# Intratumoral heterogeneity in microsatellite instability status at single-cell resolution

## TL;DR

This study shows that tumors can have mixed microsatellite instability (MSI) levels within them, challenging the idea that MSI is a simple yes/no trait.

## Contribution

A new computational method reveals that MSI status is heterogeneous within tumors at single-cell resolution.

## Key findings

- 15 out of 49 individuals showed intratumoral heterogeneity in MSI status.
- Both MSI-H and MSS tumors contained subclones with opposing MSI statuses.
- Current binary classification of MSI may be insufficient for accurate biomarker use.

## Abstract

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.

•Novel computational pipeline quantifies ITH and MSI at single-cell resolution•15 out of 49 individuals have evidence of ITH in MSI•Both MSI-H and MSS individuals have tumors with distinct MSI-H and MSS subclones•Findings challenge the current binary classification of MSI status

Novel computational pipeline quantifies ITH and MSI at single-cell resolution

15 out of 49 individuals have evidence of ITH in MSI

Both MSI-H and MSS individuals have tumors with distinct MSI-H and MSS subclones

Findings challenge the current binary classification of MSI status

Cancer; Cell biology; Genetics