DNA variants in region for noncoding interfering transcript of dihydrofolate reductase gene and outcome in childhood acute lymphoblastic leukemia.
OBJECTIVE
Dihydrofolate reductase (DHFR) is the major target of methotrexate, a key component in childhood acute lymphoblastic leukemia (ALL) treatment. We recently reported an association of DHFR promoter polymorphisms with ALL outcome. Lower event-free survival correlated with haplotype *1, defined by A(-317) and C(-1610) alleles. Haplotype *1 was also associated higher DHFR expression.


METHODS
Here, we analyzed adjacent 400-bp region participating in DHFR regulation as both a major promoter and a noncoding minor transcript.


RESULTS
Six polymorphisms were identified, of which five were single nucleotide polymorphisms and one was length polymorphism composed of variable number of 9-bp elements and 9-bp insertion/deletion. Haplotype analysis including all promoter polymorphisms revealed diversification of haplotype *1 into five subtypes (*1a-*1e). DNA variations of major promoter/noncoding transcript region and haplotype *1 subtypes were subsequently analyzed for the association with ALL outcome. Lower event-free survival was associated with an A allele of G(308)A polymorphism (P = 0.02) and with *1b haplotype (P = 0.01). This association was particularly striking in high-risk patients (P = 0.001) and was subsequently confirmed in independent patient cohort (P = 0.02). Haplotype *1b was the only haplotype *1 subtype associated with higher mRNA levels.


CONCLUSIONS
The study provides a new insight into DHFR regulatory variations predisposing to an event in ALL patients.
Research Center, CHU Sainte-Justine, University of Montreal, Montreal, Quebec, Canada.
Fidaa
F
Al-Shakfa
Stéphanie
S
Dulucq
Ivan
I
Brukner
Iva
I
Milacic
Marc
M
Ansari
Patrick
P
Beaulieu
Albert
A
Moghrabi
Caroline
C
Laverdière
Stephen E
SE
Sallan
Lewis B
LB
Silverman
Donna
D
Neuberg
Jeffery L
JL
Kutok
Daniel
D
Sinnett
Maja
M
Krajinovic
D000328:Adult; D016022:Case-Control Studies; D002648:Child; D015331:Cohort Studies; D004247:DNA / Q000235:genetics*; D005260:Female; D014644:Genetic Variation; D006239:Haplotypes; D006801:Humans; D008297:Male; D008727:Methotrexate / Q000494:pharmacology; D008875:Middle Aged; D010597:Pharmacogenetics; D011110:Polymorphism, Genetic; D054198:Precursor Cell Lymphoblastic Leukemia-Lymphoma / Q000235:genetics* / Q000628:therapy*; D011401:Promoter Regions, Genetic; D013762:Tetrahydrofolate Dehydrogenase / Q000235:genetics*
D004247:DNA; D013762:Tetrahydrofolate Dehydrogenase; D008727:Methotrexate