Prediction of immune checkpoint inhibition with immune oncology-related gene expression in gastrointestinal cancer using a machine learning classifier

Abstract

Immune checkpoint inhibitors (ICIs) have revolutionized the therapeutic landscape of gastrointestinal cancer. However, biomarkers correlated with the efficacy of ICIs in gastrointestinal cancer are still lacking. In this study, we performed 395-plex immune oncology (IO)-related gene target sequencing in tumor samples from 96 patients with metastatic gastrointestinal cancer patients treated with ICIs, and a linear support vector machine learning strategy was applied to construct a predictive model. ResultsAll 96 patients were randomly assigned into the discovery (n=72) and validation (n=24) cohorts. A 24-gene RNA signature (termed the IO-score) was constructed from 395 immune-related gene expression profiling using a machine learning strategy to identify patients who might benefit from ICIs. The durable clinical benefit rate was higher in patients with a high IO-score than in patients with a low IO-score (discovery cohort: 92.0% vs 4.3%, p<0.001; validation cohort: 85.7% vs 17.6%, p=0.004). The IO-score may exhibit a higher predictive value in the discovery (area under the receiver operating characteristic curve (AUC)=0.97)) and validation (AUC=0.74) cohorts compared with the programmed death ligand 1 positivity (AUC=0.52), tumor mutational burden (AUC=0.69) and microsatellite instability status (AUC=0.59) in the combined cohort. Moreover, patients with a high IO-score also exhibited a prolonged overall survival compared with patients with a low IO-score (discovery cohort: HR, 0.29; 95% CI 0.15 to 0.56; p=0.003; validation cohort: HR, 0.32; 95% CI 0.10 to 1.05; p=0.04). Taken together, our results indicated the potential of IO-score as a biomarker for immunotherapy in patients with gastrointestinal cancers.

Keywords: gastrointestinal neoplasms; tumor biomarkers; tumor microenvironment.