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Comparison of lung cancer cell lines representing four histopathological subtypes with gene expression profiling using quantitative real-time PCR
© Watanabe et al; licensee BioMed Central Ltd. 2010
Received: 05 October 2009
Accepted: 21 January 2010
Published: 21 January 2010
Lung cancers are the most common type of human malignancy and are intractable. Lung cancers are generally classified into four histopathological subtypes: adenocarcinoma (AD), squamous cell carcinoma (SQ), large cell carcinoma (LC), and small cell carcinoma (SC). Molecular biological characterization of these subtypes has been performed mainly using DNA microarrays. In this study, we compared the gene expression profiles of these four subtypes using twelve human lung cancer cell lines and the more reliable quantitative real-time PCR (qPCR).
We selected 100 genes from public DNA microarray data and examined them by DNA microarray analysis in eight test cell lines (A549, ABC-1, EBC-1, LK-2, LU65, LU99, STC 1, RERF-LC-MA) and a normal control lung cell line (MRC-9). From this, we extracted 19 candidate genes. We quantified the expression of the 19 genes and a housekeeping gene, GAPDH, with qPCR, using the same eight cell lines plus four additional validation lung cancer cell lines (RERF-LC-MS, LC-1/sq, 86-2, and MS-1-L). Finally, we characterized the four subtypes of lung cancer cell lines using principal component analysis (PCA) of gene expression profiling for 12 of the 19 genes (AMY2A, CDH1, FOXG1, IGSF3, ISL1, MALL, PLAU, RAB25, S100P, SLCO4A1, STMN1, and TGM2). The combined PCA and gene pathway analyses suggested that these genes were related to cell adhesion, growth, and invasion. S100P in AD cells and CDH1 in AD and SQ cells were identified as candidate markers of these lung cancer subtypes based on their upregulation and the results of PCA analysis. Immunohistochemistry for S100P and RAB25 was closely correlated to gene expression.
These results show that the four subtypes, represented by 12 lung cancer cell lines, were well characterized using qPCR and PCA for the 12 genes examined. Certain genes, in particular S100P and CDH1, may be especially important for distinguishing the different subtypes. Our results confirm that qPCR and PCA analysis provide a useful tool for characterizing cancer cell subtypes, and we discuss the possible clinical applications of this approach.
Lung cancer is the leading cause of cancer-related death in men and women worldwide and continues to increase in frequency. Currently, a diagnosis of lung cancer is generally based on histopathological findings. Lung cancers are generally classified as either small-cell lung carcinoma (SC) or non-small-cell lung carcinoma (NSCLC). NSCLC is further classified into three histopathological subtypes: adenocarcinoma (AD), squamous cell carcinoma (SQ), and large cell carcinoma (LC). However, progression, metastatic susceptibility, therapeutic and radiation therapy sensitivity, and prognosis cannot be fully predicted based on initial histopathological observations. Molecular characterization of tumors, by assaying gene expression using techniques such as DNA microarray analysis, has the potential to significantly inform medical care that is otherwise based on surgical pathology and oncology. Using this technology, it may be possible to identify clinically important subsets of tumors that would otherwise be indistinguishable by conventional histopathological assessment. In principle, expression profiling should identify tumors that are more likely to invade, relapse, and metastasize, and the approach should allow improved prediction of responses to specific therapeutic regimens and clinical outcomes [1–3]. However, recent publications have raised concerns about the reliability of microarray technology for analyzing differential expression, because of the lack of reproducibility across laboratories and platforms despite the use of highly similar protocols . Initial investigations (e.g., 2000-2003) highlighted discrepancies in gene expression analyzed with different microarray technologies . Although a considerable number of studies have used DNA microarrays to genetically identify lung cancer patients and lung cancer cells [1–3, 6–10], marker gene candidates have varied depending on the report.
