Discordant Protein and mRNA Expression in Lung Adenocarcinomas

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. Twentyeight 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.

Identification of putative oncogenes in lung adenocarcinoma by a comprehensive functional genomic approach

“…Our discovery that EEF1A2 may be a putative oncogene in lung adenocarcinoma demonstrates the power of our functional genomic strategy for rapidly identifying potential oncogenes. Although the main focus of this study was to specifically identify putative oncogenes, it should be noted that 90.7% of the genes showing high protein expression did not show corresponding increases in both DNA copy number and transcript, a finding consistent with that of others that transcriptional, translational, and post-translational regulatory mechanisms can greatly influence the abundance of protein in lung tumorigenesis (Chen et al, 2002). For example, NFKB1 is a critical arbiter of immune responses, cell survival, and transformation and is often activated in several types of tumors (Chen et al, 2002).…”

“…Although the main focus of this study was to specifically identify putative oncogenes, it should be noted that 90.7% of the genes showing high protein expression did not show corresponding increases in both DNA copy number and transcript, a finding consistent with that of others that transcriptional, translational, and post-translational regulatory mechanisms can greatly influence the abundance of protein in lung tumorigenesis (Chen et al, 2002). For example, NFKB1 is a critical arbiter of immune responses, cell survival, and transformation and is often activated in several types of tumors (Chen et al, 2002). Deregulation of NFKB1 is thought to be modulated through phosphorylation of Ser337 by protein kinase A (Chen et al, 2002).…”

“…For example, NFKB1 is a critical arbiter of immune responses, cell survival, and transformation and is often activated in several types of tumors (Chen et al, 2002). Deregulation of NFKB1 is thought to be modulated through phosphorylation of Ser337 by protein kinase A (Chen et al, 2002). In our study, 68.8% of the genes showing over-representation in the genome did not show elevated transcript levels, implying that at least some of these genes are 'passenger' genes that are concurrently amplified because of their location with respect to amplicons but lack biological relevance in terms of the development of lung adenocarcinoma.…”

“…For example, genomic copy number and protein levels of KCIP-1 were previously found to be amplified and overexpressed in primary lung cancers by cDNA clonebased CGH array analysis (Jiang et al, 2004) and proteomic analysis (Chen et al, 2002), respectively. Our functional genomic approach, which integrates simultaneous CGH, transcript microarrys, proteomic analyses, and siRNA, allows us not only to quickly identify potential oncogenes but also to explore their significance as diagnostic and therapeutic targets in tumor progression -more than could be achieved by any technique alone.…”

“…However, use of transcript patterns does not allow assessment of the expression of protein products or identification of protooncogenes. Another approach, identifying differentially expressed proteins by proteomic analysis and then comparing the proteins present with mRNA expression in cDNA microarrays from the same specimens, can clarify the extent to which changes in transcript patterns reflect changes in their cognate proteins and posttranscriptional mechanisms (Chen et al, 2002), but this approach cannot be used to identify oncogenes driven by extensive increases of their gene copy number. Moreover, using individual microarrays or proteomic approaches alone cannot distinguish the cancer-driving oncogenes that directly propel tumor progression from the larger number of passenger genes that may be concurrently over-represented but are not biologically relevant in tumor development.…”