Whole-Exome Sequencing Reveals Clinical Potential of Circulating Tumor DNA from Peritoneal Fluid and Plasma in Endometrial Cancer

SIMPLE SUMMARY: Studies on biomarkers for endometrial cancer using circulating tumor DNA (ctDNA) from liquid biopsy samples are lacking. The aim of this study was to analyze gDNA from tumor tissues and ctDNA derived from peritoneal fluid and plasma samples and determine their mutational concordance via microsatellite instability, copy number alteration, and mutational signature analyses using whole-exome sequencing and P53 immunohistochemistry. ctDNA of two patients with negative cytology presented TP53 mutations concordant with those in the tissue, and the ctDNA of a patient with positive cytology harbored both TP53 and POLE mutations, although none were detected in the tissue. This study is the first to demonstrate comprehensive genomic concordance between ctDNA from the peritoneal fluid and tumor gDNA in endometrial cancer at the whole-exome level. ABSTRACT: Endometrial cancer (EC) is the most common type of gynecological cancer. Studies comparing tumor gDNA and ctDNA isolated from the plasma and peritoneal fluid of EC patients are limited. Whole-exome sequencing and P53 immunohistochemistry of 24 paired tissue, plasma, and peritoneal fluid samples from 10 EC patients were performed to analyze somatic mutations, copy number alterations, microsatellite instability, and mutational signatures. Mutations in cancer-related genes (KMT2C, NOTCH2, PRKAR1A, SDHA, and USP6) and genes related to EC (ARID1A, CTNNB1, PIK3CA, and PTEN) were identified with high frequencies among the three samples. TP53 and POLE mutations, which are highly related to the molecular classification of EC, were identified based on several key observations. The ctDNA of two patients with negative peritoneal fluid presented TP53 mutations concordant with those in tissues. ctDNA from the plasma and peritoneal fluid of a patient with positive cytology harbored both TP53 and POLE mutations, although none were detected in tissues. Additionally, the patient presented with wild type P53 immunohistochemistry, with a focal “high” expression in a “low” wild type background. The tissues and peritoneal fluid of 75% EC patients showed concordant microsatellite instability. Furthermore, we observed strong mutational concordance between the peritoneal fluid and tumors. Our data suggest that the ctDNA from peritoneal fluid might be a suitable biomarker for identifying the mutational landscape of EC and could complement tumor heterogeneity.