Quantitative real-time PCR (qPCR) is generally considered the "gold-standard" assay for measuring gene expression and is often used to confirm microarray data . qPCR is the most sensitive technique for detection and quantification of mRNA targets . Recently, it has been suggested that qPCR may be a simpler, more reliable, and more reproducible method than DNA microarrays . qPCR has been used as a supplementary technique for characterizing lung cancer cells . The recent development of DNA databases and bioinformatics techniques has made it possible to determine gene pathways and gene networks . Statistical analyses, such as principal component analysis (PCA), have recently proven useful in this field. Establishing molecular profiles of the four histopathological subtypes of lung cancer cells in relation to gene networks and statistical analysis would be a valuable and meaningful undertaking. Because the analysis of DNA microarrays is expensive and complex, it is often not practical for routine diagnosis to use high-throughput DNA microarrays containing more than 10,000 genes. A diagnostic approach designed for less than 100 marker genes using either a smaller, less-expensive DNA microarray or qPCR would be more practical. To classify the four histopathological subtypes, we selected 100 candidate marker genes that showed relatively consistent differential expression in reports that analyzed a total of 580 clinical lung cancer tissues and 64 lung cancer cell lines [1–3, 6–10]. We first selected candidate genes using DNA microarrays and then quantified their expression by qPCR. Although clinical application is the ultimate goal, there are some issues to consider when examining clinical tissues with DNA microarrays or qPCR. First, tissues contain varying amounts of contamination from neighboring stromal cells. Second, RNA amplification is required if the amount of clinical tissue is limited, for instance when samples are obtained by microdissection of cancer cells. While these issues are not problematic for analyzing lung cancer cell lines, they become significant barriers when analyzing clinical samples. Finally, the use of epithelial tissue from sites adjacent to tumors as the normal control has drawn criticism , as this tissue often includes histologically normal but genetically abnormal cells .
In this study, we first selected 100 genes from published studies and used DNA microarrays to examine their expression in eight test cell lines (A549 [AD], ABC-1 [AD], EBC-1 [SQ], LK-2 [SQ], LU65 [LC], LU99 [LC], STC 1 [SC], RERF-LC-MA [SC]) representing four histopathological subtypes of lung cancer cells plus a normal control lung cell line (MRC-9). From this, we identified 19 candidate genes for subtype-specific markers. Second, we quantified the expression of these 19 genes in the different cell lines using qPCR. Third, we evaluated the 19 genes with an additional four validation lung cancer cell lines (RERF-LC-MS [AD], LC-1/sq [SQ], 86-2 [LC], and MS-1-L [SC]) and MRC-9 cell by qPCR. Fourth, we analyzed the data using statistical, bioinformatics, PCA, and gene pathway analysis (Ingenuity Pathways Analysis, IPA). We selected 12 optimal marker genes and demonstrated that these profiles could discriminate the four histopathological subtypes of tumors. In addition, we confirmed the results using immunohistochemical analysis.
Identification of candidate genes by microarray analysis
Selection of candidate genes by DNA microarray
Cell lines by histopathological subtype
Quantification of 19 candidate genes by qPCR
Evaluation by qPCR using validation cell lines
We evaluated the expression profiling of the 19 genes using four validation cell lines (RERF-LC-MS [AD], LC-1/sq [SQ], 86-2 [LC], and MS-1-L [SC]) and the normal control (MRC-9). The results of expression profiling are shown in Figure 1. The validation AD cell line showed similar upregulation in the same 12 genes (AMY2A, BEX1, CDH1, CSTA, DUSP4, FOXG1, IGSF3, INADL, ISL1, MALL, S100P, and SLCO4A1) and downregulation in PLAU. The validation SQ cell line showed similar upregulation in 10 genes (AMY2A, BEX1, CDH1, HMGA1, IGSF3, INADL, ISL1, MALL, RAB25 and SLCO4A1) and downregulation in PLAU. The validation LC cell line showed similar upregulation in 10 genes (AMY2A, CDH1, FOSL1, HMGA1, IGSF3, ISL1, MALL, RAB25, S100A2, and SLCO4A1). The validation SC cell line showed similar upregulation in the same nine genes (AMY2A, BEX1, FOXG1, IGSF3, INADL, ISL1, RAB25, SLCO4A1, and STMN1) and downregulation in TGM2. Thus, the concordance rates were 100% for the AD, and SC validation lines, 92% (11/12) for the SQ line, 77% (10/13) for the LC line, and 92% (44/48) overall. CSTA, DUSP4, and S100P were upregulated consistently in only AD cells, and FOSL1 and S100A2 were upregulated in only LC cells. STMN1 was upregulated and TGM2 was downregulated in only SC cells.
