Genome-wide screening of genes regulated by DNA methylation in colon cancer development.
Tumorigenesis is accompanied by changes in the DNA methylation pattern. Our aim was to test a novel approach for identification of transcripts at whole transcript level which are regulated by DNA methylation. Our approach is based on comparison of data obtained from transcriptome profiling of primary human samples and in vitro cell culture models. Epithelial cells were collected by LCM from normal, adenoma, and tumorous colonic samples. Using gene expression analysis, we identified downregulated genes in the tumors compared to normal tissues. In parallel 3000 upregulated genes were determined in HT-29 colon adenocarcinoma cell culture model after DNA demethylation treatment. Of the 2533 transcripts showing reduced expression in the tumorous samples, 154 had increased expression as a result of DNA demethylation treatment. Approximately 2/3 of these genes had decreased expression already in the adenoma samples. Expression of five genes (GCG, NMES-1, LRMP, FAM161B and PTGDR), was validated using RT-PCR. PTGDR showed ambiguous results, therefore it was further studied to verify the extent of DNA methylation and its effect on the protein level. Results confirmed that our approach is suitable for genome-wide screening of genes which are regulated or inactivated by DNA methylation. Activity of these genes possibly interferes with tumor progression, therefore genes identified can be key factors in the formation and in the progression of the disease.
Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary. spisak@abc.hu
Sándor
S
Spisák
Alexandra
A
Kalmár
Orsolya
O
Galamb
Barna
B
Wichmann
Ferenc
F
Sipos
Bálint
B
Péterfia
István
I
Csabai
Ilona
I
Kovalszky
Szabolcs
S
Semsey
Zsolt
Z
Tulassay
Béla
B
Molnár
D000230:Adenocarcinoma / Q000235:genetics* / Q000378:metabolism*; D003110:Colonic Neoplasms / Q000235:genetics* / Q000378:metabolism*; D019175:DNA Methylation / Q000235:genetics / Q000502:physiology*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics / Q000502:physiology*; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D007150:Immunohistochemistry; D008565:Membrane Proteins / Q000378:metabolism; D046228:Microarray Analysis; D009363:Neoplasm Proteins / Q000378:metabolism; D009687:Nuclear Proteins / Q000378:metabolism; D025341:Principal Component Analysis; D011971:Receptors, Immunologic / Q000378:metabolism; D011982:Receptors, Prostaglandin / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014407:Tumor Cells, Cultured
D008565:Membrane Proteins; D009363:Neoplasm Proteins; D009687:Nuclear Proteins; D011971:Receptors, Immunologic; D011982:Receptors, Prostaglandin; C486311:IRAG2 protein, human; C465665:C15orf48 protein, human; C036293:prostaglandin D2 receptor