Intratumoral heterogeneity in microsatellite instability status at single-cell resolution

Intratumoral heterogeneity complicates the interpretation of single-test biomarkers. Microsatellite instability (MSI) is one such biomarker, which is used to guide immune checkpoint inhibitor treatment by classifying samples as having high microsatellite instability (MSI-H) or as microsatellite stable (MSS). However, it is unknown whether MSI itself is a heterogeneous phenomenon. To test this, we curated data from several single-cell RNA sequencing studies with clinical MSI status and developed a computational pipeline that quantifies intratumoral heterogeneity in MSI. Out of 49 individuals, 15 showed evidence of divergence in MSI status between clusters of cancer cells, and most had distinct MSI-H and MSS subclones. These results question the use of MSI as a binary biomarker, and we hypothesize that accounting for heterogeneity could improve its use as a predictive biomarker. Further studies are required to determine the frequency of MSI heterogeneity at the population level and whether it can have clinical implications.