Abstract 3604: Identification of genes involved in pathogenesis of esophageal adenocarcinoma using RNA sequencing from laser capture micro-dissected formalin-fixed paraffin-embedded tissue specimens
Authors: Guggenbiller Matthew , Hassan Md Sazzad , Yan Min , Li Jun , Makuru Victoria , von Holzen Urs 
Published: September 2020

Abstract
Esophageal adenocarcinoma (EAC) is one of the most aggressive human cancers and the only major cancer in the United States with increasing incidence. The overall 5-year survival rate of EAC is below 20 percent and treatment remains largely ineffective due to the high resistance to chemotherapy, despite recent advances in systemic treatment options as well as surgical techniques. Gastroesophageal reflux disease (GERD) causes Barrett's esophagus (BE), a columnar metaplasia containing goblet cells of the esophagus strongly associated with the development of EAC. However, the mechanisms driving EAC development remains poorly understood. In this study, transcriptomic profiling was performed using RNA-sequencing (RNA-seq) on normal, premalignant Barrett's and malignant adenocarcinoma esophageal tissues for better understanding the pathogenesis of EAC. Pure population of cells were collected by laser capture microdissection (LCM) of histologically confirmed formalin-fixed paraffin-embedded (FFPE) esophageal tissues. Total RNA was extracted from micro-dissected sections using the Ambion RecoverAll kit followed by RNA quality assessment using Bioanalyzer to determine the RNA integrity number (RIN) and DV200 metric. 15 RNA samples with sufficient purity and appropriate concentrations were sent for library preparations and sequenced on an Illumina NextSeq500. Differential gene expression and network analysis methods were then applied to discover novel driver genes and pathways for EAC development. Clustering for RNA-seq data shows nice clustering of normal esophagus (NE), Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC) samples in relation to gene expression patters. Comparing differentially expressed genes using FDR&lt;0.001 we found many genes differentially expressed, especially between each of the BE and EAC when compared to the NE. Interestingly, there are much less differentially expressed genes when comparing each of the BE and EAD to each other. This shows that BE and EAC are closer to each other than to the normal esophagus, but there are still key differences between them. Using pathway analysis and functional annotation we have identified differentially expressed candidate genes and pathways in BE and EAC involving quite a few pathways including PI3 kinase, focal adhesion kinase and metabolic pathways. In summary, this transcriptomic profiling will improve our understanding of EAC pathogenesis and these candidate genes could be diagnostic and therapeutic targets for EAC.
Citation Format: Matthew Guggenbiller, Md Sazzad Hassan, Min Yan, Jun Li, Victoria Makuru, Urs von Holzen. Identification of genes involved in pathogenesis of esophageal adenocarcinoma using RNA sequencing from laser capture micro-dissected formalin-fixed paraffin-embedded tissue specimens [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 3604.