TY - JOUR
T1 - Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues.
AU - Simmer, Femke
AU - Brinkman, Arie B.
AU - Assenov, Yassen
AU - Matarese, Filomena
AU - Kaan, Anita
AU - Sabatino, Lina
AU - Villanueva, Alberto
AU - Huertas, Dori
AU - Esteller, Manel
AU - Lengauer, Thomas
AU - Bock, Christoph
AU - Colantuoni, Vittorio
AU - Altucci, Lucia
AU - Stunnenberg, Hendrik G.
N1 - Funding Information:
CancerDIP EU Collaborative project HEALTH-F2-2007-200620, Breast Cancer Somatic Genetics Study [BASIS] HEALTH-2009-2.1.1-2-242006, Dutch Cancer Foundation (KWF) grant KUN 2008-4130.
Funding Information:
We thank E.M. Janssen-Megens, Y. Tan, and K.-J. Francoijs for technical support. This work was supported by the CancerDIP EU Collaborative project HEALTH-F2-2007-200620.
PY - 2012/12/1
Y1 - 2012/12/1
N2 - Aberrant DNA methylation often occurs in colorectal cancer (CRC). In our study we applied a genome-wide DNA methylation analysis approach, MethylCap-seq, to map the differentially methylated regions (DMRs) in 24 tumors and matched normal colon samples. In total, 2687 frequently hypermethylated and 468 frequently hypomethylated regions were identified, which include potential biomarkers for CRC diagnosis. Hypermethylation in the tumor samples was enriched at CpG islands and gene promoters, while hypomethylation was distributed throughout the genome. Using epigenetic data from human embryonic stem cells, we show that frequently hypermethylated regions coincide with bivalent loci in human embryonic stem cells. DNA methylation is commonly thought to lead to gene silencing; however, integration of publically available gene expression data indicates that 75% of the frequently hypermethylated genes were most likely already lowly or not expressed in normal tissue. Collectively, our study provides genome-wide DNA methylation maps of CRC, comprehensive lists of DMRs, and gives insights into the role of aberrant DNA methylation in CRC formation.
AB - Aberrant DNA methylation often occurs in colorectal cancer (CRC). In our study we applied a genome-wide DNA methylation analysis approach, MethylCap-seq, to map the differentially methylated regions (DMRs) in 24 tumors and matched normal colon samples. In total, 2687 frequently hypermethylated and 468 frequently hypomethylated regions were identified, which include potential biomarkers for CRC diagnosis. Hypermethylation in the tumor samples was enriched at CpG islands and gene promoters, while hypomethylation was distributed throughout the genome. Using epigenetic data from human embryonic stem cells, we show that frequently hypermethylated regions coincide with bivalent loci in human embryonic stem cells. DNA methylation is commonly thought to lead to gene silencing; however, integration of publically available gene expression data indicates that 75% of the frequently hypermethylated genes were most likely already lowly or not expressed in normal tissue. Collectively, our study provides genome-wide DNA methylation maps of CRC, comprehensive lists of DMRs, and gives insights into the role of aberrant DNA methylation in CRC formation.
UR - http://www.scopus.com/inward/record.url?scp=84878632825&partnerID=8YFLogxK
U2 - 10.4161/epi.22562
DO - 10.4161/epi.22562
M3 - Article
C2 - 23079744
AN - SCOPUS:84878632825
VL - 7
SP - 1355
EP - 1367
JO - Unknown Journal
JF - Unknown Journal
IS - 12
ER -