Genome-wide DNA methylation profiling of chronic lymphocytic leukemia allows identification of epigenetically repressed molecular pathways with clinical impact.
We performed a genome-wide analysis of aberrant DNA methylation in chronic lymphocytic leukemia (CLL) using methylated CpG island amplification (MCA) coupled with a promoter microarray. We identified 280 potential targets of aberrant DNA methylation in CLL. These genes were located more frequently in chromosomes 19 (16%, p=0.001), 16 (11%, p=0.001), 17 (10%, p=0.02) and 11 (9%, p=0.02) and could be grouped in several functional networks. Methylation status was confirmed for 22 of these genes (SOX11, DLX1, FAM62C, SOX14, RSPO1, ADCY5, HAND2,SPOCK, MLL, ING1, PRIMA1, BCL11B, LTBP2, BNC1, NR2F2, SALL1, GALGT2, LHX1, DLX4, KLK10, TFAP2 and APP) in 78 CLL patients by pyrosequencing. As a proof of principle, we analyzed the expression of 2 genes, PRIMA1 and APP, in primary cells and of GALGT2, TFAP2C and PRIMA1 in leukemia cells. There was an inverse association between methylation and gene expression. This could be reversed by treatment with 5-aza-2'-deoxycytidine in cell lines. Treatment in a clinical trial with 5-azacitidine resulted in decreased methylation of LINE, DLX4 and SALL1 in the peripheral blood B-cells of patients with CLL. IgVH mutational status or ZAP-70 expression were not associated with specific methylation profiles. By multivariate analysis, methylation of LINE and APP was associated with shorter overall survival (p = 0.045 and 0.0035, respectively). This study demonstrates that aberrant DNA methylation is common and has potential prognostic and therapeutic value in CLL.
Tong
Wei-Gang
WG
Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.
Wierda
William G
WG
Lin
E
E
Kuang
Shao-Qing
SQ
Bekele
B Nebiyou
BN
Estrov
Zeev
Z
Wei
Yue
Y
Yang
Hui
H
Keating
Michael J
MJ
Garcia-Manero
Guillermo
G
D000328:Adult; D000368:Aged; D014408:Biomarkers, Tumor / Q000032:analysis / Q000235:genetics; D016022:Case-Control Studies; D045744:Cell Line, Tumor; D019175:DNA Methylation / Q000502:physiology; D015536:Down-Regulation / Q000235:genetics; D044127:Epigenesis, Genetic / Q000502:physiology*; D005260:Female; D005500:Follow-Up Studies; D020869:Gene Expression Profiling / Q000379:methods*; D015973:Gene Expression Regulation, Leukemic; D020868:Gene Silencing / Q000502:physiology; D055106:Genome-Wide Association Study; D018922:HL-60 Cells; D006801:Humans; D015451:Leukemia, Lymphocytic, Chronic, B-Cell / Q000175:diagnosis* / Q000235:genetics* / Q000473:pathology; D008297:Male; D046228:Microarray Analysis / Q000379:methods; D008875:Middle Aged; D011379:Prognosis; D015398:Signal Transduction / Q000235:genetics; D054928:Validation Studies as Topic
D014408:Biomarkers, Tumor