Susceptibility of nonpromoter CpG islands to de novo methylation in normal and neoplastic cells.
BACKGROUND
Many cancers display alterations in methylation patterns of CpG islands--stretches of DNA rich in CpG dinucleotides often associated with gene promoters that are involved in initiation of gene transcription. This methylation may perturb expression of genes critical to the regulation of cell proliferation. Aberrant methylation is not limited to a few genes or to promoter regions but has been found on a genome-wide scale in a variety of neoplasias, including colorectal cancer and acute myelogenous leukemia. Our goal was to characterize, in a quantitative manner, the profiles of abnormally methylated genes that may be specific for different cancers.


METHODS
Using a quantitative assay, methylation-sensitive single nucleotide primer extension (MS-SNuPE), we have analyzed the methylation levels of promoter and exonic (coding region) CpG islands of two cyclin-dependent kinase inhibitors [p15(INK4B) and p16(INK4A)] and the PAX6 gene, which encodes a transcriptional factor involved in neuronal proliferation, in DNA samples taken from patients with chronic myelogenous leukemia, acute myelogenous leukemia, myelodysplastic syndrome, and colorectal cancer.


RESULTS
De novo methylation of all three exonic loci in tumors--relative to baseline levels found in nontumor tissue or blood--was observed in hematologic neoplasias and in solid tumors as well as in normal colonic tissue. However, methylation of promoter regions was more limited. Moreover, two different patterns of promoter methylation distinguished the leukemias from colorectal cancer: p15 promoter hypermethylation was found only in the leukemias, and p16 promoter hypermethylation occurred only in colon tumors. However, we did not address this issue prospectively; therefore, such an observation is only hypothesis generating.


CONCLUSIONS
The methylation patterns that we observed suggest that exonic CpG islands are more susceptible to de novo methylation than promoter islands and that methylation may be seeded in exonic regions, from which it can spread to other islands, including promoter regions. Subsequent selection of cells with a growth advantage conferred by spread of methylation into and inactivation of a particular promoter might then contribute to the genesis of a specific type of cancer.
Nguyen
C
C
Department of Biochemistry and Molecular Biology, University of Southern California/Norris Comprehensive Cancer Center, Keck School of Medicine of the USC, Los Angeles, USA.
Liang
G
G
Nguyen
T T
TT
Tsao-Wei
D
D
Groshen
S
S
Lübbert
M
M
Zhou
J H
JH
Benedict
W F
WF
Jones
P A
PA
D000208:Acute Disease; D000230:Adenocarcinoma / Q000235:genetics; D001752:Blast Crisis / Q000235:genetics; D001773:Blood Cells / Q000737:chemistry; D001854:Bone Marrow Cells / Q000737:chemistry; D018797:Cell Cycle Proteins / Q000235:genetics; D015179:Colorectal Neoplasms / Q000235:genetics; D018899:CpG Islands; D050762:Cyclin-Dependent Kinase Inhibitor p15; D019941:Cyclin-Dependent Kinase Inhibitor p16 / Q000235:genetics; D019175:DNA Methylation; D004273:DNA, Neoplasm / Q000737:chemistry*; D005091:Exons; D005136:Eye Proteins; D005801:Genes, Homeobox; D016147:Genes, Tumor Suppressor; D019942:Genes, p16; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D007951:Leukemia, Myeloid / Q000235:genetics; D015465:Leukemia, Myeloid, Accelerated Phase / Q000235:genetics; D015466:Leukemia, Myeloid, Chronic-Phase / Q000235:genetics; D013058:Mass Spectrometry; D009190:Myelodysplastic Syndromes / Q000235:genetics; D014411:Neoplastic Stem Cells / Q000737:chemistry*; D000071841:PAX6 Transcription Factor; D051761:Paired Box Transcription Factors; D011401:Promoter Regions, Genetic; D012097:Repressor Proteins; D025521:Tumor Suppressor Proteins
C493966:CDKN2B protein, human; D018797:Cell Cycle Proteins; D050762:Cyclin-Dependent Kinase Inhibitor p15; D019941:Cyclin-Dependent Kinase Inhibitor p16; D004273:DNA, Neoplasm; D005136:Eye Proteins; D018398:Homeodomain Proteins; D000071841:PAX6 Transcription Factor; C000605730:PAX6 protein, human; D051761:Paired Box Transcription Factors; D012097:Repressor Proteins; D025521:Tumor Suppressor Proteins