SpatialSNV: A novel method for identifying and analyzing spatially resolved SNVs in tumor microenvironments

Abstract

Background The dynamics of single-nucleotide variants (SNVs) play a critical role in understanding tumor development, yet their influence on shaping tumor microenvironments remains largely unexplored. Spatial transcriptomics offers an opportunity to map SNVs within the tumor context, potentially uncovering new insights into tumor microenvironment dynamics. Results This study developed SpatialSNV for identifying effective SNVs across tumor sections using multiple spatial transcriptomics platforms. The analysis revealed that SNVs reflect regional tumor evolutionary traces and extend beyond RNA expression changes. The tumor margins exhibited a distinct mutational profile, with novel SNVs diminishing in a distance-dependent manner from the tumor boundary. These mutations were significantly linked to inflammatory and hypoxic microenvironments. Furthermore, spatially correlated SNV groups were identified, exhibiting distinct spatial patterns and implicating specific roles in tumor-immune system crosstalk. Among these, critical SNVs such as S100A11L40P in colorectal cancer were identified as tumor region-specific mutations. This mutation, located within exonic nonsynonymous regions, may produce neoantigens presented by HLAs, marking it as a potential therapeutic target. Conclusions SpatialSNV represents a promising framework for unraveling the mechanisms underlying tumor-immune crosstalk within the tumor microenvironment by leveraging spatial transcriptomics and SNV-based tissue domain characterization. This approach is designed to be scalable, integrative, and adaptable, making it accessible to researchers aiming to explore tumor heterogeneity and identify therapeutic targets.