What does this research mean for the field?

Microsatellite instability exhibits intratumoral heterogeneity, with distinct high microsatellite instability (MSI-H) and microsatellite stable (MSS) subclones coexisting within the same tumor. Novelty: ClaimNovelty.NOVEL_FINDING. Consensus alignment: ConsensusAlignment.CHALLENGES_CONSENSUS.

March 3, 2026Open Access

Intratumoral heterogeneity in microsatellite instability status at single-cell resolution

Key Result

In 49 patients, 15 showed intratumoral heterogeneity in microsatellite instability, with distinct MSI-H and MSS subclones within tumors.

Key Points

Evidence shows 15 out of 49 individuals exhibited divergence in microsatellite instability status across cancer cell clusters.
Most individuals displayed distinct subclones categorized as microsatellite unstable (MSI-H) and microsatellite stable (MSS).
Analysis utilized curated single-cell RNA sequencing studies to quantify intratumoral heterogeneity in MSI status.
Study suggests that understanding MSI heterogeneity could enhance the utility of MSI as a predictive biomarker in clinical settings.

Structured PICO

Is microsatellite instability (MSI) a heterogeneous phenomenon within tumors?

Population

49 individuals from curated single-cell RNA sequencing studies with clinical microsatellite instability (MSI) status

Intervention

Computational pipeline quantifying intratumoral heterogeneity in MSI

Outcome

Evidence of divergence in MSI status between clusters of cancer cellssurrogate

Intratumoral heterogeneity in microsatellite instability exists, questioning its use as a binary biomarker and suggesting that accounting for this heterogeneity could improve its predictive value.

Main Result

Absolute Event Rate: 0% vs 0%

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.