Fatty Acid Metabolism in Immune Cells: A Bioinformatics Analysis of Genes Involved in Ulcerative Colitis

Identification and immunoinfiltration analysis of key genes in ulcerative colitis using WGCNA

Objective

Ulcerative colitis (UC) is a chronic non-specific inflammatory bowel disease characterized by an unclear pathogenesis. This study aims to screen out key genes related to UC pathogenesis.

Methods

Bioinformatics analysis was conducted for screening key genes linked to UC pathogenesis, and the expression of the screened key genes was verified by establishing a UC mouse model.

Results

Through bioinformatics analysis, five key genes were obtained. Subsequent infiltration analysis revealed seven significantly different immune cell types between the UC and general samples. Additionally, animal experiment results illustrated markedly decreased body weight, visible colonic shortening and damage, along with a significant increase in the DAI score of the DSS-induced mice in the UC group in comparison with the NC group. In addition, H&E staining results demonstrated histological changes including marked inflammatory cell infiltration, loss of crypts, and epithelial destruction in the colon mucosa epithelium. qRT-PCR analysis indicated a down-regulation of ABCG2 and an up-regulation of IL1RN, REG4, SERPINB5 and TRIM29 in the UC mouse model. Notably, this observed trend showed a significant dependence on the concentration of DSS, with the mouse model of UC induced by 7% DSS demonstrating a more severe disease state compared to that induced by 5% DSS.

Conclusion

ABCG2, IL1RN, REG4, SERPINB5 and TRIM29 were screened out as key genes related to UC by bioinformatics analysis. The expression of ABCG2 was down-regulated, and that of IL1RN, REG4, SERPINB5 and TRIM29 were up-regulated in UC mice as revealed by animal experiments.

Fatty acids and lipid mediators in inflammatory bowel disease: from mechanism to treatment

Inflammatory Bowel Disease (IBD) is a chronic, relapsing inflammatory disorder of the gastrointestinal tract. Though the pathogenesis of IBD remains unclear, diet is increasingly recognized as a pivotal factor influencing its onset and progression. Fatty acids, essential components of dietary lipids, play diverse roles in IBD, ranging from anti-inflammatory and immune-regulatory functions to gut-microbiota modulation and barrier maintenance. Short-chain fatty acids (SCFAs), products of indigestible dietary fiber fermentation by gut microbiota, have strong anti-inflammatory properties and are seen as key protective factors against IBD. Among long-chain fatty acids, saturated fatty acids, trans fatty acids, and ω-6 polyunsaturated fatty acids exhibit pro-inflammatory effects, while oleic acid and ω-3 polyunsaturated fatty acids display anti-inflammatory actions. Lipid mediators derived from polyunsaturated fatty acids serve as bioactive molecules, influencing immune cell functions and offering both pro-inflammatory and anti-inflammatory benefits. Recent research has also highlighted the potential of medium- and very long-chain fatty acids in modulating inflammation, mucosal barriers, and gut microbiota in IBD. Given these insights, dietary intervention and supplementation with short-chain fatty acids are emerging as potential therapeutic strategies for IBD. This review elucidates the impact of various fatty acids and lipid mediators on IBD and delves into potential therapeutic avenues stemming from these compounds.

Biomarkers of ulcerative colitis disease activity CXCL1, CYP2R1, LPCAT1, and NEU4 and their relationship to immune infiltrates

