Analysis of discordance between mismatch repair and microsatellite instability testing in endometrial cancer

Accurate molecular classification of endometrial carcinoma (EC) is critical for guiding therapy, particularly concerning mismatch repair-deficient (MMRd). However, the consistency of MMRd detection across different diagnostic modalities and the molecular basis of discordant results remain insufficiently characterized. In this retrospective study, 220 EC patients treated at Zhejiang Cancer Hospital from January 2021 to March 2024 underwent histopathological review, immunohistochemistry (IHC), and targeted next-generation sequencing (NGS) with a 196-gene panel. Discordant cases were further assessed by polymerase chain reaction (PCR)-based microsatellite instability (MSI) testing, MLH1 promoter methylation analysis, and extended mutational profiling. The median age of the study cohort was 57.0 years. IHC revealed deficient mismatch repair (dMMR) in 65 cases (29.6 %), while NGS detected high MSI (MSI-H) in 44 cases (20.0 %), yielding an overall 90.5 % concordance. All 21 discordant cases (9.5 %) displayed dMMR by IHC but microsatellite stable (MSS) by NGS. PCR reclassified five cases as MSI-H, whose MSIsensor scores were significantly higher than proficient MMR (pMMR)/MSS tumors (p = 0.01) but lower than dMMR/MSI-H tumors (p = 0.0007). Of the remaining 16 unresolved cases, 43.8 % exhibited isolated MSH6 loss, likely due to the functional compensation of MSH3, while 56.2 % showed MLH1 loss, predominantly due to MLH1 promoter methylation (77.8 %). In conclusion, discordance between IHC- and NGS-based MMR/MSI detection is primarily attributable to MSH6 loss with MSH3 compensation and MLH1 promoter methylation. Recognizing these mechanisms is essential for accurate molecular subtyping and clinical decision-making in EC.