Transcriptomic Profiling of Laser Capture Microdissected FFPE Esophageal Tissues Identifies Candidate Genes and Pathways Associated with Esophageal Adenocarcinoma

Esophageal adenocarcinoma (AC) incidence has increased markedly in the United States and other Western countries over recent decades. Gastro-esophageal reflux disease (GERD) can cause Barrett’s esophagus, which is strongly associated with the development of AC. However, the mechanisms underlying the pathogenesis of AC remain poorly elucidated. In this exploratory pilot study, we performed transcriptomic profiling by RNA sequencing (RNA-seq) on six normal esophagus (WT), four Barrett’s esophagus with low-grade dysplasia (BL), and six esophageal adenocarcinoma (AC) samples using RNA extracted via laser capture microdissection (LCM) of histologically confirmed formalin-fixed paraffin-embedded (FFPE) esophageal biopsies. Differential gene expression analysis demonstrated partial separation according to histological group, with overlap between BL and AC. BL and AC groups displayed a multitude of differentially expressed genes relative to WT samples; however, fewer differentially expressed genes were found when comparing BL and AC groups. We identified 3062 differentially expressed genes across comparisons (2289 WT vs. AC; 1854 WT vs. BL; 130 BL vs. AC). Using KEGG pathway analysis and functional annotation, candidate genes and pathways were identified. Genes related to the extracellular matrix, focal adhesion, and PI3K-AKT pathways were upregulated in BL and AC versus WT, while genes relating to keratinization, Ras/Rap1, and Hippo signaling were downregulated in BL and AC versus WT. A small set of genes (e.g., ANPEP, REG4, MEP1A) distinguished BL from AC and represent differentially expressed candidates for further investigation. This exploratory transcriptomic profiling provides insights into gene expression changes associated with AC pathogenesis and identifies candidate genes and pathways that warrant independent validation by qRT-PCR, immunohistochemistry, and functional studies.