The diagnosis and assessment of ulcerative colitis (UC) poses significant challenges, which may result in inadequate treatment and a poor prognosis for patients. This study aims to identify potential activity biomarkers for UC and investigate the role of infiltrating immune cells in the disease. To perform gene set enrichment analysis, we utilized the cluster profiler and ggplot2 packages. Kyoto encyclopedia of genes and genomes was used to analyze degenerate enrichment genes. Significant gene set enrichment was determined using the cluster profiler and ggplot2 packages. Additionally, quantitative PCR (qRT-PCR) was employed to validate the expression of each marker in the ulcerative colitis model. We identified 651 differentially expressed genes (DEGs) and further investigated potential UC activity biomarkers. Our analysis revealed that CXCL1 (AUC = 0.710), CYP2R1 (AUC = 0.863), LPCAT1 (AUC = 0.783), and NEU4 (AUC = 0.833) were promising activity markers for the diagnosis of UC. Using rat DSS model, we validated these markers through qRT-PCR, which showed statistically significant differences between UC and normal colon mucosa. Infiltrating immune cell analysis indicated that M1 macrophages, M2 macrophages, activated dendritic cells (DCs), and neutrophils played crucial roles in the occurrence and progression of UC. Moreover, the activity markers exhibited varying degrees of correlation with activated memory CD4 T cells, M0 macrophages, T follicular helper cells, memory B cells, and activated DCs. The potential diagnostic genes for UC activity, such as CXCL1, CYP2R1, LPCAT1, and NEU4, as well as the infiltration of immune cells, may contribute to the pathogenesis and progression of UC.

Single-cell and microarray chip analysis revealed the underlying pathogenesis of ulcerative colitis and validated model genes in diagnosis and drug response

The morbidity rate of ulcerative colitis (UC) in the world is increasing year by year, recurrent episodes of diarrhea, mucopurulent and bloody stools, and abdominal pain are the main symptoms, reducing the quality of life of the patient and affecting the productivity of the society. In this study, we sought to develop robust diagnostic biomarkers for UC, to uncover potential targets for anti-TNF-ɑ drugs, and to investigate their associated pathway mechanisms. We collected single-cell expression profile data from 9 UC or healthy samples and performed cell annotation and cell communication analysis. Revealing the possible pathogenesis of ulcerative colitis by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) analysis. Based on the disease-related modules obtained from weighted correlation network analysis (WGCNA) analysis, we used Lasso regression analysis and random forest algorithm to identify the genes with the greatest impact on disease (EPB41L3, HSD17B3, NDRG1, PDIA5, TRPV3) and further validated the diagnostic value of the model genes by various means. To further explore the relationship and mechanism between model genes and drug sensitivity, we collected gene expression profiles of 185 UC patients before receiving anti-tumor necrosis factor drugs, and we performed functional analysis based on the results of differential analysis between NR tissues and R tissues, and used single-sample GSEA (ssGSEA) and CIBERSORT algorithms to explore the important role of immune microenvironment on drug sensitivity. The results suggest that our model is not only helpful in aiding diagnosis, but also has implications for predicting drug efficacy; in addition, model genes may influence drug sensitivity by affecting immune cells. We suggest that this study has developed a diagnostic model with higher specificity and sensitivity, and also provides suggestions for clinical administration and drug efficacy prediction.

The pharmacological validation of the Xiao-Jian-Zhong formula against ulcerative colitis by network pharmacology integrated with metabolomics

ETHNOPHARMACOLOGICAL RELEVANCE

Inflammatory bowel disease (IBD) is pathologically characterized by an immune response accommodative insufficiency and dysbiosis accompanied by persistent epithelial barrier dysfunction, and is divided into ulcerative colitis (UC) and Crohn's disease (CD). Its progression increases the susceptibility to colitis-associated cancer (CAC), as well as other complications. The Xiao-Jian-Zhong (XJZ) formula has a historical application in the clinic to combat gastrointestinal disorders.

AIM OF THE STUDY

The investigation aimed to explore the molecular and cellular mechanisms of XJZ.

MATERIALS AND METHODS

Dextran sodium sulfate (DSS) was diluted in drinking water and given to mice for a week to establish murine models of experimental colitis, and the XJZ solution was administered for two weeks. Network pharmacology analysis and weighted gene co-expression network analysis (WGCNA) were utilized to predict the therapeutic role of XJZ against UC and CAC. 16S rRNA sequencing and untargeted metabolomics were conducted utilizing murine feces to examine the changes in the microbiome profile. Biochemical experiments were conducted to confirm the predicted functions.

