Methylation status of long interspersed element-1 in advanced gastric cancer and its prognostic implication

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 th...

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Published in:	Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association Vol. 19; no. 1; pp. 98 - 106
Main Authors:	Song, Young Seok, Kim, Younghoon, Cho, Nam Yun, Yang, Han Kwang, Kim, Woo Ho, Kang, Gyeong Hoon
Format:	Journal Article
Language:	English
Published:	Tokyo Springer Japan 01-01-2016 Springer Nature B.V
Subjects:	Abdominal Surgery Adult Aged Aged, 80 and over Cancer Research CpG Islands Cryopreservation - methods DNA Methylation Female Gastric cancer Gastroenterology Humans Long Interspersed Nucleotide Elements - physiology Male Medicine Medicine & Public Health Middle Aged Oncology Original Article Paraffin Embedding Prognosis Stomach Neoplasms - genetics Stomach Neoplasms - mortality Stomach Neoplasms - pathology Surgical Oncology Survival Analysis Young Adult Hypomethylation Long interspersed element-1 Prognosis Gastric cancer
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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.
AbstractList	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 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. BACKGROUNDSReportedly, 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.METHODSWe 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.RESULTSOlder 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.CONCLUSIONOur 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. 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. 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. 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. 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.
Author	Yang, Han Kwang Kim, Woo Ho Kim, Younghoon Kang, Gyeong Hoon Cho, Nam Yun Song, Young Seok
Author_xml	– sequence: 1 givenname: Young Seok surname: Song fullname: Song, Young Seok organization: Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine – sequence: 2 givenname: Younghoon surname: Kim fullname: Kim, Younghoon organization: Department of Pathology, Seoul National University College of Medicine – sequence: 3 givenname: Nam Yun surname: Cho fullname: Cho, Nam Yun organization: Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine – sequence: 4 givenname: Han Kwang surname: Yang fullname: Yang, Han Kwang organization: Department of General Surgery, Seoul National University College of Medicine – sequence: 5 givenname: Woo Ho surname: Kim fullname: Kim, Woo Ho organization: Department of Pathology, Seoul National University College of Medicine – sequence: 6 givenname: Gyeong Hoon surname: Kang fullname: Kang, Gyeong Hoon email: ghkang@snu.ac.kr organization: Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Department of Pathology, Seoul National University College of Medicine
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/25609453$$D View this record in MEDLINE/PubMed
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Snippet	Backgrounds Reportedly, the pyrosequencing methylation assay can produce inconsistent results between paired snap-frozen and formalin-fixed paraffin-embedded... Reportedly, the pyrosequencing methylation assay can produce inconsistent results between paired snap-frozen and formalin-fixed paraffin-embedded archival... Backgrounds Reportedly, the pyrosequencing methylation assay can produce inconsistent results between paired snap-frozen and formalin-fixed paraffin-embedded... BACKGROUNDSReportedly, the pyrosequencing methylation assay can produce inconsistent results between paired snap-frozen and formalin-fixed paraffin-embedded... Backgrounds: Reportedly, the pyrosequencing methylation assay can produce inconsistent results between paired snap-frozen and formalin-fixed paraffin-embedded...
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SubjectTerms	Abdominal Surgery Adult Aged Aged, 80 and over Cancer Research CpG Islands Cryopreservation - methods DNA Methylation Female Gastric cancer Gastroenterology Humans Long Interspersed Nucleotide Elements - physiology Male Medicine Medicine & Public Health Middle Aged Oncology Original Article Paraffin Embedding Prognosis Stomach Neoplasms - genetics Stomach Neoplasms - mortality Stomach Neoplasms - pathology Surgical Oncology Survival Analysis Young Adult
Title	Methylation status of long interspersed element-1 in advanced gastric cancer and its prognostic implication
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