Prediction and Verification of Potential Therapeutic Targets for Non-Responders to Infliximab in Ulcerative Colitis

The Gut Microbiota Affects Anti-TNF Responsiveness by Activating the NAD+ Salvage Pathway in Ulcerative Colitis

Approximately 50% of the patients with ulcerative colitis (UC) are primarily nonresponsive to anti-tumor necrosis factor (TNF) therapy or lose their responsiveness over time. The gut microbiota plays an important role in the resistance of UC to anti-TNF therapy; however, the underlying mechanism remains unknown. Here, it is found that the transplantation of gut fecal microbiota from patients with UC alters the diversity of the gut microbiota in dextran sulfate sodium-induced colitis mice and may affect the therapeutic responsiveness of mice to infliximab. Furthermore, the abundances of Romboutsia and Fusobacterium increase in the tissues of patients with UC who do not respond to anti-TNF therapy. Differentially abundant metabolites are mainly enriched in nicotinate and nicotinamide metabolism in NCM460 cells after Fusobacterium nucleatum infection. Mechanistically, F. nucleatum promotes the nicotinamide adenine dinucleotide (NAD+) salvage pathway by upregulating NAMPT expression, which subsequently leads to the activation of the p38 mitogen-activated protein kinase (MAPK) signaling pathway and promotes the secretion of inflammatory factors, ultimately inhibiting the therapeutic response to anti-TNF drugs. These findings demonstrate that the gut microbiota can influence the response to anti-TNF therapy in patients with UC and highlight the therapeutic potential of targeting F. nucleatum and its associated pathways for preventing and treating drug resistance in UC.

IBDTransDB: a manually curated transcriptomic database for inflammatory bowel disease

Inflammatory Bowel Disease (IBD) therapies are ineffective in at least 40% patients, and transcriptomic datasets have been widely used to reveal the pathogenesis and to identify the novel drug targets for these patients. Although public IBD transcriptomic datasets are available from many web-based tools/databases, due to the unstructured metadata and data description of these public datasets, most of these tools/databases do not allow querying datasets based on multiple keywords (e.g. colon and infliximab). Furthermore, few tools/databases can compare and integrate the datasets from the query results. To fill these gaps, we have developed IBDTransDB (https://abbviegrc.shinyapps.io/ibdtransdb/), a manually curated transcriptomic database for IBD. IBDTransDB includes a manually curated database with 34 transcriptomic datasets (2932 samples, 122 differential comparisons) and a query system supporting 35 keywords from 5 attributes (e.g. tissue and treatment). IBDTransDB also provides three modules for data analyses and integration. IBDExplore allows interactive visualization of differential gene list, pathway enrichment, gene signature and cell deconvolution analyses from a single dataset. IBDCompare supports comparisons of selected genes or pathways from multiple datasets across different conditions. IBDIntegrate performs meta-analysis to prioritize a list of genes/pathways based on user-selected datasets and conditions. Using two case studies related to infliximab treatment, we demonstrated that IBDTransDB provides a unique platform for biologists and clinicians to reveal IBD pathogenesis and identify the novel targets by integrating with other omics data. Database URL: https://abbviegrc.shinyapps.io/ibdtransdb/.

Biomarkers prediction and immune landscape in ulcerative colitis: Findings based on bioinformatics and machine learning

BACKGROUND

Ulcerative colitis (UC) presents diagnostic and therapeutic difficulties. The primary objective of this study is to identify efficacious biomarkers for diagnosis and treatment, as well as acquire a deeper understanding of the immuneological characteristics associated with the disease.

METHODS

Datasets relating to UC were obtained from GEO database. Among these, three datasets were merged to create a metadata for bioinformatics analysis and machine learning. Additionally, one dataset specifically utilized for external validation. Least absolute shrinkage and selection operator (LASSO) and random forest (RF) were employed to screen signature genes. The artificial neural network (ANN) model and receiver operating characteristic (ROC) curve were used to assess the diagnostic performance of signature genes. The single sample gene set enrichment analysis (ssGSEA) was applied to reveal the immune landscape. Finally, the relationship between the signature genes, immune infiltration, and clinical characteristics was investigated through correlation analysis.

RESULT

By intersecting the result of LASSO, RF and WGCNA, 8 signature genes were identified, including S100A8, IL-1B, CXCL1, TCN1, MMP10, GREM1, DUOX2 and SLC6A14. The biological progress of this gene mostly encompasses acute inflammatory response, aggregation and chemotaxis of leukocyte, and response to lipopolysaccharide by mediating IL-17 signaling pathway, NF-kappa B signaling pathway, TNF signaling pathway, NOD-like receptor signaling pathway. Immune infiltration analysis shows 25 immune cells are significantly elevated in UC samples. Moreover, these signature genes exhibit a strong correlation with various immune cells and a mild to moderate correlation with the Mayo score.

CONCLUSION

S100A8, IL-1B, CXCL1, TCN1, MMP10, GREM1, DUOX2 and SLC6A14 have been identified as credible potential biomarkers for the diagnosis and therapy of UC. The immune response mediated by these signature biomarkers plays a crucial role in the occurrence and advancement of UC by means of the reciprocal interaction between the signature biomarkers and immune-infiltrated cells.