DNA variants in the dihydrofolate reductase gene and outcome in childhood ALL

Blood ◽  
2008 ◽  
Vol 111 (7) ◽  
pp. 3692-3700 ◽  
Author(s):  
Stéphanie Dulucq ◽  
Geneviève St-Onge ◽  
Vincent Gagné ◽  
Marc Ansari ◽  
Daniel Sinnett ◽  
...  
Keyword(s):  
Dihydrofolate Reductase ◽  
Lymphoblastic Leukemia ◽  
Luciferase Expression ◽  
Nucleotide Polymorphisms ◽  
Promoter Polymorphisms ◽  
Single Nucleotide ◽  
Childhood All ◽  
Reductase Gene ◽  
Haplotype 1 ◽  
Folate Cycle

Abstract Dihydrofolate reductase (DHFR) is the major target of methotrexate (MTX), a key component in childhood acute lymphoblastic leukemia (ALL) treatment. A total of 15 polymorphisms in DHFR promoter were analyzed, and 3 sites (C−1610G/T, C−680A, and A−317G) were identified as sufficient to define observed haplotypes (tag single nucleotide polymorphisms [tagSNPs]). These polymorphisms were investigated for association with treatment response in 277 children with ALL. Lower event-free survival (EFS) was associated with homozygosity for the allele A−317 and C−1610 (P = .03 and .02), and with the haplotype *1, defined by both C−1610 and A−317 alleles (P = .03). The haplotype *1 conferred higher transcriptional activity (P < .01 compared with haplotypes generating minimal luciferase expression). Quantitative mRNA analysis showed higher DHFR levels for particular haplotype *1 carriers (P < .01). The analysis combining haplotype *1 with thymidylate synthase (TS) and cyclin D1 (CCND1) genotypes previously shown to affect ALL outcome showed that the number of event-predisposing genotypes was associated with increasingly lower EFS (P < .001). In conclusion, DHFR promoter polymorphisms are associated with worse ALL outcome, likely due to a higher DHFR expression. Combined effects among genes of the folate cycle can further accentuate differences in the response to the treatment.

Single Nucleotide Polymorphisms of DNA Synthetic and Repair Enzymes and Risk of Childhood Acute Lymphoblastic Leukemia.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 4447-4447
Author(s):  
Samart Pakakasama ◽  
Thanasan Sirirat ◽  
Saowanee Kajanachumpol ◽  
Ampaiwan Chaunsumrit ◽  
Suradej Hongeng
Keyword(s):  
Dna Repair ◽  
Acute Lymphoblastic Leukemia ◽  
Single Nucleotide Polymorphisms ◽  
Lymphoblastic Leukemia ◽  
Metabolic Enzymes ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Dna Repair Enzymes ◽  
Childhood All ◽  
Repair Enzymes

Abstract Although the outcome of children with acute lymphoblastic leukemia (ALL) has been improving, the origin of this disease is still unknown. It is likely that individual genetic susceptibility and environmental exposure play a role in carcinogenesis. To maintain normal hematopoiesis, DNA synthesis and repair systems need to be intact. Folate metabolism, producing purines and pyrimidines, is the source of nucleotides while base excision and nucleotide excision repair enzymes, i.e. XRCC1 and XPD, have important roles in protection of DNA damage. Single nucleotide polymorphisms (SNPs) of enzymes involving these processes alter their enzymatic structures and functions. We hypothesized that SNPs of folate metabolic enzymes including methylenetetrahydrofolate reductase (MTHFR 677 C&gt;T; 1298 A&gt;C), methionine synthase (MS 2756 A&gt;G), and tandem repeats of thymidylate synthase (TS 2R or 3R) and of DNA repair enzymes (XRCC1 26304 C&gt;T; 27466 G&gt;A; 28152 G&gt;A and XPD 23591 G&gt;A; 35931 A&gt;C) could effect the risk of ALL in children. We performed genotyping of these SNPs in 108 ALL and 317 normal controls by using PCR RFLP method. Genotype frequencies of folate metabolic enzymes SNPs were not different between cases and controls. However, TS 2R allele showed a trend to decrease risk of ALL (OR=0.66; 95% CI 0.41–1.07). We observed a 4.5 fold reduction in the risk of ALL in individuals with the XRCC1 26304 TT genotype (OR=0.22; 95% CI 0.5–0.96). XRCC1 26304 T allele showed a protective effect to this disease (OR=0.67; 95% CI 0.47–0.97). In contrast, individuals with XRCC1 28152 A allele had an increased risk of ALL (OR=1.67; 95% CI 1.2–2.33) compared to those with G allele. XRCC1 28152 GA and GA+AA genotypes were significantly higher among patients with ALL compared to controls (OR=2.17; 95% CI 1.37–3.45 and OR=2.18; 95%CI 1.38–3.42). No association between genotype or allele frequencies of both XPD SNPs and risk of ALL was shown in this study. In conclusion, our data demonstrated that SNPs of DNA repair enzymes (XRCC1 26304 C&gt;T and 28152 G&gt;A) but not folate-dependent DNA synthetic enzymes may influence risk of childhood ALL.

