Ribonucleic Acid Microarray Analysis From Lymph Node Samples Obtained by Endobronchial Ultrasonography-Guided Transbronchial Needle Aspiration

Abstract

The aim of this study was to evaluate the feasibility of messenger RNA (mRNA) and microRNA (miRNA) expression analysis by microarray using samples obtained by endobronchial ultrasonography-guided transbronchial needle aspiration (EBUS-TBNA). We isolated total RNA from 24 archived clinical EBUS-TBNA samples. The purified RNA that met the quality threshold was used for two different kinds of microarray analyses: whole transcript-based (WT) array for mRNA expression and miRNA expression array. The RNA from 17 of the 24 samples (71%; 12 adenocarcinoma, 3 squamous cell carcinoma, 2 poorly differentiated carcinoma) met the quality threshold. After performing a one-way analysis of variance, we found genes with significant differences in histologic subtype (p<0.01) for each of the WT and miRNA expression data sets. The samples clustered discretely according to their histologic subtypes by hierarchical clustering. After adjusting for multiple testing using the Benjamini-Hochberg false discovery rate correction, there remained 16 WT genes and 4 miRNAs with a false discovery rate of 5% or less. Samples of EBUS-TBNA can be used for comprehensive WT and miRNA expression analysis using microarray technology.