title: Inter-locus as well as intra-locus heterogeneity in LINE-1 promoter methylation in common human cancers suggests selective demethylation pressure at specific CpGs.
abstract: BACKGROUND
  Hypomethylation of long interspersed element (LINE)-1 has been observed in tumorigenesis when using degenerate assays, which provide an average across all repeats. However, it is unknown whether individual LINE-1 loci or different CpGs within one specific LINE-1 promoter are equally affected by methylation changes. Conceivably, studying methylation changes at specific LINE-1 may be more informative than global assays for cancer diagnostics. Therefore, with the aim of mapping methylation at individual LINE-1 loci at single-CpG resolution and exploring the diagnostic potential of individual LINE-1 locus methylation, we analyzed methylation at 11 loci by pyrosequencing, next-generation bisulfite sequencing as well as global LINE-1 methylation in bladder, colon, pancreas, prostate, and stomach cancers compared to paired normal tissues and in blood samples from some of the patients compared to healthy donors.
  
  
  RESULTS
  Most (72/80) tumor samples harbored significant methylation changes at at least one locus. Notably, our data revealed not only the expected hypomethylation but also hypermethylation at some loci. Specific CpGs within the LINE-1 consensus sequence appeared preferentially hypomethylated suggesting that these could act as seeds for hypomethylation. In silico analysis revealed that these CpG sites more likely faced the histones in the nucleosome. Multivariate logistic regression analysis did not reveal a significant clinical advantage of locus-specific methylation markers over global methylation markers in distinguishing tumors from normal tissues.
  
  
  CONCLUSIONS
  Methylation changes at individual LINE-1 loci are heterogeneous, whereas specific CpGs within the consensus sequence appear to be more prone to hypomethylation. With a broader selection of loci, locus-specific LINE-1 methylation could become a tool for tumor detection.
authors: Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Sigmund-Freud Str. 25, 53127 Bonn, Germany.
authors: Nicole
authors: N
authors: Nüsgen
authors: Department of Urology, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany.
authors: Wolfgang
authors: W
authors: Goering
authors: Institute for Digestive Research, Lithuanian University of Health Sciences, Eiveniu g. 2, Kaunas, 50009 Lithuania.
authors: Albertas
authors: A
authors: Dauksa
authors: Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Sigmund-Freud Str. 25, 53127 Bonn, Germany.
authors: Arijit
authors: A
authors: Biswas
authors: Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Sigmund-Freud Str. 25, 53127 Bonn, Germany ; Bonn-Aachen International Center for IT (B-IT) Algorithmic Bioinformatics, University of Bonn, Dahlmannstr. 2, 53113 Bonn, Germany.
authors: Muhammad Ahmer
authors: MA
authors: Jamil
authors: Institute of Medical Biometry, Informatics and Epidemiology (IMBIE), University of Bonn, Sigmund-Freud-Straße 25, D-53127 Bonn, Germany.
authors: Ioanna
authors: I
authors: Dimitriou
authors: Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Sigmund-Freud Str. 25, 53127 Bonn, Germany.
authors: Amit
authors: A
authors: Sharma
authors: Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Sigmund-Freud Str. 25, 53127 Bonn, Germany.
authors: Heike
authors: H
authors: Singer
authors: Institute of Medical Biometry, Informatics and Epidemiology (IMBIE), University of Bonn, Sigmund-Freud-Straße 25, D-53127 Bonn, Germany.
authors: Rolf
authors: R
authors: Fimmers
authors: Bonn-Aachen International Center for IT (B-IT) Algorithmic Bioinformatics, University of Bonn, Dahlmannstr. 2, 53113 Bonn, Germany.
authors: Holger
authors: H
authors: Fröhlich
authors: Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Sigmund-Freud Str. 25, 53127 Bonn, Germany.
authors: Johannes
authors: J
authors: Oldenburg
authors: Institute for Digestive Research, Lithuanian University of Health Sciences, Eiveniu g. 2, Kaunas, 50009 Lithuania.
authors: Antanas
authors: A
authors: Gulbinas
authors: Department of Urology, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany.
authors: Wolfgang A
authors: WA
authors: Schulz
authors: Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Sigmund-Freud Str. 25, 53127 Bonn, Germany.
authors: Osman
authors: O
authors: El-Maarri
keywords: Bisulfite sequencing; Cancer; Cancer classification; DNA methylation; Global methylation; L1 loci; LINE-1; Methylation patterns; Pyrosequencing