Genome-Wide Analysis of DNA Methylation and the Gene Expression Change in Lung Cancer Yong-Jae Kwon, PhD, Seog Joo Lee, MSc, Jae Soo Koh, MD, PhD, Sung.

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Genome-Wide Analysis of DNA Methylation and the Gene Expression Change in Lung Cancer Yong-Jae Kwon, PhD, Seog Joo Lee, MSc, Jae Soo Koh, MD, PhD, Sung Han Kim, PhD, Hae Won Lee, MD, Moon Chul Kang, MD, Jae Bum Bae, PhD, Young-Joon Kim, PhD, Jong Ho Park, MD, PhD Journal of Thoracic Oncology Volume 7, Issue 1, Pages 20-33 (January 2012) DOI: 10.1097/JTO.0b013e3182307f62 Copyright © 2012 International Association for the Study of Lung Cancer Terms and Conditions

FIGURE 1 Schematic diagram showing all the steps to identify the target genes. The outline of the procedures to find the genes regulated by DNA methylation in squamous cell carcinoma (SCC). Two independent experiments (whole-genome DNA methylation assay and microarray) were performed, and then the results were combined. According to this flowchart, we selected the target genes from the whole-genome scale combining assay, and we confirmed the data of the clinical samples. At the end, we can obtain the clinical meanings by statistical analysis. Journal of Thoracic Oncology 2012 7, 20-33DOI: (10.1097/JTO.0b013e3182307f62) Copyright © 2012 International Association for the Study of Lung Cancer Terms and Conditions

FIGURE 2 Genes confirmed to be in accordance with the whole-genome scale combining analysis in the 30 squamous cell carcinoma (SCC) samples by semiquantitative reverse-transcriptase polymerase chain reaction (RT-PCR). CCDC37 (A), CYTL1 (B), CDO1 (C), LMO3 (D), and SLIT2 (E) are hypermethylated and down-regulated genes in the whole-genome scale combining assay. SERPINB5 (F) is a hypomethylated and up-regulated gene in the same assay. DLEC1 (G) is a positive control for the hypermethylated and down-regulated genes. SCC1–30 is frozen tissues from patients with squamous cell carcinoma. N, normal lung tissue; T, tumor. Journal of Thoracic Oncology 2012 7, 20-33DOI: (10.1097/JTO.0b013e3182307f62) Copyright © 2012 International Association for the Study of Lung Cancer Terms and Conditions

FIGURE 3 Differences in DNA methylation between normal lung and squamous cell carcinoma (SCC). These graphs show the DNA methylation pattern of CCDC37 (A), CYTL1 (B), LMO3 (C), and SERPINB5 (D) in both normal lung and SCC. Four genes among the selected six genes were confirmed to have different DNA methylation patterns as compared between normal lung and SCC. In detail, CCDC37, CYTL1, and LMO3 were hypermethylated, and SERPINB5 was hypomethylated in SCC. Each dot represents the DNA methylation of each sample, which was from frozen tissue or a paraffin block. For statistical analysis, Student's t test was applied, and p values <0.05 were considered to be significant. The promoter region (the transcription start site is +1) was examined, and the mean value and standard error of the mean of the normal lung and lung cancer are also depicted. Each graph displays the number of samples used and qualified by pyrosequencing. Although the DNA methylation of 20 SCC samples was examined by pyrosequencing, each graph has different sample numbers because of the quality check for pyrosequencing. In each panel, the upper three graphs and lower three graphs are the results from the frozen tissues and SCC paraffin blocks, respectively. In the lower three graphs in each panel, the dotted line means the DNA methylation level of the purified epithelial cells of the representative normal lung. Journal of Thoracic Oncology 2012 7, 20-33DOI: (10.1097/JTO.0b013e3182307f62) Copyright © 2012 International Association for the Study of Lung Cancer Terms and Conditions

FIGURE 4 The correlation of DNA methylation of CYTL1 with the squamous cell carcinoma (SCC) stages. The DNA methylation level of CYTL1 (+168) was compared after dividing the samples according to their pathologic stage. The difference of the DNA methylation levels was 6.49 between stage I and stage II and 4.38 between stage II and stage III. Their p value of one-way analysis of variance (ANOVA) analysis was 0.0471. Therefore, the CpG site (+168) of the CYTL1 promoter region was recognized as a hot spot that has correlation with the SCC stage. The dotted line is the DNA methylation level of normal lung. Journal of Thoracic Oncology 2012 7, 20-33DOI: (10.1097/JTO.0b013e3182307f62) Copyright © 2012 International Association for the Study of Lung Cancer Terms and Conditions

FIGURE 5 Restoration of the gene expression by 5-aza-2′-deoxycytidine treatment in the SCC cell lines. A, The total RNA was extracted from the normal lung tissues and two SCC cell lines, and the complementary DNAs (cDNAs) were synthesized. By using the cDNA as a template, semiquantitative RT-PCR was done, and GAPDH was used as a loading control. CCDC37, CDO1, LMO3, CYTL1, and SLIT2 were down-regulated, and SERPINB5 was up-regulated in the SCC cell lines in accordance with the data from the tissue samples. B, To validate whether these results were caused by DNA methylation, 5-aza-2′-deoxycytidine treatment was performed in the SCC cell lines. The SCC cell lines were treated with a demethylating agent (20 μM 5-aza-2′-deoxycytidine) for 4 days, and the expression levels of the five genes that were found to be hypermethylated in the previous experiment were recovered to their original expression level in the SCC cell lines. SCC-13N and SCC-15N: normal lung tissue; HCC-95, HCC-1588, Calu-1, SK-MES-1, and SW900: squamous cell carcinoma cell lines. Journal of Thoracic Oncology 2012 7, 20-33DOI: (10.1097/JTO.0b013e3182307f62) Copyright © 2012 International Association for the Study of Lung Cancer Terms and Conditions