Variation at the von Willebrand Factor (vWF) Gene Locus Is Associated With Plasma vWF:Ag Levels: Identification of Three Novel Single Nucleotide Polymorphisms in the vWF Gene Promoter

Blood ◽  
1999 ◽  
Vol 93 (12) ◽  
pp. 4277-4283 ◽  
Author(s):  
Angela M. Keightley ◽  
Y. Miu Lam ◽  
Jolene N. Brady ◽  
Cherie L. Cameron ◽  
David Lillicrap
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Von Willebrand Factor ◽  
Gene Locus ◽  
Strong Linkage Disequilibrium ◽  
Nucleotide Polymorphisms ◽  
Polymorphic Variation ◽  
Single Nucleotide ◽  
Haplotype 1 ◽  
Von Willebrand ◽  
Willebrand Factor

Abstract Both genetic and environmental factors contribute to the normal population variability of plasma von Willebrand Factor (vWF) levels, however, regulatory mechanisms at the vWF gene locus itself have not yet been identified. We have investigated the association between polymorphic variation in the 5′-regulatory region of the vWF gene and levels of plasma vWF:Ag in a study of 261 group O blood donors. Three novel single nucleotide polymorphisms (SNPs) were identified in the vWF promoter: C/T at -1234, A/G at -1185, and G/A at -1051. These SNPs had identical allele frequencies of 0.36 for the -1234C, -1185A, and -1051G alleles and 0.64 for the -1234T, -1185G, and -1051A alleles and were in strong linkage disequilibrium. In fact, these polymorphisms segregated as two distinct haplotypes: -1234C/-1185A/-1051G (haplotype 1) and -1234T/-1185G/-1051A (haplotype 2) with 12.6% of subjects homozygous for haplotype 1, 40.6% homozygous for haplotype 2, and 42.5% of subjects heterozygous for both haplotypes. Only 4.3% of individuals had other genotypes. A significant association between promoter genotype and level of plasma vWF:Ag was established (analysis of covariance [ANCOVA], P = .008; Kruskal-Wallis test,P = .006); individuals with the CC/AA/GG genotype had the highest mean vWF:Ag levels (0.962 U/mL), intermediate values of vWF:Ag (0.867 U/mL) were observed for heterozygotes (CT/AG/GA), and those with the TT/GG/AA genotype had the lowest mean plasma vWF:Ag levels (0.776 U/mL). Interestingly, when the sample was subgrouped according to age, the significant association between promoter genotype and plasma vWF:Ag level was accentuated in subjects &gt; 40 years of age (analysis of variance [ANOVA], P = .003; Kruskal-Wallis test, P= .001), but was not maintained for subjects ≤ 40 years of age (ANOVA, P &gt; .4; Kruskal-Wallis test, P &gt; .4). In the former subgroup, mean levels of plasma vWF:Ag for subjects with the CC/AA/GG, CT/AG/GA, and TT/GG/AA genotypes were 1.075, 0.954, and 0.794 U/mL, respectively. By searching a transcription factor binding site profile database, these polymorphic sequences were predicted to interact with several transcription factors expressed in endothelial cells, including Sp1, GATA-2, c-Ets, and NFκB. Furthermore, the binding sites at the -1234 and -1051 SNPs appeared to indicate allelic preferences for some of these proteins. Electrophoretic mobility shift assays (EMSAs) performed with recombinant human NFκB p50 showed preferential binding of the -1234T allele (confirmed by supershift EMSAs), and EMSAs using bovine aortic endothelial cell (BAEC) nuclear extracts produced specific binding of a nuclear protein to the -1051A allele, but not the -1051G allele. These findings suggest that circulating levels of vWF:Ag may be determined, at least in part, by polymorphic variation in the promoter region of the vWF gene, and that this association may be mediated by differential binding of nuclear proteins involved in the regulation of vWF gene expression.

