Abstract PO019: Identification of differentially expressed genes in primary samples of endometrial hyperplasia and endometrioid endometrial carcinoma responsive to progestin therapy
Authors: Craig M. Rush, Jeffery M. Vahrenkamp, Kathryn Szczotka, Mark K. Dodson, Elke A. Jarboe, Andrew P. Soisson, Jay Gertz
Journal: Clinical Cancer Research (2021)

Abstract One of the oldest and most common therapies for endometrial complex atypical hyperplasia (CAH) and low-stage, low-grade endometrioid endometrial carcinoma (EEC) is the use of progestins. Importantly, the use of progestins remains the only fertility-sparing treatment available. Despite frequent initial response to progestins, relapse rates are high (35-50%). This study aims to identify gene expression signatures indicative of the likelihood of successful progestin therapy. Primary samples (n = 63) were obtained from a total of 31 patients with either CAH or EEC who underwent progestin therapy. Samples were acquired pre- and post-treatment with progestins. Pathological review of the FFPE samples was performed to identify regions of high hyperplastic or neoplastic content for core punches and RNA extraction. RNA-seq was then performed on the FFPE RNA using the TruSeq RNA Exome approach (Illumina), a method that uses targeted capture to improve sequencing from fragmented samples. Differential expression (DE) analysis was performed using two methods: DESeq2 a parametric method and Noiseq a non-parametric method. Both methods were used to obtain an overlapping subset of DE genes to reduce spurious results due to samples with outlier expression. Gene set enrichment was performed using ENRICHR. Analysis of all samples using DESeq2 identified 843 genes significantly associated with outcome, while Noiseq identified 318 genes, with an overlap between the two methods of 137. These 137 genes were largely increased in post-treatment samples from progestin responders and were enriched for the DSigDB terms “progesterone”, “medroxyprogesterone acetate”, and “estradiol”, indicating a strong hormonal gene expression response to progestin therapy. Importantly, post-treatment samples from non-responding patients did not show this expression pattern, demonstrating that this set of genes may indicate successful hormone response in post-treatment samples. Additionally, a small gene signature (61 genes) was specifically decreased in post-treatment responders compared to all other groups. This gene set is enriched for the GO molecular function “enhancer binding”, BioPlanet 2019 sets “BMP signaling pathway in stem cells” and “Signaling events mediated by the hedgehog family”. The genes in this set may be related to failure on progestin therapies and surprisingly include both ESR1 (estrogen receptor a) and PGR (progesterone receptor). Analysis of RNA-seq data from our cohort of CAH and EEC samples identified a 137 gene signature post-progestin treatment that indicate successful clinical response. We also identified a 61 gene signature that remains high in non-responders after treatment compared to responders. Overall, we find that responders show a coordinated change in expression during progestin therapy that is missing from non-responders and this signature could be used in the early evaluation of progestin treatment success. Citation Format: Craig M. Rush, Jeffery M. Vahrenkamp, Kathryn Szczotka, Mark K. Dodson, Elke A. Jarboe, Andrew P. Soisson, Jay Gertz. Identification of differentially expressed genes in primary samples of endometrial hyperplasia and endometrioid endometrial carcinoma responsive to progestin therapy [abstract]. In: Proceedings of the AACR Virtual Special Conference: Endometrial Cancer: New Biology Driving Research and Treatment; 2020 Nov 9-10. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(3_Suppl):Abstract nr PO019.