Abstract 4275: Analysis of gene and protein expression in lymphoma cell lines using multiple platforms
Authors: Cascione Luciano , Benvento Marco , Gaudio Eugenio , Tarantelli Chiara , Spriano Filippo , Arribas Alberto , Rinaldi Andrea , Kwee Ivo , Luecke Jonh , Geiger Roger , Bertoni Francesco 
Published: August 2018

Abstract
Introduction. Published studies on the correlation of mRNA and protein levels in complex samples are relatively limited, especially in lymphoma cells. Here, we present a large-scale analysis of gene expression and protein abundance across a panel of human lymphoma cell lines. We integrated mass spectrometry data with expression profiles obtained with a next generation sequencing (NGS) and a microarray based platform.
Methods. Transcriptome analysis of 51 cell lines derived from activated B cell (n=7) and germinal center B cell (n=15) diffuse large B cell lymphoma (DLBCL), Type 3 DLBCL (n=3), mantle cell lymphoma (n=10), marginal zone lymphoma (n=5), prolymphocytic leukemia (n=1), anaplastic large-cell lymphoma (n=7), primary mediastinal large b-cell lymphoma (n=1) were analyzed using the HTG EdgeSeq Oncology Biomarker Panel Assay, and the Illumina HumanHT 12 Expression BeadChips. Proteome analysis was performed by digesting each cell lysate with LysC and trypsin endoprotease. Subsequently, peptides were analyzed by LC-MS/MS with a QExactive HF mass spectrometer. The Pearson correlation was calculated between gene and protein measurements.
Results. High correlations (median rho 0.65, 95% CI 0.61-0.66) were observed between the gene expression profiles generated by the microarray and the NGS - based platforms (Illumina and HTG), with the latter demonstrating a broader dynamic range and ability in detecting low abundance transcripts. A comprehensive cell- and gene-specific analysis revealed that across cell lines, correlation between mRNA and protein expression was positive with a median correlation of 0.49 (95% CI 0.48-0.50) for the NGS assay, and of 0.43 (95% CI 0.42-0.44) for the microarray-based platform. We identified 577 (46% of common genes n=1253) and 3890 (51% of common genes n=7592) genes whose RNA and protein expression was significantly correlated across all cell lines for NGS and microarray, respectively. Most genes had high and concordant RNA-protein expression (rho values ranged from 0.34 to 0.91), showing that expression of target genes corresponded well to protein levels in lymphoma cell lines. In this group, we found representatives of essential cellular functions, such as cell cycle (CDK1 and CDC34), apoptosis (CASP8 and CD27), and the NFkB pathway (TBK1 and TNFAIP3). A low number of discordant genes (high expression-low protein level or low expression-high protein level) was identified (less than 1% of tested genes; 31 for microarray and 4 for NGS).
Conclusion. We observed a positive correlation between mRNAs and protein levels. In particular, we identified a set of known biomarkers and therapeutic genes whose expression were highly correlated with protein levels, implying that mRNA expression of those genes is sufficient to determine protein abundance. Moreover, we found few genes with discordant mRNA-protein ratios and further analyses are needed to better understand this phenomenon.
Citation Format: Luciano Cascione, Marco Benvento, Eugenio Gaudio, Chiara Tarantelli, Filippo Spriano, Alberto Arribas, Andrea Rinaldi, Ivo Kwee, Jonh Luecke, Roger Geiger, Francesco Bertoni. Analysis of gene and protein expression in lymphoma cell lines using multiple platforms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4275.