title: LINE-1 hypomethylation in cancer is highly variable and inversely correlated with microsatellite instability.
abstract: BACKGROUND
  Alterations in DNA methylation in cancer include global hypomethylation and gene-specific hypermethylation. It is not clear whether these two epigenetic errors are mechanistically linked or occur independently. This study was performed to determine the relationship between DNA hypomethylation, hypermethylation and microsatellite instability in cancer.
  
  
  RESULTS
  We examined 61 cancer cell lines and 60 colorectal carcinomas and their adjacent tissues using LINE-1 bisulfite-PCR as a surrogate for global demethylation. Colorectal carcinomas with sporadic microsatellite instability (MSI), most of which are due to a CpG island methylation phenotype (CIMP) and associated MLH1 promoter methylation, showed in average no difference in LINE-1 methylation between normal adjacent and cancer tissues. Interestingly, some tumor samples in this group showed increase in LINE-1 methylation. In contrast, MSI-showed a significant decrease in LINE-1 methylation between normal adjacent and cancer tissues (P<0.001). Microarray analysis of repetitive element methylation confirmed this observation and showed a high degree of variability in hypomethylation between samples. Additionally, unsupervised hierarchical clustering identified a group of highly hypomethylated tumors, composed mostly of tumors without microsatellite instability. We extended LINE-1 analysis to cancer cell lines from different tissues and found that 50/61 were hypomethylated compared to peripheral blood lymphocytes and normal colon mucosa. Interestingly, these cancer cell lines also exhibited a large variation in demethylation, which was tissue-specific and thus unlikely to be resultant from a stochastic process.
  
  
  CONCLUSIONS
  Global hypomethylation is partially reversed in cancers with microsatellite instability and also shows high variability in cancer, which may reflect alternative progression pathways in cancer.
authors.affiliation: Department of Leukemia, University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America.
authors.forename: Marcos R H
authors.initials: MR
authors.lastname: Estécio
authors.forename: Vazganush
authors.initials: V
authors.lastname: Gharibyan
authors.forename: Lanlan
authors.initials: L
authors.lastname: Shen
authors.forename: Ashraf E K
authors.initials: AE
authors.lastname: Ibrahim
authors.forename: Ketan
authors.initials: K
authors.lastname: Doshi
authors.forename: Rong
authors.initials: R
authors.lastname: He
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Jelinek
authors.forename: Allen S
authors.initials: AS
authors.lastname: Yang
authors.forename: Pearlly S
authors.initials: PS
authors.lastname: Yan
authors.forename: Tim H-M
authors.initials: TH
authors.lastname: Huang
authors.forename: Eloiza H
authors.initials: EH
authors.lastname: Tajara
authors.forename: Jean-Pierre J
authors.initials: JP
authors.lastname: Issa
mesh_terms: D001483:Base Sequence; D019175:DNA Methylation; D017931:DNA Primers; D006801:Humans; D020084:Long Interspersed Nucleotide Elements; D018895:Microsatellite Repeats / Q000235:genetics*; D009369:Neoplasms / Q000235:genetics*
chemical_list: D017931:DNA Primers