Young Seok Song1, Younghoon Kim2, Nam Yun Cho1, Han Kwang Yang3, Woo Ho Kim2, Gyeong Hoon Kang4,5. 1. Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea. 2. Department of Pathology, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-744, South Korea. 3. Department of General Surgery, Seoul National University College of Medicine, Seoul, Korea. 4. Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea. ghkang@snu.ac.kr. 5. Department of Pathology, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-744, South Korea. ghkang@snu.ac.kr.
Abstract
BACKGROUNDS: Reportedly, the pyrosequencing methylation assay can produce inconsistent results between paired snap-frozen and formalin-fixed paraffin-embedded archival tissue samples. In this study, we assayed the methylation levels at four individual CpG sites of L1 using pyrosequencing and found that the methylation levels at individual CpG sites were different but were closely correlated between paired snap-frozen and formalin-fixed paraffin-embedded tissue samples. We aimed to determine whether low methylation status of L1 is associated with gastric cancer patient prognosis. METHODS: We analyzed 434 formalin-fixed paraffin-embedded tissue samples of advanced gastric cancer for their methylation status at four CpG sites of L1 [nucleotide positions 328, 321, 318, and 306 of X58075 (Genbank)] using pyrosequencing, and correlated the L1 methylation level with clinicopathological features. RESULTS: Older age at onset, males, tumor location at antrum or lower body, intestinal type, and lymphatic or venous invasion were associated with a low average methylation level of L1 at the two CpG sites 1 and 4 combined. The average methylation level of L1 at CpG sites 1 and 4 combined was significantly lower in microsatellite-stable and EBV-negative gastric cancers than in EBV-positive or microsatellite-unstable gastric cancers. Low methylation status of L1 was independently correlated with shorter overall survival and disease-free survival time. CONCLUSION: Our findings indicate that the discrepancy in the methylation level of L1 between fresh tissue and formalin-fixed paraffin-embedded tissue samples depends on the CpG sites considered, and that the methylation status of L1 at CpG sites 1 and 4 combined could be utilized as a prognostic parameter for advanced gastric cancers.
BACKGROUNDS: Reportedly, the pyrosequencing methylation assay can produce inconsistent results between paired snap-frozen and formalin-fixed paraffin-embedded archival tissue samples. In this study, we assayed the methylation levels at four individual CpG sites of L1 using pyrosequencing and found that the methylation levels at individual CpG sites were different but were closely correlated between paired snap-frozen and formalin-fixed paraffin-embedded tissue samples. We aimed to determine whether low methylation status of L1 is associated with gastric cancerpatient prognosis. METHODS: We analyzed 434 formalin-fixed paraffin-embedded tissue samples of advanced gastric cancer for their methylation status at four CpG sites of L1 [nucleotide positions 328, 321, 318, and 306 of X58075 (Genbank)] using pyrosequencing, and correlated the L1 methylation level with clinicopathological features. RESULTS: Older age at onset, males, tumor location at antrum or lower body, intestinal type, and lymphatic or venous invasion were associated with a low average methylation level of L1 at the two CpG sites 1 and 4 combined. The average methylation level of L1 at CpG sites 1 and 4 combined was significantly lower in microsatellite-stable and EBV-negative gastric cancers than in EBV-positive or microsatellite-unstable gastric cancers. Low methylation status of L1 was independently correlated with shorter overall survival and disease-free survival time. CONCLUSION: Our findings indicate that the discrepancy in the methylation level of L1 between fresh tissue and formalin-fixed paraffin-embedded tissue samples depends on the CpG sites considered, and that the methylation status of L1 at CpG sites 1 and 4 combined could be utilized as a prognostic parameter for advanced gastric cancers.
Entities:
Keywords:
Gastric cancer; Hypomethylation; Long interspersed element-1; Prognosis
Authors: Quan Zhu; Gerald M Pao; Alexis M Huynh; Hoonkyo Suh; Nina Tonnu; Petra M Nederlof; Fred H Gage; Inder M Verma Journal: Nature Date: 2011-09-07 Impact factor: 49.962
Authors: Kosuke Yoshihara; Maria Shahmoradgoli; Emmanuel Martínez; Rahulsimham Vegesna; Hoon Kim; Wandaliz Torres-Garcia; Victor Treviño; Hui Shen; Peter W Laird; Douglas A Levine; Scott L Carter; Gad Getz; Katherine Stemke-Hale; Gordon B Mills; Roel G W Verhaak Journal: Nat Commun Date: 2013 Impact factor: 14.919