Integration of Single-Cell Analysis and Bulk RNA Sequencing Data Using Multi-Level Attention Graph Neural Network for...

Background: The prognosis management of thyroid cancer remains a significant challenge. This study highlights the critical role of T cells in the tumor microenvironment and aims to improve prognostic precision by integrating bulk RNA-seq and single-cell RNA-seq (scRNA-seq) data, providing a more comprehensive view of tumor biology at the single-cell level. Method: 15 thyroid cancer scRNA-seq samples were analyzed from GEO and 489 patients from TCGA. A multi-level attention graph neural network (MLA-GNN) model was applied to integrate T-cell-related differentially expressed genes (DEGs) for predicting disease-free survival (DFS). Patients were divided into training and validation cohorts in an 8:2 ratio. Result: We systematically characterized the immune microenvironment of metastatic thyroid cancer by using single-cell transcriptomics and identified the important role of T-cell subtypes in the development of thyroid cancer. T-cell-based DEGS between tumor tissues and normal tissues were also identified. Subsequently, T-cell-based risk signatures were selected for establishing a risk model using MLA-GNN. Finally, our MLA-GNN-based model demonstrated an excellent ability to predict the DFS of thyroid cancer patients (1-year AUC: 0.965, 3-years AUC: 0.979, and 5-years AUC: 0.949 in training groups, and 1-year AUC: 0.879, 3-years AUC: 0.804, and 5-years AUC: 0.804 in validation groups). Conclusions: Risk features based on T-cell genes have demonstrated the effectiveness in predicting the prognosis of thyroid cancer. By conducting a comprehensive characterization of T-cell features, we aim to enhance our understanding of the tumor's response to immunotherapy and uncover new strategies for the treatment of cancer.