Discordant protein and mRNA expression in lung adenocarcinomas.

Guoan Chen,David G Beer,Jeremy M.G Taylor,David E Misek,Mark B Orringer,Mark D Iannettoni,Thomas J Giordano,Samir M Hanash,Tarek G Gharib,Chiang-Ching Huang,Sharon L.R Kardia

doi:10.1074/mcp.m200008-mcp200

Guoan Chen, David G Beer + Show 9 more

Open Access

https://doi.org/10.1074/mcp.m200008-mcp200

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Abstract

The relationship between gene expression measured at the mRNA level and the corresponding protein level is not well characterized in human cancer. In this study, we compared mRNA and protein expression for a cohort of genes in the same lung adenocarcinomas. The abundance of 165 protein spots representing 98 individual genes was analyzed in 76 lung adenocarcinomas and nine non-neoplastic lung tissues using two-dimensional polyacrylamide gel electrophoresis. Specific polypeptides were identified using matrix-assisted laser desorption/ionization mass spectrometry. For the same 85 samples, mRNA levels were determined using oligonucleotide microarrays, allowing a comparative analysis of mRNA and protein expression among the 165 protein spots. Twenty-eight of the 165 protein spots (17%) or 21 of 98 genes (21.4%) had a statistically significant correlation between protein and mRNA expression (r > 0.2445; p < 0.05); however, among all 165 proteins the correlation coefficient values (r) ranged from -0.467 to 0.442. Correlation coefficient values were not related to protein abundance. Further, no significant correlation between mRNA and protein expression was found (r = -0.025) if the average levels of mRNA or protein among all samples were applied across the 165 protein spots (98 genes). The mRNA/protein correlation coefficient also varied among proteins with multiple isoforms, indicating potentially separate isoform-specific mechanisms for the regulation of protein abundance. Among the 21 genes with a significant correlation between mRNA and protein, five genes differed significantly between stage I and stage III lung adenocarcinomas. Using a quantitative analysis of mRNA and protein expression within the same lung adenocarcinomas, we showed that only a subset of the proteins exhibited a significant correlation with mRNA abundance.

Highlights

The relationship between gene expression measured at the mRNA level and the corresponding protein level is not well characterized in human cancer
Correlation of Individual Proteins and mRNA Expression within Each Tumor—We have examined quantitatively 165 protein spots on 2D gels representing 98 genes and compared protein levels with mRNA levels for a cohort of 85 lung adenocarcinomas and normal lung samples
The proteins whose expression levels were correlated with their mRNA abundance included those involved in signal transduction, carbohydrate metabolism, apoptosis, protein post-translational modification, structural proteins, and heat shock proteins (Table III)

Summary

The abbreviations used are

2D, two-dimensional; MALDI-MS, matrix-assisted laser desorption/ionization mass spectrometry. T-complex protein I, ␣ subunit B23/numatrin Hsp E-FABP/FABP5 Calreticulin 32 Glutathione S-transferase M4 (GST m4) Macropain subunit ⌬. Protein levels were determined using quantitative 2D-PAGE analysis, and the separated protein polypeptides were identified using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The corresponding mRNA levels for the identified proteins within the same samples were determined using oligonucleotide microarrays. Correlation analyses showed that protein abundance is likely a reflection of the transcription for a subset of proteins, but translation and post-translational modifications appear to influence the expression levels of many individual proteins in lung adenocarcinomas

EXPERIMENTAL PROCEDURES

RESULTS

DISCUSSION