Interpreting Lung Cancer Health Disparity at Transcriptome Level

Abstract

Lung cancer is a leading cause of cancer-related mortality, with disparities in incidence and outcomes observed across different racial and sex groups. Understanding the genetic factors of these disparities is critical for developing targeted treatment therapies. This study aims to identify both patient-specific and cohort-specific biomarker genes that contribute to lung cancer health disparities among African American males (AAMs), European American males (EAMs), African American females (AAFs), and European American females (EAFs). The real-world data is highly imbalanced with respect to race, and the lung cancer dataset is no exception. So, classification with race labels will generate highly biased results toward the larger cohort. We developed a computational framework by designing the classification problems with disease conditions instead of races and leveraging the local interpretability of explainable AI, SHAP (SHapley Additive exPlanations). This study used three disease conditions of lung cancer, including Lung Adenocarcinoma (LUAD), Lung Squamous Cell Carcinoma (LUSC), and Healthy samples (HEALTHY) to design four classification tasks: one 3-class problem (LUAD-LUSC-HEALTHY) and three 2-class problems (LUAD-LUSC, LUAD-HEALTHY, and LUSC-HEALTHY). This multiple-classification approach allows a LUAD patient to be interrogated via three classification problems, namely LUAD-LUSC-HEALTHY, LUAD-LUSC, and LUAD-HEALTHY, thus providing a robust approach of retrieving disparity information for individual patients through the local interpretation of SHAP. The proposed method successfully discovered the sets of genes and pathways related to health disparities in lung cancer between two cohorts, including AAMs vs. EAMs, AAFs vs. EAFs, AAMs vs. AAFs, and EAMs vs. EAFs. The discovered list of genes and pathways provide a short list for biological scientists to conduct wet lab experiment.