Inter-locus as well as intra-locus heterogeneity in LINE-1 promoter methylation in common human cancers suggests selective demethylation pressure at specific CpGs

Clinical Epigenetics
Nicole NüsgenOsman El-Maarri

Abstract

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. 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 fo...Continue Reading

References

Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
Aug 1, 2006·Journal of Biomedicine & Biotechnology·Wolfgang A Schulz
Jun 26, 2007·Journal of Molecular Biology·Alfonso G Fernandez, John N Anderson
Apr 1, 2008·The Lancet Oncology·Wolfgang A Schulz
Aug 30, 2008·PLoS Computational Biology·Shobhit GuptaWilliam Stafford Noble
Sep 9, 2008·Nucleic Acids Research·Chureerat PhokaewApiwat Mutirangura
Oct 16, 2008·Cell·John L Goodier, Haig H Kazazian
Dec 19, 2008·Nature·Noam KaplanEran Segal
Sep 24, 2009·Genome Biology·Sanjida H RangwalaHaig H Kazazian
Mar 11, 2010·Nucleic Acids Research·Victoria P BelancioPrescott Deininger
Jun 1, 2010·Nature·Ramakrishna K ChodavarapuMatteo Pellegrini
Jul 16, 2010·Genome Research·Katherine Elena Varley, Robi David Mitra
Feb 1, 2011·Nucleic Acids Research·Hehuang XieMarcelo B Soares
Mar 30, 2011·International Journal of Cancer. Journal International Du Cancer·Haley L CashKarl T Kelsey
Jun 28, 2011·Nature Genetics·Kasper Daniel HansenAndrew P Feinberg
Jul 5, 2011·Genome Research·Jung H KimArul M Chinnaiyan
Aug 11, 2011·Carcinogenesis·Wolfgang GoeringWolfgang A Schulz
Sep 14, 2011·Methods in Molecular Biology·Heike SingerOsman El-Maarri
Jan 10, 2012·Journal of Molecular Medicine : Official Organ of the Gesellschaft Deutscher Naturforscher Und Ärzte·Walter PavicicPäivi Peltomäki
Apr 28, 2012·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Dana van BemmelLee E Moore
Jun 30, 2012·Science·Eunjung LeeUNKNOWN Cancer Genome Atlas Research Network
Nov 9, 2012·Cancer Prevention Research·Kevin Brennan, James M Flanagan
Nov 28, 2012·Gastric Cancer : Official Journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association·Hironobu ShigakiHideo Baba
Jan 29, 2013·Nucleic Acids Research·Clayton K CollingsJohn N Anderson
Oct 18, 2013·Frontiers in Oncology·Ulrike KreimerWolfgang Goering

❮ Previous
Next ❯

Citations

Nov 20, 2015·Environmental and Molecular Mutagenesis·Maurizio MauroCatherine B Klein
Jun 29, 2016·British Journal of Cancer·Brian T JoyceLifang Hou
Sep 15, 2016·Epigenomics·Wolfgang A Schulz, Wolfgang Goering
Jan 31, 2017·International Journal of Radiation Biology·Isabelle R MiousseIgor Koturbash
Jun 3, 2017·Radiation Research·Ricardo Cortez Cardoso PenhaLuis Felipe Ribeiro Pinto
Sep 16, 2017·Nucleic Acids Research·Yinan ZhengLifang Hou
Sep 21, 2018·Frontiers in Microbiology·Ananda Ayyappan Jaguva VasudevanWolfgang Goering
Jan 8, 2021·Cancer Investigation·Amit SharmaIngo G H Schmidt-Wolf
Dec 17, 2020·International Journal of Molecular Sciences·Patcharawalai WhongsiriWolfgang A Schulz

❮ Previous
Next ❯

Datasets Mentioned

BETA
X58075

Methods Mentioned

BETA
PCA
PCR
methylation profiling
454 Genome

Software Mentioned

SAS
ZDOCK
GraphPad
Jalview
Java
YASARA
Prism
Bioinformatics Analysis Web Services system ( JABAWS )
GraphPad Prism
SymCurv

Related Concepts

Related Feeds

Bladder Carcinoma In Situ

Bladder Carcinoma In Situ is a superficial bladder cancer that occurs on the surface layer of the bladder. Discover the latest research on this precancerous condition in this feed.