Abstract 2507: Understanding endometrial cancer heterogeneity at single-cell resolution

Abstract

Abstract Endometrial cancer is the fourth most common gynecologic malignancy in the US. Tumor- associated genetic signatures are known to be associated with poorer prognosis of patients with endometrial cancer. In general, frequent gene alterations are enrichments of p53 and KRAS, PTEN, PIK3CA and PI3K/AKT mutations with variable CNV. Considerable evidence for intratumor heterogeneity indicate that bulk genomic sequencing approaches may be insufficient since endometrial cancer is characterized by extensive tumor heterogeneity. Here, to get new insight about endometrial cancer heterogeneity, we applied single cell sequencing since it has the potential to improve our understanding of this genetic feature by providing clonotype and variant information in high resolution. We examined cancer heterogeneity using single cell DNA sequencing Copy Number Variation (sc-DNAseq-CNV) analysis and clonotype detection in three tumors from patients with endometrial cancer. The technology used for processing single cell was 10x ChromiumTM Technology that provides detection of 100 Kb CNV events, calling clonotypes down to 10 of 1000 cell inputs. By processing these samples resulted in the sequencing of around 800 cells. Genome-wide ploidy analysis of the tumor cells showed variable median ploidies per sample. The regional copy number was estimated by processing our data in 20 Kb cases of reads. Multiple sub-clones were identified per sample number one where four clusters of sub-clones characterized cancer heterogeneity. Copy number changes on entire chromosome arms and mutations at variant detection level were detected since the resolution provided by single cell technology applied. Among the variant detection we identified previously reported mutations in POLE, POLE2, TP53, FGFR2, ARID1A, CTNNBI, PIK3CA, PIK3RI, KRAS and SWI/SNF in specific sub clones. Our study addresses the predominant challenge to determine tumor heterogeneity by performing better approaches to detect genomic differences and identifying molecular signatures among women with endometrial cancer. Better understanding of tumor heterogeneity may benefit patients diagnosed with endometrial cancer, or patients with specific molecular characteristics linked to endometrial cancer. Citation Format: Enrique I. Velazquez Villarreal, John D. Carpten, David W. Craig. Understanding endometrial cancer heterogeneity at single-cell resolution [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2507.