BioFormosa（2009）44(1): 11-22 *Corresponding author: Yi-Ching Wang; FAX: 886-6-2749296; E-mail: ycw5798@mail.ncku.edu.tw Ming-Tsan Su; FAX: 886-2-29312904; E-mail: mtsu@ntnu.edu.tw Application of Array-Based Epigenomic Technology for the Identification of Hypermethylated CpG Site in Lung Cancer Patients Jer-Wei Chang 1 , Pei-Ing Hwang 2 , Han-Shui Hsu 3 , Chiao-Kai Wen 4 , Yu-Sun Chang 5 , Ming-Tsan Su 1＊ , Yi-Ching Wang 4＊ 1 Department of Life Science, National Taiwan Normal University Taipei, Taiwan 2 Institute of Statistical Science, Academia Sinica Taipei, Taiwan 3 Division of Thoracic Surgery, Taipei Veterans General Hospital Taipei, Taiwan 4 Department of Pharmacology, National Cheng Kung University Tainan, Taiwan 5 Graduate Institute of Basic Medical Sciences, Chang-Gung University Tao-Yuan, Taiwan (Received: 20 April 2009, accepted: 7 May 2009) ABSTRACT Cancer is caused by the accumulation of both genetic and epigenetic changes. Promoter hypermethylation is one of the major epigenetic changes that cause gene inactivation. Aberrant promoter hypermethylation of CpG islands associated with tumor suppressor genes (TSGs) can lead to transcriptional silencing and result in tumorigenesis. The genomic regions with hypermethylation status may possess novel candidate TSGs. We used a microarray-based epigenome-wide methylation analysis called differential methylation hybridization (DMH) to identify the regions of hypermethylation and a chromatin immunoprecipitation (ChIP)-on-chip analysis to identify the regions of condensed or open chromatin in 20 non-small cell lung cancer (NSCLC) patients and several lung cell lines, and have successfully detected several cancer subtype- and stage-specific hypermethylated genes. They may serve as biomarkers for the early detection or prognosis prediction of lung cancer. Using DMH, we identified promoter hypermethylation of the COL14A1 (collagen, type XIV, alpha 1) gene, which has cell anti-proliferative activity and plays a role in cell quiescence and differentiation. Using ChIP-on-chip, COL14A1 promoter region was shown to be in compact chromatin structure in cancer cell lines. In addition, we found that 60.4% of 48 NSCLC patients showed COL14A1 promoter hypermethylation and coincided with low mRNA and protein expression. Moreover, COL14A1 promoter hypermethylation was significantly associated with late stage lung cancer patients. In conclusion, our study provides the evidence that hypermethylation of specific genes are involved in lung tumor initiation or progression and may serve as tumor biomarkers. Key words: tumor suppressor gene, differential methylation hybridization, promoter hypermethylation, prognosis, NSCLC Introduction Cancer is caused by the accumulation of both genetic and epigenetic changes. However, epigenetic changes remain less well examined. In mammals, DNA methylation usually occurs at cytosines located 5’ of guanines, known as CpG dinucleotides. The CpG islands contain cluster of CpG dinucleotides that are about 1-2 kb in length in or near the promoter and first exon regions of genes (Antequera et al., 1993). In cancer, methylation of CpG islands in promoter is considered to be one of