scholarly journals Association of GATA3 Polymorphisms With Minimal Residual Disease and Relapse Risk in Childhood Acute Lymphoblastic Leukemia

2020 ◽  
Author(s):  
Hui Zhang ◽  
Anthony Pak-Yin Liu ◽  
Meenakshi Devidas ◽  
Shawn H R Lee ◽  
Xueyuan Cao ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Validation Cohort ◽  
Residual Disease ◽  
Lymphoblastic Leukemia ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Dichotomous Variable ◽  
Genome Wide ◽  
A Genome ◽  
Minimal Residual

Abstract Background Minimal residual disease (MRD) after induction therapy is one of the strongest prognostic factors in childhood acute lymphoblastic leukemia (ALL), and MRD-directed treatment intensification improves survival. Little is known about the effects of inherited genetic variants on interpatient variability in MRD. Methods A genome-wide association study was performed on 2597 children on the Children’s Oncology Group AALL0232 trial for high-risk B-cell ALL. Association between genotype and end-of-induction MRD levels was evaluated for 863 370 single nucleotide polymorphisms (SNPs), adjusting for genetic ancestry and treatment strata. Top variants were further evaluated in a validation cohort of 491 patients from the Children’s Oncology Group P9905 and 6 ALL trials. The independent prognostic value of single nucleotide polymorphisms was determined in multivariable analyses. All statistical tests were 2-sided. Results In the discovery genome-wide association study, we identified a genome-wide significant association at the GATA3 locus (rs3824662, odds ratio [OR] = 1.58, 95% confidence interval [CI] = 1.35 to 1.84; P = 1.15 × 10-8 as a dichotomous variable). This association was replicated in the validation cohort (P = .003, MRD as a dichotomous variable). The rs3824662 risk allele independently predicted ALL relapse after adjusting for age, white blood cell count, and leukemia DNA index (P = .04 and .007 in the discovery and validation cohort, respectively) and remained prognostic when the analyses were restricted to MRD-negative patients (P = .04 and .03 for the discovery and validation cohorts, respectively). Conclusion Inherited GATA3 variant rs3824662 strongly influences ALL response to remission induction therapy and is associated with relapse. This work highlights the potential utility of germline variants in upfront risk stratification in ALL.

scholarly journals MTHFR (methylenetetrahydrofolate reductase: EC 1.5.1.20) SNPs (single-nucleotide polymorphisms) and homocysteine in patients referred for investigation of fertility

2021 ◽  
Author(s):  
Yves Ménézo ◽  
Pasquale Patrizio ◽  
Silvia Alvarez ◽  
Edouard Amar ◽  
Michel Brack ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Methylenetetrahydrofolate Reductase ◽  
Compound Heterozygous ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Men And Women ◽  
Male Gametes ◽  
Folate Cycle ◽  
The Impact

Abstract Purpose MTHFR, one of the major enzymes in the folate cycle, is known to acquire single-nucleotide polymorphisms that significantly reduce its activity, resulting in an increase in circulating homocysteine. Methylation processes are of crucial importance in gametogenesis, involved in the regulation of imprinting and epigenetic tags on DNA and histones. We have retrospectively assessed the prevalence of MTHFR SNPs in a population consulting for infertility according to gender and studied the impact of the mutations on circulating homocysteine levels. Methods More than 2900 patients having suffered at least two miscarriages (2 to 9) or two failed IVF/ICSI (2 to 10) attempts were included for analysis of MTHFR SNPs C677T and A1298C. Serum homocysteine levels were measured simultaneously. Results We observed no difference in the prevalence of different genetic backgrounds between men and women; only 15% of the patients were found to be wild type. More than 40% of the patients are either homozygous for one SNP or compound heterozygous carriers. As expected, the C677T SNP shows the greatest adverse effect on homocysteine accumulation. The impact of MTHFR SNPs on circulating homocysteine is different in men than in women. Conclusions Determination of MTHFR SNPs in both men and women must be seriously advocated in the presence of long-standing infertility; male gametes, from MTHFR SNPs carriers, are not exempted from exerting a hazardous impact on fertility. Patients should be informed of the pleiotropic medical implications of these SNPs for their own health, as well as for the health of future children.

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