TY - JOUR
T1 - Association of aberrant DNA methylation in Apcmin/+ mice with the epithelial-mesenchymal transition and Wnt/β-catenin pathways
T2 - Genome-wide analysis using MeDIP-seq
AU - Guo, Yue
AU - Lee, J. Hun
AU - Shu, Limin
AU - Huang, Ying
AU - Li, Wenji
AU - Zhang, Chengyue
AU - Yang, Anne Yuqing
AU - Boyanapalli, Sarandeep S.S.
AU - Perekatt, Ansu
AU - Hart, Ronald P.
AU - Verzi, Michael
AU - Kong, A. N.Tony
N1 - Publisher Copyright:
© 2015 Guo et al.
PY - 2015/5/27
Y1 - 2015/5/27
N2 - Background: Aberrant DNA methylation at the 5-carbon on cytosine residues (5mC) in CpG dinucleotides is probably the most extensively characterized epigenetic modification in colon cancer. It has been suggested that the loss of adenomatous polyposis coli (APC) function initiates tumorigenesis and that additional genetic and epigenetic events are involved in colon cancer progression. We aimed to study the genome-wide DNA methylation profiles of intestinal tumorigenesis in Apcmin/+ mice. Results: Methylated DNA immunoprecipitation (MeDIP) followed by next-generation sequencing was used to determine the global profile of DNA methylation changes in Apcmin/+ mice. DNA was extracted from adenomatous polyps from Apcmin/+ mice and from normal intestinal tissue from age-matched Apc+/+ littermates, and the MeDIP-seq assay was performed. Ingenuity Pathway Analysis (IPA) software was used to analyze the data for gene interactions. A total of 17,265 differentially methylated regions (DMRs) displayed a≥2-fold change (log2) in methylation in Apcmin/+ mice; among these DMRs, 9,078 (52.6 %) and 8,187 (47.4 %) exhibited increased and decreased methylation, respectively. Genes with altered methylation patterns were mainly mapped to networks and biological functions associated with cancer and gastrointestinal diseases. Among these networks, several canonical pathways, such as the epithelial-mesenchymal transition (EMT) and Wnt/β-catenin pathways, were significantly associated with genome-wide methylation changes in polyps from Apcmin/+ mice. The identification of certain differentially methylated molecules in the EMT and Wnt/β-catenin pathways, such as APC2 (adenomatosis polyposis coli 2), SFRP2 (secreted frizzled-related protein 2), and DKK3 (dickkopf-related protein 3), was consistent with previous publications. Conclusions: Our findings indicated that Apcmin/+ mice exhibited extensive aberrant DNA methylation that affected certain signaling pathways, such as the EMT and Wnt/β-catenin pathways. The genome-wide DNA methylation profile of Apcmin/+ mice is informative for future studies investigating epigenetic gene regulation in colon tumorigenesis and the prevention of colon cancer.
AB - Background: Aberrant DNA methylation at the 5-carbon on cytosine residues (5mC) in CpG dinucleotides is probably the most extensively characterized epigenetic modification in colon cancer. It has been suggested that the loss of adenomatous polyposis coli (APC) function initiates tumorigenesis and that additional genetic and epigenetic events are involved in colon cancer progression. We aimed to study the genome-wide DNA methylation profiles of intestinal tumorigenesis in Apcmin/+ mice. Results: Methylated DNA immunoprecipitation (MeDIP) followed by next-generation sequencing was used to determine the global profile of DNA methylation changes in Apcmin/+ mice. DNA was extracted from adenomatous polyps from Apcmin/+ mice and from normal intestinal tissue from age-matched Apc+/+ littermates, and the MeDIP-seq assay was performed. Ingenuity Pathway Analysis (IPA) software was used to analyze the data for gene interactions. A total of 17,265 differentially methylated regions (DMRs) displayed a≥2-fold change (log2) in methylation in Apcmin/+ mice; among these DMRs, 9,078 (52.6 %) and 8,187 (47.4 %) exhibited increased and decreased methylation, respectively. Genes with altered methylation patterns were mainly mapped to networks and biological functions associated with cancer and gastrointestinal diseases. Among these networks, several canonical pathways, such as the epithelial-mesenchymal transition (EMT) and Wnt/β-catenin pathways, were significantly associated with genome-wide methylation changes in polyps from Apcmin/+ mice. The identification of certain differentially methylated molecules in the EMT and Wnt/β-catenin pathways, such as APC2 (adenomatosis polyposis coli 2), SFRP2 (secreted frizzled-related protein 2), and DKK3 (dickkopf-related protein 3), was consistent with previous publications. Conclusions: Our findings indicated that Apcmin/+ mice exhibited extensive aberrant DNA methylation that affected certain signaling pathways, such as the EMT and Wnt/β-catenin pathways. The genome-wide DNA methylation profile of Apcmin/+ mice is informative for future studies investigating epigenetic gene regulation in colon tumorigenesis and the prevention of colon cancer.
KW - DNA methylation
KW - Epigenetic
KW - Epithelial-mesenchymal transition pathway
KW - MeDIP-seq
KW - Wnt/β-catenin pathway
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U2 - 10.1186/s13578-015-0013-2
DO - 10.1186/s13578-015-0013-2
M3 - Article
AN - SCOPUS:85027926963
VL - 5
JO - Cell and Bioscience
JF - Cell and Bioscience
IS - 1
M1 - 24
ER -