Machine Learning and Mendelian Randomization Identify Six Cell Death-Related Genes Driving Ulcerative Colitis Progression and Treatment Response.

The pathogenesis of ulcerative colitis (UC) is thought to involve abnormal regulation of cell death. However, key cell death-related genes (CDGs) that drive disease progression have not been fully characterized. The identification of these CDGs is thought to potentially reveal new therapeutic targets. Machine learning (ML) and Mendelian randomization (MR) methods were integrated to identify CDGs with causal effects in UC progression. The validation included immune-related analysis, drug response assessment (infliximab/vedolizumab/golimumab), patient stratification based on consensus clustering, and functional validation. Six key CDG genes (VNN1, PTGDS, MMP9, IL13RA2, S100A8, and IL1B) were identified by ML. VNN1 and MMP9 were confirmed by MR to be pathogenic risk factors for UC progression. All six genes were significantly associated with immune cell infiltration, pro-inflammatory cytokines, and intestinal barrier dysfunction. Compared with non-responders, the expression of these six CDGs was significantly downregulated in biologic therapy responders. Based on these genes, patients with UC were classified into two groups: the C1 group with severe disease activity and the C2 group with reduced Mayo scores and enhanced treatment sensitivity. Additionally, knocking down VNN1 functionally alleviated intestinal inflammation. These six genes can be used to assess the severity of UC and predict treatment outcomes.