Principal component analysis (PCA)
Gene networks and gene pathways
IPA network 1 of ABC-1 cell
Genes in network
AGER, Ap1, ↑ BEX1, CDC42EP5, ↑ CDH1, Ck2, deoxycholate, ↑ DUSP4, ERK, ↓ FOSL1, ↑ FOXG1, FSH, FXYD5, GDF15, HMGA1, Il8r, ↑ ISL1, Jnk, LCN2, MAD2L2, Mapk, MGAT3, MKP2/5, NFkB, PDGF BB, PI3K, ↓ PLAU, PTPRF, PVR, RAGE, S100A1, ↑ S100P, SLC12A6, ↓ STMN1, ↓ TGM2
Cancer, Cellular Movement, Cellular Growth and Proliferation
We compared four histopathological subtypes of 12 lung cancer cell lines using a statistical processing method, PCA, which is based on gene expression profiling determined by qPCR. Four subtypes were optimally classified by PCA using 12 genes (AMY2A, CDH1, FOXG1, IGSF3, ISL1, MALL, PLAU, RAB25, S100P, SLCO4A1, STMN1, and TGM2) from the 19 candidate genes shown in Figure 1. PCA analysis revealed that the loading number of component 1 (PC1) was negatively correlated with the expression of PLAU, SLCO4A1, and TGM2, and positively correlated with IGSF3, STMN1, FOXG1, and RAB25. The loading number of component 2 (PC2) was negatively correlated with the expression of STMN1, AMY2A, and ISL1, and positively correlated with S100P, RAB25, and CDH1. The loading number of component 3 (PC3) was negatively correlated with the expression of RAB25 and AMY2A, and positively correlated with TGM2, MALL, and IGSF3. The four subtypes were divided into two prominent groups with PC2, corresponding to positive PC2 values (AD and SQ) and negative PC2 values (LC and SC). Because PC2 was positively correlated with the expression of CDH1, S100P, and RAB25, these genes may be significant in the classification of the four subtypes. Three SC cell lines were close to each other in PC1, PC2, and PC3. As the presence of subclasses in AD and SQ clinical tissues was suggested [6, 7, 18], it was probable that there was some diversity in the present AD and SQ cell lines. Gene expression of these 12 genes was generally consistent with some exceptions in the four subtypes. Even when gene expression was not fully consistent among the subtypes, PCA with the present 12 genes could be used effectively to classify the four subtypes.
Using DNA microarrays and qPCR, Kuner et al.  recently compared gene expression in 42 AD and 18 SQ clinical tumor samples and systematically analyzed their expression patterns using gene ontology. This group identified 14 tight junction genes and 9 epithelial-mesenchymal transition genes that were upregulated or downregulated in AD samples, SQ samples, or both. Among these genes, the epithelial-mesenchymal transition gene CDH1, which codes for E-cadherin, was upregulated in both AD and SQ samples. We also examined gene ontology. Although our overall results were unclear, our data suggest that CDH1 is associated with cell adhesion, and that the AD and SQ cell lines are associated with greater cell adhesion, while LC and SC cell lines are associated with weaker cell adhesion. Taken together, these studies demonstrate a remarkable upregulation of CDH1 in AD and SQ cells, but not LC and SC cells, making this a candidate marker for differentiating lung cancer subtypes. CDH1 was the only gene studied in both the Kuner et al. report and in ours.
Using cDNA microarrays and gene ontology, Inamura et al.  analyzed 48 SQ clinical tissue samples and classified them into two subclasses. Subclass A genes were related to processes such as cell proliferation and cell cycle progression, while subclass B genes were related to processes such as the MAPKKK cascade and apoptosis. They focused on 30 possible marker genes that were completely different from the 23 genes identified in the Kuner et al. report and the 12 genes we studied.
Using bioinformatics, Kim et al.  extracted differentially expressed lung cancer candidate genes from published data examined by SAGE method. Next, they used qPCR to compare candidate gene expression in 18 AD and 18 SQ samples from microdissected clinical tissues. They extensively examined seven genes and identified two, CBLC and CYP24A1, as novel candidate biomarkers for AD and SQ cells. They also suggested that S100P, which encodes S100 calcium-binding protein P, may be a good biomarker for AD cells. The expression ratio of S100P in cancer/normal cells was high in AD samples and low in SQ samples. In our study, all three AD cell lines showed a robust increase in S100P expression, while the three SQ cell lines showed less or no increase. Taking our data and the Kim et al. data together, the remarkable and specific upregulation of S100P in AD cells suggests that this is a candidate marker for distinguishing the AD subtype. Although the Kim and Kuner groups both analyzed AD and SQ samples, their gene sets (7 and 30, respectively) were non-overlapping.
