Survival prediction of colorectal cancer using 101 machine learning methods based on immune-related genes: A machine learning study

Clinical Snapshot

Key Findings

• P Value: P < 0.001 for survival difference between risk groups

• Effect Size: Ridge regression model achieved highest performance

• Primary Outcome: Overall survival prediction using immune-related gene risk score

• Nnt Or Sensitivity: Concordance index 0.67 (moderate discriminative ability)

• Confidence Interval: Not reported in abstract

Clinical Application

Requires access to gene expression profiling technology and bioinformatics expertise; may be challenging in routine practice Relevant to Australian oncology practice; gene expression profiling increasingly available through public pathology services; aligns with precision medicine initiatives supported by NHMRC Colorectal cancer patients suitable for genomic profiling and risk stratification

Abstract

Colorectal cancer (CRC) is characterized by high incidence and mortality rates. Early identification of high-risk CRC patients and timely intervention are crucial for reducing mortality rates. This study aims to develop a prognostic model incorporating immune-related genes using 101 machine learning algorithms. We utilized data from 630 CRC patients in The Cancer Genome Atlas Program database and the Gene Expression Omnibus database as a validation set. We identified immune-related genes from the ImmPort repository and conducted differential gene expression analysis. We developed 101 machine learning models, including random survival forest, elastic net, LASSO, Ridge regression, stepwise Cox, Coxboost, partial least squares regression for Cox, supervised principal component analysis, generalized boosted modeling, and survival support vector machines. The model with the highest mean concordance index was selected as the optimal prognostic model. The Ridge regression model demonstrated the most robust performance with a mean concordance index of 0.67. Patients with higher immune-related gene risk score (IRGRS) had significantly lower survival rates (log-rank test, P < .001). Univariate and multivariate Cox regression analyses confirmed IRGRS as an independent prognostic factor. Nomograms successfully predicted overall survival at 1, 2, and 3 years. IRGRS correlated with immune cell infiltration levels and stromal activity in the tumor microenvironment. High IRGRS scores were associated with higher tumor immune dysfunction and exclusion scores, suggesting potential differences in response to immune checkpoint inhibitors. In addition, high IRGRS patients exhibited greater sensitivity to certain chemotherapy drugs. The IRGRS score is a potent predictor of survival in CRC patients. This study offers a new perspective for CRC prognosis and supports the development of personalized treatment strategies.