Revealing Fibrosis Genes as Biomarkers of Ulcerative Colitis: A Bioinformatics Study Based on ScRNA and Bulk RNA Datasets.

Abstract

Objective: This study aimed to uncover biomarkers associated with fibroblasts to diagnose ulcerative colitis (UC) and predict sensitivity to TNFα inhibitors.

Methods: We identified fibrosis-related genes by analyzing eight bulk RNA and one single-cell RNA sequencing dataset from UC patients. Three machine learning algorithms were employed to identify common significant genes. We utilized five machine learning models, namely Random Forest (RF), Support Vector Machine (SVM), Xgboost, Multilayer Perceptron (MLP), and Logistic Regression, to develop diagnostic models for UC. Following hyperparameter tweaking using grid search, we evaluated Matthew's Correlation Coefficient (MCC) of each model on the validation set. Finally, we identified five hub genes in UC patients and evaluated their response to infliximab or golimumab.

Results: We identified 23 genes associated with fibroblasts. Further analysis using three ML models revealed BIRC3, IFITM2, ANXA1, ISG20, and MSN as critical fibroblast genes. Following hyperparameter adjustment, the SVM model exhibited the most favorable characteristics in the validation set, achieving an MCC of 0.7. ANXA1 contributed the most to the model that predicts UC. The optimal model was implemented on the website. Among UC patients receiving TNFα inhibitor treatment, the ineffective group showed considerably increased expression of the five critical genes than the responsive group.

Conclusion: BIRC3, IFITM2, ANXA1, ISG20, and MSN may serve as potential diagnostic biomarkers in UC. Through the interaction between characteristic biomarkers and immune infiltrating cells, the immune response mediated by these characteristic biomarkers plays a crucial role in the occurrence and development of UC.