Identification of molecular markers often leads to important clinical applications, such as earlier diagnosis, better prognosis, and more effective drug targeting. Although numerous papers examining lung cancer tissues and/or lung cancer cell lines using DNA microarrays and/or qPCR have been published e.g.[1–3, 6–10, 19, 20], lung cancers still lack reliable molecular markers . The genes examined varied between paper, and the results were not necessarily consistent. This variability may result from technical limitations, differences in methodology, and the broad biological heterogeneity of lung cancers themselves. Continued accumulation of data will help resolve this question. The studies described were conducted primarily with AD and SQ samples. Many fewer studies looked at LC and SC samples, and direct comparison of all four histopathological subtypes using the same method(s) was rare. Our study is unique because we examined 12 lung cancer cell lines representing all four subtypes, and we used both qPCR and PCA of 12 genes (AMY2A, CDH1, FOXG1, IGSF3, ISL1, MALL, PLAU, RAB25, S100P, SLCO4A1, STMN1, and TGM2). Although none of these 12 genes represent novel candidate markers because they were all selected from earlier microarray studies [1–3, 6–10], this is the first report that systematically analyzed them together in all four subtypes.
The gene network was analyzed using Ingenuity Pathways Analysis software and is displayed graphically in Figure 3. The first connection including CDH1, PLAU, and SMAD4 was suggested to be related to cell adhesion [21, 22]. It was reported that SMAD4 reduced the expression level of endogenous PLAU  and induced CDH1 expression . The second connection including RAB25, SNAI1, and CDH1 was suggested to be related to tumor invasion. It was reported that RAB25 enhanced the ability of tumor cells to invade the extracellular matrix . The first and second connection may be applicable to AD and SQ cell lines in this study. It was reported that STMN1 influenced cell motility  and S100P was associated with cell growth . STMN1 and S100P may work in SC cell lines and AD cell lines, respectively, in this study. The third connection including TGM2, IL1B, and PLAU was suggested to be tumor invasion. It was reported that IL1B increased the expression level of TGM2 , which might be involved in establishing a barrier to tumor spreading . The third connection may not be effective in cell lines in this study, because TGM2 was rather downregulated in this study.
Six of the genes analyzed (CDH1, PLAU, RAB25, S100P, STMN1, and TGM2) have attracted recent attention relating to therapeutic drug sensitivity and prognosis. In gene expression profiling studies of lung cancer cell lines to study therapeutic drug sensitivity, PLAU and CDH1 have been suggested as novel biomarkers of cetuximab sensitivity , and TGM2 was suggested as a potential marker of doxorubicin sensitivity . STIMN1 was reported to be a novel therapeutic target for anticancer activity . Additionally, RAB25 may be linked to tumor aggressiveness and metastasis , and S100P may be a diagnostic marker of non-small-cell lung cancer [30, 31]. PLAU has also been examined in relation to lung cancer prognosis . The set of 12 well-characterized cell lines described in this study, representing the four histopathological subtypes, should prove useful for screening therapeutic drugs and their effects on specific genes.
We performed additional immunohistochemical studies to examine S100P and RAB25 (Figure 4). The results were generally consistent with the gene expression data (Figure 1). In immunostained tumor tissues, AD cells showed immunostaining of S100P in the cytoplasm and the nucleus, while SQ cells showed immunostaining of RAB25 in the cytoplasm. The localization of S100P and RAB25 in tumor tissues was similar to that in cultured cells (data not shown).
Although DNA microarray technology is a powerful tool for characterizing gene expression on a genome scale, issues of reliability, reproducibility, and the correlation of data across different DNA microarrays still need to be addressed. Recently, qPCR was described as being simpler and more reliable than DNA microarrays . Our experiments confirmed that qPCR was simpler, more reproducible, and more reliable than DNA microarrays. In the future, identification of reliable marker genes will hopefully allow for the development of automatic qPCR systems for routine clinical cancer diagnosis.
We examined the characteristics of four histopathological subtypes in lung cancer cell lines using both statistical analysis and biological network analysis. In the future, studies with cultured lung cancer cells should improve our ability to predict the response of different lung cancer types to specific therapeutic regimens.
Our results showed that the four histopathological subtypes, represented by 12 lung cancer cell lines, were well characterized by qPCR and PCA using 12 genes: AMY2A, CDH1, FOXG1, IGSF3, ISL1, MALL, PLAU, RAB25, S100P, SLCO4A1, STMN1, and TGM2. Based on their upregulation and the results of the PCA analysis, S100P and CDH1 were identified as candidate markers for AD tumors and for AD and SQ tumors, respectively.
