DNA hypermethylation accompanied by transcriptional repression in follicular lymphoma.
High-throughput microarray technologies were used to study DNA methylation accompanied by transcriptional changes in follicular lymphoma (FL). Using Methylated CpG Island Amplification with Microarrays to study CpG Island DNA methylation in FL, we discovered widespread hypermethylation of homeobox genes and previously identified targets of polycomb repressive complex 2 (PRC2) in cell lines and primary tumors, but not in benign follicular hyperplasia (BFH). DNA methylation for HOXA11, HOXD10, HOXB7, HOXC12, PAX6, LHX9, SFMBT2, EN2, and PAX7 was independently validated in the RL cell line and HOXA11, HOXD10, PAX6, and EN2 in primary tumors. Combined Bisulfite Restriction Analysis (COBRA) also established DNA methylation for the previously identified PRC2 targets DCC, DES, GAD2, AQP5, GPR61, GRIA4, GJD2, and AMPH in FL but not in BFH. Gene expression analyses revealed 411 genes that were hypermethylated and transcriptionally repressed in RL, 74% of which were reactivated by the demethylating agent 5-aza-2'-deoxycytidine (5-azaD) plus or minus the histone deacetylase inhibitor trichostatin A (TSA). Forty genes were also downregulated in primary FL. Our results suggest that extensive hypermethylation in promoters of polycomb target genes is a characteristic of FL and that loss of expression of certain SUZ12 target genes could be functionally relevant for lymphomagenesis.
Bennett
Lynda B
LB
Department of Pathology and Anatomical Sciences, University of Missouri-Columbia School of Medicine, Columbia, MO 65212, USA. bennettlb@health.missouri.edu
Schnabel
Jennifer L
JL
Kelchen
Jean M
JM
Taylor
Kristen H
KH
Guo
Juyuan
J
Arthur
Gerald L
GL
Papageorgio
Christos N
CN
Shi
Huidong
H
Caldwell
Charles W
CW
D002352:Carrier Proteins / Q000235:genetics; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D018899:CpG Islands; D019938:Cyclin D1 / Q000235:genetics; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005260:Female; D005801:Genes, Homeobox; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D006965:Hyperplasia / Q000235:genetics; D008198:Lymph Nodes / Q000473:pathology; D008224:Lymphoma, Follicular / Q000235:genetics*; D008297:Male; D008875:Middle Aged; D009363:Neoplasm Proteins; D009687:Nuclear Proteins / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D063151:Polycomb Repressive Complex 2; D063146:Polycomb-Group Proteins; D011401:Promoter Regions, Genetic; D012097:Repressor Proteins / Q000235:genetics; D015203:Reproducibility of Results; D014157:Transcription Factors; D014158:Transcription, Genetic
C530104:CCND1 protein, human; D002352:Carrier Proteins; C484298:HOXA11 protein, human; D018398:Homeodomain Proteins; D009363:Neoplasm Proteins; D009687:Nuclear Proteins; D063146:Polycomb-Group Proteins; D012097:Repressor Proteins; C430461:SUZ12 protein, human; D014157:Transcription Factors; D019938:Cyclin D1; D063151:Polycomb Repressive Complex 2