A transformer-based deep learning survival prediction model and an explainable XGBoost anti-PD-1/PD-L1 outcome prediction model based on the cGAS-STING-centered pathways in hepatocellular carcinoma.
Journal:
Briefings in bioinformatics
PMID:
39749665
Abstract
Recent studies suggest cGAS-STING pathway may play a crucial role in the genesis and development of hepatocellular carcinoma (HCC), closely associated with classical pathways and tumor immunity. We aimed to develop models predicting survival and anti-PD-1/PD-L1 outcomes centered on the cGAS-STING pathway in HCC. We identified classical pathways highly correlated with cGAS-STING pathway and constructed transformer survival model preserving raw structure of pathways. We also developed explainable XGBoost model for predicting anti-PD-1/PD-L1 outcomes using SHAP algorithm. We trained and validated transformer survival model on pan-cancer cohort and tested it on three independent HCC cohorts. Using 0.5 as threshold across cohorts, we divided each HCC cohort into two groups and calculated P values with log-rank test. TCGA-LIHC: C-index = 0.750, P = 1.52e-11; ICGC-LIRI-JP: C-index = 0.741, P = .00138; GSE144269: C-index = 0.647, P = .0233. We trained and validated [area under the receiver operating characteristic curve (AUC) = 0.777] XGBoost model on immunotherapy datasets and tested it on GSE78220 (AUC = 0.789); we also tested XGBoost model on HCC anti-PD-L1 cohort (AUC = 0.719). Our deep learning model and XGBoost model demonstrate potential in predicting survival risks and anti-PD-1/PD-L1 outcomes in HCC. We deployed these two prediction models to the GitHub repository and provided detailed instructions for their usage: deep learning survival model, https://github.com/mlwalker123/CSP_survival_model; XGBoost immunotherapy model, https://github.com/mlwalker123/CSP_immunotherapy_model.