Analysis of microsatellite instability intensity in single-cell resolution with scMnT reveals tumor heterogeneity in colorectal cancer

Abstract

Although microsatellite instability (MSI) is traditionally regarded as a binary trait, growing evidence indicates that it exists on a continuum, with higher intensity of MSI correlating with better prognosis. However, accurate quantification of MSI intensity is challenging due to the heterogeneous cellular composition of the tumor microenvironment. To this end, we introduce scMnT, a bioinformatic method for identifying MSI cells at single-cell resolution and quantifying MSI intensity based on microsatellite allele lengths. Applying scMnT to scRNA-seq datasets produced robust results and revealed substantial variation in MSI intensity among colorectal cancer patients, with higher MSI intensity correlating with improved responses to immunotherapy. Our approach provides a novel framework for analyzing MSI at the single-cell level, allowing new opportunities for MSI research. scMnT is publicly available at https://github.com/18parkky/scMnT. © The Author(s) 2026. Published by Oxford University Press.