BackgroundMicrosatellite instability–high (MSI‐H)/mismatch repair deficiency (dMMR) is a biomarker for responses to immune checkpoint inhibitors (ICIs). Whether mechanisms underlying microsatellite instability alter responses to ICIs is unclear. This article reports data from a prospective phase 2 pilot study of pembrolizumab in patients with recurrent MSI‐H endometrial cancer (EC) analyzed by whole exome sequencing (WES) and potential mechanisms of primary/secondary ICI resistance (NCT02899793).MethodsPatients with measurable MSI‐H/dMMR EC confirmed by polymerase chain reaction/immunohistochemistry were evaluated by WES and received 200 mg of pembrolizumab every 3 weeks for ≤2 years. The primary end point was the objective response rate (ORR). Secondary end points included progression‐free survival (PFS) and overall survival (OS).ResultsTwenty‐five patients (24 evaluable) were treated. Six patients (25%) harbored Lynch/Lynch‐like tumors, whereas 18 (75%) had sporadic EC. The tumor mutation burden was higher in Lynch‐like tumors (median, 2939 mutations/megabase [Mut/Mb]; interquartile range [IQR], 867‐5108 Mut/Mb) than sporadic tumors (median, 604 Mut/Mb; IQR, 411‐798 Mut/Mb; P = .0076). The ORR was 100% in Lynch/Lynch‐like patients but only 44% in sporadic patients (P = .024). The 3‐year PFS and OS proportions were 100% versus 30% (P = .017) and 100% versus 43% (P = .043), respectively.ConclusionsThis study suggests prognostic significance of Lynch‐like cancers versus sporadic MSI‐H/dMMR ECs for ORR, PFS, and OS when patients are treated with pembrolizumab. Larger confirmatory studies in ECs and other MSI‐H/dMMR tumors are necessary. Defective antigen processing/presentation and deranged induction in interferon responses serve as mechanisms of resistance in sporadic MSI‐H ECs. Oligoprogression in MSI‐H/dMMR patients appears salvageable with surgical resection and/or local treatment and the continuation of pembrolizumab off study. Clinical studies evaluating separate MSI‐H/dMMR EC subtypes treated with ICIs are warranted.