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Table 1 Summary of the promoter hypermethylation frequencies and expression analysis of candidate genes in ALL.

From: A Genome-wide screen identifies frequently methylated genes in haematological and epithelial cancers

Gene Cell lines T-ALL (%) B-ALL (%) PB/BM controls Expression upregulation after 5azaDC
ARHGAP20 6/10 4/12 (33) 33/51 (65) 0/8 YES
ATG16L2 3/7 5/12 (42) 14/52 (27) 0/8 ND
BARHL2† 5/6 3/12 (25) 39/51 (77) 0/9 YES
BMP2† 6/7 7/12 (58) 2/52 (4) 0/8 YES
CDC14B 5/7 4/12 (33) 21/48 (44) 0/9 YES
CYP1B1† 5/6 5/12 (42) 40/52 (77) 0/10 YES
DUSP4 1/6 3/12 (25) 13/52 (25) 0/6 ND
EBF2 5/6 10/12 (83) 49/52 (94) 1/10 YES
EYA2 5/7 3/12 (25) 15/47 (32) 0/10 YES
FAT1† 1/6 3/12 (25) 34/52 (65) 0/10 YES
FOXF2 4/6 3/12 (25) 15/52 (29) 0/9 YES
GPR123 5/7 4/12 (33) 10/48 (21) 0/9 YES
HLA-F 4/6 4/12 (33) 7/52 (14) 1/10 ND
KNDC1 4/7 1/12 (8) 9/40 (23) 0/9 YES
MYO10† 6/8 6/12 (50) 8/51 (16) 1/8 YES
NKX2-1 5/6 5/12 (42) 32/51 (63) 0/9 YES
N2RE1 6/6 4/12 (33) 19/49 (39) 0/8 YES
NR4A2† 3/7 6/12 (50) 5/51 (10) 0/9 ND
PAX2 6/7 2/10 (20) 15/34 (44) 0/9 YES
PAX6 3/6 6/12 (50) 35/52 (67) 0/10 YES
POU4F1 1/6 5/12 (42) 22/51 (43) 0/8 YES
PRDM12 6/6 6/12 (50) 30/45 (67) 0/9 YES
PTGS2† 4/6 6/12 (50) 48/52 (92) 0/10 YES
SALL3 5/6 4/12 (33) 25/52 (48) 0/9 YES
SSPN 7/9 4/12 (33) 32/52 (62) 0/8 YES
TCF2† 5/6 6/12 (50) 5/52 (10) 0/10 YES
TFAP2A 5/6 5/11 (46) 33/49 (67) 0/10 YES
TFAP2C 2/6 10/12 (83) 43/50 (86) 0/10 YES
TP53I11 3/6 3/12 (25) 8/52 (15) 0/9 ND
TRPC4 5/5 9/12 (75) 48/52 (92) 0/10 YES
TSHZ3† 4/6 0/12 (0) 16/52 (31) 0/10 ND
UBE2C 3/6 2/12 (17) 12/52 (23) 0/10 YES
  1. The table summarises the genes showing a methylation frequency of 25% or above (with the exception of UBE2C and KNDC1) in either T or B-ALL or both, that were unmethylated or showed much lower frequency of methylation in control blood/bone marrow DNA. Also indicated are the genes showing upregulated expression in methylated leukemia cell lines (but were not upregulated in unmethylated cell lines) after 5-azaDC treatment ('YES' in the expression upregulation after 5-azaDC column). PB; peripheral blood lymphocytes from healthy donors. BM; bone marrow DNA from healthy donors. ND; not determined. †; significantly differential methylation in T-ALL vs B-ALL.