Cell lines and RNA isolation
The human lung cancer cell lines ABC-1 (AD), RERF-LC-MS (AD), EBC-1 (SQ), LK-2 (SQ), LC-1/sq (SQ), LU65 (LC), LU99 (LC), STC 1 (SC), RERF-LC-MA (SC), MS-1-L (SC), and MRC-9 (normal control lung cell line) were purchased from the Japanese Collection Research Resources Bank (JCRB, Osaka Japan). The 86-2 (LC) lung cancer cell line was purchased from Riken Bioresource Center (Tsukuba, Japan), and the A549 (AD) lung cancer cell line was a generous gift provided by Dr. Akira Yasui of Tohoku University (Sendai, Japan). Total RNA samples were isolated from each cultured cell line using Micro Smash MS-100 (Tomy Digital Biology Co., Ltd. Tokyo) and QuickGene-800 (Fujifilm, Tokyo). RNA quality assurance was performed by measuring the 260:280 nm ratio with a spectrophotometer (NanoDrop Technologies, LLC, Wilmington, DE, USA) and by gel electrophoresis using the Bioanalyzer and Agilent RNA 6000 Nano kit (Agilent Technologies Inc., Santa Clara, CA, USA).
DNA microarray design and production
The 100 candidate marker genes, which were selected based on previous reports [1–3, 6–10], are shown in additional file 1http://www.chem.aoyama.ac.jp/Chem/ChemHP/Furihatalab/. Synthesis of newly designed probes (Japan Patent No. 2007-234363) was outsourced to Invitrogen Corp. (Carlsbad, CA, USA). The probes were spotted onto a GeneSlide platform (Toyo Kohan Co., Ltd. Tokyo) using a Genex Arrayer Type-M (Kaken Geneqs, Inc., Chiba, Japan). GeneSlides were prehybridized at 80°C for 1 hour, washed in 2× SSC/0.2% SDS and then ultrapure water, and then dried by centrifugation.
cDNA synthesis and gene expression profiling by DNA microarray
Alexa-labeled target cDNA was prepared from 20 μg total RNA using a SuperScript Plus Indirect cDNA System kit (Invitrogen Corp., Carlsbad, CA, USA). cDNA obtained from cancer cell lines was labeled with Alexa 555, and cDNA obtained from the control cell line was labeled with Alexa 647. The two Alexa-labeled cDNA samples were mixed and hybridized to a single DNA microarray that was then scanned in a DNA microarray scanner (FLA-8000, Fujifilm). To identify upregulated and downregulated genes, the ratio of relative intensities of the two fluorophores (Alexa 555: Alexa 647) was calculated after global normalization using ArrayGauge (Fujifilm). DNA microarray array data were deposited into the Center for Information Biology Gene Expression Database (CIBEX; accession: CBX 100).
Quantification of genes using qPCR
Primer sequences of 20 genes examined in the study
Gene pathways, networks, and ontology analysis
Biological networks were generated with Ingenuity Pathways Analysis 7.0 (IPA), a web-based application http://www.Ingenuity.com that enables the visualization and analysis of biologically relevant networks to enable the discovery, visualization, and exploration of therapeutically relevant networks as described previously . Ontology analysis was performed with IPA and http://geneontology.org/.
Routine immunohistochemistry was performed using formalin-fixed, paraffin-embedded sections as described in the manufacturer's protocol. We could obtain only RAB25 and S100P antibodies. The following antibodies, dilutions, and pretreatment conditions were used: anti-RAB25 (1:100), trypsin pretreatment; Abnova Corporation, Taipei, Taiwan) and anti-S100P (polyclonal rabbit anti-S100, (1:400), trypsin pretreatment; DakoCytomation, Copenhagen, Denmark).
For statistical analysis program, we performed a logarithmic (log2) transformation of the data to stabilize the variance and the gene expression profile of each cancer cell line, which was normalized to the median gene expression level for the entire sample set. DNA microarray results of the eight test cell lines were analyzed with a Dunnett's test. qPCR results of the 19 candidate genes in 12 cell lines were analyzed with a Dunnett's test and principal component analysis (PCA). PCA was performed using both the PCA program in R (2.8.0; http://www.r-project.org/) and Microsoft Office Excel 2003 (Microsoft, Redmond, WA, USA).
This work was supported in part by Regional New Consortium R&D Projects, The Ministry of Economy, Trade and Industry, Japan (C. Furihata), and a Grant-in-Aid from the Private School High-tech Research Center Program of the Ministry of Education, Culture, Sports, Science, and Technology, Japan (C. Furihata). We thank Dr. Takayuki Negishi, School of Science and Engineering, Aoyama Gakuin University, for collaboration with the Bioanalyzer experiment, and Dr. Kazuhiko Matsumoto, Torii Pharmaceutical Co. Ltd. for his advice on Dunnett's test.
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