RESULTS

XJZ treatment markedly attenuated DSS-induced experimental colitis progression, and the targets were enriched in inflammation, infection, and tumorigenesis, predicted by network pharmacology analysis. Based on The Cancer Genome Atlas (TCGA) database, the XJZ-targets were related to the survival probability in patients with colorectal cancer, underlying a potential therapeutic value in cancer intervention. Moreover, the XJZ therapy successfully rescued the decreased richness and diversity of microbiota, suppressed the potentially pathogenic phenotype of the gut microorganisms, and reversed the declined linoleic acid metabolism and increased cytochrome P450 activity in murine colitis models. Our in-vitro experiments confirmed that the XJZ treatment suppressed Caspase1-dependent pyroptosis and increased peroxisome proliferators-activated receptor-γ(PPAR-γ) expression in the colon, facilitated the alternative activation of macrophages (Mφs), inhibited tumor necrosis factor-α (TNFα)-induced reactive oxygen species (ROS) level in intestinal organoids (IOs), thereby favoring the mucosal healing.

CONCLUSION

The XJZ formula is efficacious for colitis by a prompt resolution of inflammation and dysbiosis, and by re-establishing a microbiome profile that favors re-epithelization, and prevents carcinogenesis.

Effects of Milk-Derived Extracellular Vesicles on the Colonic Transcriptome and Proteome in Murine Model

Evidence shows that effective nutritional intervention can prevent or mitigate the risk and morbidity of inflammatory bowel disease (IBD). Bovine milk extracellular vesicles (mEVs), a major bioactive constituent of milk, play an important role in maintaining intestinal health. The aims of this study were to assess the effects of mEV pre-supplementation on the colonic transcriptome and proteome in dextran sulphate sodium (DSS)-induced acute colitis, in order to understand the underlying molecular mechanisms of mEV protection against acute colitis. Our results revealed that dietary mEV supplementation alleviated the severity of acute colitis, as evidenced by the reduced disease activity index scores, histological damage, and infiltration of inflammatory cells. In addition, transcriptome profiling analysis found that oral mEVs significantly reduced the expression of pro-inflammatory cytokines (IL-1β, IL-6, IL-17A and IL-33), chemokine ligands (CXCL1, CXCL2, CXCL3, CXCL5, CCL3 and CCL11) and chemokine receptors (CXCR2 and CCR3). Moreover, oral mEVs up-regulated 109 proteins and down-regulated 150 proteins in the DSS-induced murine model, which were involved in modulating amino acid metabolism and lipid metabolism. Collectively, this study might provide new insights for identifying potential targets for the therapeutic effects of mEVs on colitis.

Capparis spinosa Alleviates DSS-Induced Ulcerative Colitis via Regulation of the Gut Microbiota and Oxidative Stress

Ulcerative colitis (UC) is a chronic inflammatory disease. Here, the potential effects of Capparis spinosa water extract (CSWE) on colonic histopathology, inflammation, and gut microbiota composition in dextran sulfate sodium (DSS) induced UC mice were evaluated. Our results showed that CSWE treatment improved the colonic histopathology of UC mice, increased the levels of tight junction protein gene ZO-1 and Occludin in intestinal epithelial cells, and inhibited the expression of proinflammatory cytokines (IL-1β, IL-6, and TNF-α). Furthermore, CSWE administration alleviated oxidative stress in the colon of UC mice. The effects of CSWE on the compositions and metabolomic profiles of the gut microbiota in UC mice were investigated. It was found that CSWE could enhance the diversity of gut microbes and the abundance of probiotics and metabonomics had the strongest association with Firmicutes. Our results indicated that CSWE might be an ideal candidate as a potential therapeutic natural product for the treatment of UC.

