Abstract B06: Understanding of the ovarian endometriosis and gene expression functions in neoplastic transformation
Authors: Monteiro Janice Barros , López Alexandra M. Maldonado , Peng Lirong , Flores Idhaliz , Seto Ed 
Published: May 2016

Abstract
Background: Endometriosis is a benign gynecologic condition that is known to have transformation potential. Women with ovarian endometriosis have twice the risk for developing ovarian cancer of the endometrioid or clear cell types. However, the carcinogenic pathways by which endometriosis associated ovarian carcinoma (EAOC) develops remain poorly understood. Epigenetics are emerging as an important player in the progression from a pre-malignant to a malignant phenotype. Previously, we showed that endometriosis cells and tissues are characterized by increased levels of HDAC1 and 2, histone acetylation at lysine 9 and 16 (H3K9, H4K16), and that promoter sequences of candidate genes for endometriosis are enriched in these histone marks. Aim: We sought to investigate the role of these histone modifications in modulation of gene expression in ovarian endometriosis (OE), endometriosis-associated ovarian cancer (EAOC), and adjacent histologically normal tissues (normal adjacent, NA).
Methods: Series of formalin-fixed paraffin-embedded tissue (FFPE) blocks from EAOC patients containing these three histological tissues were studied. DNA extracted from these three tissues were subjected to chromatin immunoprecipitation using either anti-Ac-H3K9 or anti-Ac-H4K16, and then next generation sequencing. We are analyzing if these three histological tissues are characterized by a different pattern of histone modification enrichment in gene promoters and gene expression profile and identify the genes involved. Also, we assessed the effects of HDAC inhibitors (HDACis) in endometriotic and normal endometrial cells, by measuring its effects in proliferation, invasion and cell viability.
Results: The analysis of ChIP-seq data was mapped of the short reads. Unmapped reads: raw reads were mapped to human genome using BWA. Many unmapped reads (have 30%) were found. Further analysis of unmapped reads using blast against NCBI notation database. Peaks (binding sites of histone): MACS2 software was used to call peaks. Most samples (P018-OEH3K9Ac P018-OEH4K16Ac) have less than 10k peaks detected, indicating a non-successful experiment. Code for IDR analysis was done to check how well biological replicates are reproducible. The p104-AN-H3K09 and p018-AN-H3K09 have good reproducible results, the rests have poor correlations. Based in this find NanoString molecular technology the assay will be necessary to validate our ChIP-Seq results and screening large sample sets against focused sets of loci involved in chromatin remodeling and gene expression.
Citation Format: Janice Barros Monteiro, Alexandra M. Maldonado López, Lirong Peng, Idhaliz Flores, Ed Seto. Understanding of the ovarian endometriosis and gene expression functions in neoplastic transformation. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr B06.