PURPOSE: 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). DESCRIPTION: 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. EVALUATION: 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. CONCLUSIONS: Samples of EBUS-TBNA can be used for comprehensive WT and miRNA expression analysis using microarray technology.
PURPOSE: 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). DESCRIPTION: 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. EVALUATION: 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. CONCLUSIONS: Samples of EBUS-TBNA can be used for comprehensive WT and miRNA expression analysis using microarray technology.
Authors: Travis Dotson; Christina Bellinger; Jing Su; Kris Hansen; Graham E Parks; James O Cappellari; Lou Craddock; Hollins Clark; Clifford Howard; W Jeffrey Petty; Bharat Prakash; Kounosuke Watabe; Michael Chan; Jonathan Hovda; Lance D Miller; Jimmy Ruiz Journal: Lung Cancer Date: 2018-11-20 Impact factor: 5.705
Authors: Gillian S Tomlinson; Niclas Thomas; Benjamin M Chain; Katharine Best; Nandi Simpson; Georgia Hardavella; James Brown; Angshu Bhowmik; Neal Navani; Samuel M Janes; Robert F Miller; Mahdad Noursadeghi Journal: Chest Date: 2016-01-12 Impact factor: 9.410
Authors: Juliana Guarize; Fabrizio Bianchi; Elena Marino; Elena Belloni; Manuela Vecchi; Stefano Donghi; Giorgio Lo Iacono; Chiara Casadio; Roberto Cuttano; Massimo Barberis; Pier Paolo Di Fiore; Francesco Petrella; Lorenzo Spaggiari Journal: J Thorac Dis Date: 2018-01 Impact factor: 2.895