensive unresolved inflammation, failed mucosal repairment, and aberrant lipid metabolism, particularly lower levels of palmitoleic acid (POA). Dietary POA repaired gut mucosal barriers, reduced inflammatory cell infiltrations and expressions of TNF-α and IL-6, and improved efficacy of anti-TNF-α therapy in both acute and chronic IBD mouse models. Ex vivo treatment with POA in cultured inflamed colon tissues derived from Crohn's disease (CD) patients reduced pro-inflammatory signaling/cytokines and conferred appreciable tissue repairment. Mechanistically, POA significantly upregulated the transcriptional signatures of cell division and biosynthetic process of Akkermansia muciniphila, selectively increased the growth and abundance of Akkermansia muciniphila in gut microbiota, and further reprogrammed the composition and structures of gut microbiota. Oral transfer of such POA-reprogrammed, but not control, gut microbiota induced better protection against colitis in anti-TNF-α mAb-treated recipient mice, and co-administration of POA with Akkermansia muciniphila showed significant synergistic protections against colitis in mice. Collectively, this work not only reveals the critical importance of POA as a polyfunctional molecular force to shape the magnitude and diversity of gut microbiota and therefore promote the intestinal homeostasis, but also implicates a new potential therapeutic strategy against intestinal or abenteric inflammatory diseases.