Immune activation and response to pembrolizumab in POLE-mutant endometrial cancer

Abstract

Antibodies that target the immune checkpoint receptor programmed cell death protein 1 (PD-1) have resulted in prolonged and beneficial responses toward a variety of human cancers. However, anti-PD-1 therapy in some patients provides no benefit and/or results in adverse side effects. The factors that determine whether patients will be drug sensitive or resistant are not fully understood; therefore, genomic assessment of exceptional responders can provide important insight into patient response. Here, we identified a patient with endometrial cancer who had an exceptional response to the anti-PD-1 antibody pembrolizumab. Clinical grade targeted genomic profiling of a pretreatment tumor sample from this individual identified a mutation in DNA polymerase epsilon (POLE) that associated with an ultramutator phenotype. Analysis of The Cancer Genome Atlas (TCGA) revealed that the presence of POLE mutation associates with high mutational burden and elevated expression of several immune checkpoint genes. Together, these data suggest that cancers harboring POLE mutations are good candidates for immune checkpoint inhibitor therapy.

Figure 1. Histologic, radiologic, and genomic characteristics of a patient with POLE-mutant endometrial cancer responding to pembrolizumab.

(A) Histology from surgical resection of primary endometrial cancer. Top inset shows region of peritumoral lymphocytic infiltration; bottom inset shows separate region with peritumoral lymphocytic micronodules. Original magnification, ×10 (left); ×20 (right). T, tumor; L, lymphocytic infiltrate. (B) Histology from supraclavicular LN biopsy taken 4 years after original diagnosis. Original magnification, ×20. (C) Sections of LN metastasis: hematoxylin counterstain (negative control; top image); IHC staining with anti–PD-L1 antibody clone 22C3 (Merck) (bottom image). Original magnification, ×20. (D) Representative abdominal (top) and thoracic (bottom) CT images taken prior to pembrolizumab treatment and 8 weeks after initiation of therapy. Arrows highlight paraaortic and supraclavicular tumor masses, which substantially decreased. (E) Number of nonsynonymous somatic variants, including somatic variants of unknown significance, found in 315 cancer-related genes shown for primary and recurrent tumor samples.

Figure 2. Comparison of immune markers in POLE, MSI, and MSS endometrial cancers in the TCGA data set.

(A) The relative numbers of nonsynonymous mutations found in POLE-mutant, MSI, and MSS endometrial cancers. (B) Heat map showing relative expression of differentially expressed immune-related genes in POLE-mutant, MSI, and MSS endometrial cancers. Number of samples: 27 POLE, 64 MSI, 104 MSS. Box plots (shown in A) use the following default convention: the horizontal line represents the median value, the box covers the interquartile range (IQR), the whiskers cover values within 1.5 IQR beyond the box, and values beyond 1.5 IQR are represented as dots.

Figure 3. Expression of immune signatures in MSS, MSI, and POLE endometrial cancers in the TCGA endometrial cancer data set.

(A) Expression of a set of immune checkpoint and lymphocyte-associated genes as assayed by RNA sequencing in POLE-mutant, MSI, and MSS endometrial cancers. (B) Estimated proportion representation of some leukocyte subsets, as calculated by CIBERSORT, for POLE-mutant, MSI, and MSS endometrial cancers. (C) Distribution of lymphocyte infiltration scores in histological images of a set of POLE-mutant, MSI, and MSS endometrial cancers. Representative images associated with scores of 1 and 3 are shown to the right. Original magnification, ×20. A 2-sided Wilcoxon rank-sum test was used in all cases to determine P values. P <0.05 was considered statistically significant. Number of samples: 27 POLE, 64 MSI, 104 MSS (A); 12 POLE, 20 MSI, 28 MSS (B); 12 POLE, 10 MSI, 10 MSS (C). For the remaining samples not shown in B, CIBERSORT provided a P value ≥ 0.05. Box plots (shown in B and C) use the following default convention: the horizontal line represents the median value, the box covers the interquartile range (IQR), the whiskers cover values within 1.5 IQR beyond the box, and values beyond 1.5 IQR are represented as dots. *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001.