Abstract 2965: Relationship between LINE-1 methylation level, allelic imbalance and PIK3CA mutation in esophageal squamous cell carcinoma.
Authors: Baba Yoshifumi , Watanabe Masayuki , Murata Asuka , Shigaki Hironobu , Iwagami Shiro , Iwatsuki Masaaki , Ishimoto Takatsugu , Baba Hideo 
Published: August 2014

Abstract
Background: Epigenetic changes such as DNA methylation, histone modification, and loss of genome imprinting play a crucial role in esophageal squamous cell carcinogenesis, along with genomic and genetic alterations. DNA methylation is a fundamental epigenetic process that modulates gene expression. Cancer cells exhibit two types of DNA methylation alterations: global DNA hypomethylation and site-specific CpG island promoter hypermethylation. Genome-wide DNA hypomethylation plays a crucial role in genomic instability and carcinogenesis. Since LINE-1 or the L1 retrotransposon constitutes a substantial portion (17%) of the human genome, the level of LINE-1 methylation is regarded to be a surrogate marker of global DNA methylation. Our group has reported that esophageal squamous cell carcinomas (ESCCs) patients with LINE-1 hypomethylated tumor experience poorer prognosis compared with those with LINE-1 hypermethylated tumors (Ann Surg, 2012).
Method: To examine the potential mechanism by which LINE-1 hypomethylation affects tumor aggressive behavior, we performed an array-based comparative genomic hybridization (array-CGH; Agilent 400K) analysis utilizing LINE-1 hypomethylated ESCC tissues (n=3) and LINE-1 hypermethylated ESCC tissues (n=3). In addition, we assessed the relationship between LINE-1 methylation level and mutations of KRAS, BRAF, and PIK3CA using a non-biased cohort of 202 ESCCs and Pyrosequencing technology.
Results: Array-CGH analysis revealed that genomic gains and losses frequently occurred only in LINE-1 hypomethylated ESCCs; genomic gains were found at 1q42, 1q44, 2p16, 3q13, 3q29, 6q22, 7p21-22, 7q11, 7q31, 8q11, 8q21, 9q21-22, 10q11, 10q26, 11p11, 11q22, 17q11-12, 17q21, and 20p12, while losses were found at 2q35, 3p21, 3p14, 4q25, 4q28, 5p31 and 6p21. On the other hand, LINE-1 hypermethylated tumors showed no significant genomic gain and bare genomic loss (10q11). KRAS mutation was extremely rare (1/202; 0.5%), and BRAF mutation was absent (0/202; 0%). PIK3CA in exon 9 and/or 20 mutation was detected in 45 of 202 cases (22%). Interestingly, PIK3CA wild-type tumors showed significantly lower LINE-1 methylation level compared with PIK3CA mutated tumors (p=0.027).
Conclusion: Our data suggest a relationship between LINE-1 methylation level (global DNA methylation level), allelic imbalances (copy number alterations) and oncogene mutation (PIK3CA). This relationship may confer a poor prognosis in ESCCs. Further studies are necessary to elucidate mechanism(s) by which LINE-1 hypomethylation affects tumor behavior.
Citation Format: Yoshifumi Baba, Masayuki Watanabe, Asuka Murata, Hironobu Shigaki, Shiro Iwagami, Masaaki Iwatsuki, Takatsugu Ishimoto, Hideo Baba. Relationship between LINE-1 methylation level, allelic imbalance and PIK3CA mutation in esophageal squamous cell carcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2965. doi:10.1158/1538-7445.AM2013-2965