Epigenetic regulation of microRNAs in acute lymphoblastic leukemia.
OBJECTIVE
To identify microRNAs (miRNAs) epigenetically regulated in acute lymphoblastic leukemia (ALL).


METHODS
We first examined ALL-derived cell lines for the presence of abnormal levels of two different histone modifications (trimethylation of H3 lysine 4 [K4H3me3] and dimethylation of H3 lysine 9 [K9H3me2]) in the 5'UTR regions around CpG islands of 78 miRNAs by chromatin immunoprecipitation (ChIP)-on-ChIP analysis. Methylation status (methylation-specific polymerase chain reaction [PCR]) and expression (quantitative PCR) of miRNAs showing a pattern of histone modifications linked to a closed chromatin structure were analyzed in a panel of six ALL cell lines and in 353 ALL patients.


RESULTS
CpG islands around 13 miRNAs disclosed high levels of K9H3me2 and/or low levels of K4H3me3, a pattern of histone modifications underlying a closed chromatin structure associated with repressive gene expression. Complete consistency in the correlation between both histone marks, the presence of DNA methylation around these miRNAs, and their expression patterns was confirmed in the six ALL cell lines. Treatment with 5-Aza-2'-deoxycytidine upregulated the expression levels of these genes, suggesting that epigenetic mechanisms deregulate the expression of these miRNAs. A total of 65% of the ALL samples had at least one miRNA methylated (methylated group). Estimated disease-free survival (DFS) and overall survival (OS) at 14 years were 78% and 71% for nonmethylated patients and 24% and 28% for methylated patients (P = .00001 for both). Multivariate analysis demonstrated that methylation profile was an independent prognostic factor for predicting DFS (P = .0001) and OS (P = .0001).


CONCLUSIONS
Aberrant miRNA methylation is a common phenomenon in ALL that affects the clinical outcome of these patients.
Roman-Gomez
Jose
J
Hematology Department. Reina Sofia Hospital. Avda. Menendez Pidal s/n. 14004 Cordoba. Spain. peperosa@teleline.es
Agirre
Xabier
X
Jiménez-Velasco
Antonio
A
Arqueros
Victor
V
Vilas-Zornoza
Amaia
A
Rodriguez-Otero
Paula
P
Martin-Subero
Iñaki
I
Garate
Leire
L
Cordeu
Lucia
L
San José-Eneriz
Edurne
E
Martin
Vanesa
V
Castillejo
Juan Antonio
JA
Bandrés
Eva
E
Calasanz
María José
MJ
Siebert
Reiner
R
Heiniger
Anabel
A
Torres
Antonio
A
Prosper
Felipe
F
D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D045744:Cell Line, Tumor; D018899:CpG Islands; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005260:Female; D006801:Humans; D008297:Male; D035683:MicroRNAs / Q000235:genetics*; D008875:Middle Aged; D015999:Multivariate Analysis; D054198:Precursor Cell Lymphoblastic Leukemia-Lymphoma / Q000235:genetics*; D011379:Prognosis
D035683:MicroRNAs