The Fatty Acid-Based Erythrocyte Membrane Lipidome in Dogs with Chronic Enteropathy

Canine chronic enteropathies (CEs) are inflammatory processes resulting from complex interplay between the mucosal immune system, intestinal microbiome, and dietary components in susceptible dogs. Fatty acids (FAs) play important roles in the regulation of physiologic and metabolic pathways and their role in inflammation seems to be dual, as they exhibit pro-inflammatory and anti-inflammatory functions. Analysis of red blood cell (RBC) membrane fatty acid profile represents a tool for assessing the quantity and quality of structural and functional molecular components. This study was aimed at comparing the FA membrane profile, determined by Gas Chromatography and relevant lipid parameter of 48 CE dogs compared with 68 healthy dogs. In CE patients, the levels of stearic (p < 0.0001), dihomo-gamma-linolenic, eicosapentaenoic (p = 0.02), and docosahexaenoic (p = 0.02) acids were significantly higher, and those of palmitic (p < 0.0001) and linoleic (p = 0.0006) acids were significantly lower. Non-responder dogs presented higher percentages of vaccenic acid (p = 0.007), compared to those of dogs that responded to diagnostic trials. These results suggest that lipidomic status may reflect the "gut health", and the non-invasive analysis of RBC membrane might have the potential to become a candidate biomarker in the evaluation of dogs affected by CE.

Eriodictyol attenuates TNBS-induced ulcerative colitis through repressing TLR4/NF-kB signaling pathway in rats

Ulcerative colitis (UC) is a chronic disease characterized by mucosal and submucosal inflammation, which has a low cure rate and is prone to relapse, due to the immune imbalance of the body. Inhibition of inflammation-related pathways can delay the progression of UC. Toll-like receptor 4 (TLR4) pathway is considered to be one of the important signaling pathways involved in colon inflammation. Eriodictyol (EDT) is a natural flavonoid widely distributed in foodborne plants. EDT plays an important role in the regulation of inflammation and related signaling pathways. However, whether EDT plays a role in UC remains unknown. Herein, we established a TNBS induced animal model of enteritis in Wistar rats. Our data confirmed the establishment of TNBS induced animal model of enteritis and the administration Eriodictyol in Wistar rats. EDT treatment alleviated TNBS-induced intestinal tissue injury in rats. We further found that EDT reduced MPO expression and regulated the cytokine parameters in TNBS-induced intestinal tissues of rats. The levels of TNF-α, IL-1β, IL-6, IL-10, IL-2, and IL-12 were also affected by the treatment of EDT. EDT also affected SOD, CAT, GSH-Px, and MDA level in rats with colitis. Moreover, EDT regulated TNBS-induced TLR4/NF-κB pathway activation, therefore inhibiting the progression of UC. Our results suggest that EDT could be a potential therapeutic agent for UC.

Capparis spinosa Alleviates DSS-Induced Ulcerative Colitis via Regulation of the Gut Microbiota and Oxidative Stress

Ulcerative colitis (UC) is a chronic inflammatory disease. Here, the potential effects of Capparis spinosa water extract (CSWE) on colonic histopathology, inflammation, and gut microbiota composition in dextran sulfate sodium (DSS) induced UC mice were evaluated. Our results showed that CSWE treatment improved the colonic histopathology of UC mice, increased the levels of tight junction protein gene ZO-1 and Occludin in intestinal epithelial cells, and inhibited the expression of proinflammatory cytokines (IL-1β, IL-6, and TNF-α). Furthermore, CSWE administration alleviated oxidative stress in the colon of UC mice. The effects of CSWE on the compositions and metabolomic profiles of the gut microbiota in UC mice were investigated. It was found that CSWE could enhance the diversity of gut microbes and the abundance of probiotics and metabonomics had the strongest association with Firmicutes. Our results indicated that CSWE might be an ideal candidate as a potential therapeutic natural product for the treatment of UC.