Toward Graph-Based Decoding of Tumor Evolution: Spatial Inference of Copy Number Variations

Background/Objectives: Constructing a comprehensive spatiotemporal map of tumor heterogeneity is essential for understanding tumor evolution, with copy number variation (CNV) being a significant feature. Existing studies often rely on tools originally developed for single-cell data, which fail to utilize spatial information, often leading to an incomplete map of clonal architecture. Our study aims to develop a model that fully leverages spatial omics data to elucidate spatio-temporal changes in tumor evolution. Methods: Here, we introduce SCOIGET (Spatial COpy number Inference by Graph on Evolution of Tumor), a novel framework using graph neural networks with graph attention layers to learn spatial neighborhood features of gene expression and infer copy number variations. This approach integrates spatial multi-omics features to create a comprehensive spatial map of tumor heterogeneity. Results: Notably, SCOIGET achieves a substantial reduction in error metrics (e.g., mean squared error, cosine similarity, and distance measures) and produces superior clustering performance, as indicated by higher Silhouette Scores compared to existing methods, validated by both simulated data with spot-level ground truth and patient cohorts. Our model significantly enhances the accuracy of tumor evolution depiction, capturing detailed spatial and temporal changes within the tumor microenvironment. It is versatile and applicable to various downstream tasks, demonstrating strong generalizability across different spatial omics platforms, including 10× Visium and Visium HD and various cancer types, including colorectal cancer and prostate cancer. This robust performance improves research efficiency and provides valuable insights into tumor progression. Conclusions: SCOIGET offers an innovative solution by integrating multiple features and advanced algorithms, providing a detailed and accurate representation of tumor heterogeneity and evolution, aiding in the development of personalized cancer treatment strategies.