Development Of Pediatric Acute Lymphoblastic Leukemia Research Articles

Evaluation of DNA Methylation at Birth in Monozygotic Twin Pairs Discordant for Acute Lymphoblastic Leukemia

Background: Aberrant patterns of DNA methylation constitute a key feature of pediatric acute lymphoblastic leukemia (ALL) at diagnosis, however its role as a predisposing or early contributor to the development of ALL remains unknown. We employed a discordant monozygotic twin model to identify epigenetic variation associated with future development of pediatric ALL through evaluation of DNA methylation at birth.Methods: Twin pairs discordant for the development of pediatric ALL were identified using linked data from the California Cancer Registry and California Birth Statistical Master File spanning from 1989 to 2015. Archived dried neonatal blood spots were obtained from 86 same-gender twin pairs with available materials from the California Biobank Program. Following isolation of genomic DNA from DBS samples, monozygosity was confirmed in 43 of 86 twin pairs through an identity-by-descent analysis from a genome-wide SNP-array. Epigenome-wide DNA methylation assessment of the 43 discordant monozygotic twin pairs was conducted using the Illumina Infinium MethylationEPIC BeadChip kit (Illumina, San Diego, CA, USA). Data preprocessing and quality control measures were conducted in R, using SeSAMe for data normalization. Two twin pairs were omitted due to failure to pass quality control measures. Within-pair analysis was conducted through identification of array probes with absolute differences in methylation beta values greater than 15% between case and control siblings of a twin pair unit. Differentially methylated probes (DMP) were identified using a conditional logistic regression model accounting for array-specific variation, nucleated cell proportions, and appropriate control for the paired nature of the dataset. Differentially methylated regions (DMR) were defined by regional correlation of p-values from the conditional logistic regression model. Gene set enrichment analysis was conducted on significant probes identified through the within pair and regression analysis.Results: The discordant twin cohort (n = 41 pairs) included 24 female and 17 male pairs. Median gestational age was 258 days, ranging from 184 to 306 days. Age of diagnosis in the case twin ranged from <1 to 23 years (median = 5). There was no significant association between birthweight and case status (paired Wilcoxon signed rank test p = 0.22). No significant differences in nucleated cell proportions were identified in deconvolution analysis. Within-pair analysis identified a total of 18,001 probes with absolute methylation variation greater than 15% across the 41 twin pairs, with 3,984 recurrently variable across more than one pair. Gene ontology analysis of these recurrently variable sites revealed an enrichment of immune-related processes in 7 of the top 15 terms with nominal p-value <0.05, though no terms were significant after correction for multiple comparisons. Conditional logistic regression was conducted on 37 twin pairs, with T-cell cases (n=4) omitted to improve data resolution. This resulted in 240 significant DMPs with p-values below an FDR threshold of 0.05. Of these significant probes, 20 associate with genes previously reported to have altered DNA methylation in ALL at diagnosis. Regional analysis identified 10 significant DMRs with adjusted p-values below 0.05, with the top association encompassing a 454bp region on chromosome 6 located near TRIM39-RPP21 (adjusted p-value 2.39e-05). Notably, conditional regression analysis revealed a significant negative bias in coefficients (409,812 of 710,010 probes, binomial exact test p <2.2e-16), indicating a global tendency toward hypomethylation in cases compared to unaffected siblings (Figure 1). The strength of this bias was greater in probes associated with open sea regions compared to those in island regions, as well as promoter-associated probes.Conclusions: This novel analysis of DNA methylation at birth in ALL-discordant monozygotic twins identified sites of differential methylation associated with immune regulation. In addition, these results provide evidence of an association between global DNA hypomethylation and future development of ALL in one member of a genetically identical twin pair. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Association of C4125A Polymorphisms of MDR-1 gene with childhood acute lymphoblastic leukaemia in Egyptian

Acute lymphoblastic leukemia (ALL) is the most common malignancy in children, though the etiology of the leukemia is poorly understood, both genetic and environmental factors appear to be involved. To investigate the possible role of MDR-1 (C4125A) polymorphism as risk factor for the development of ALL in this study on Egyptian children and to evaluate its prognostic role. Typing of MDR-1 (C4125A) polymorphism was done using RFLP-PCR for 120 patients with ALL and 100 healthy controls. The C allele (100%) and CC genotype (100%) were insignificant in both groups. Also, no relation between clinical data and C4125A genotypes. Thus, MDR-1 (C4125A) SNP may be not risk factor for the development of pediatric ALL in Egyptian patients.

Genetic background and treatment of pediatric ALL

Molecular genomic studies for acute lymphoblastic leukemia (ALL) have been focused on genetic alterations in leukemic cells, while germline cells are mainly used as a control to identify the somatic mutation. However, recent studies demonstrate that germline mutations may contribute to the pathogenesis of ALL, and currently, the genetic background has been found to play an essential role in the development of pediatric ALL. An association between polymorphism and adverse events has already been reported, and recent genomic analyses of familial ALL cases identified inherited causative genes for ALL. Moreover, non-syndromic/familial ALL cases may present pathogenic germline variants in cancer predisposition genes. These variants could not only contribute to poor response to treatment but also lead to an increased risk of secondary neoplasms. Comprehensive understanding of the biology in both ALL cells and germline cells is required.

Tumor necrosis factor-α (TNF-α) −308 G/A and lymphotoxin-α (LT-α) +252 A/G genetic polymorphisms in Egyptian acute lymphoblastic leukemia

Acute lymphoblastic leukemia (ALL) is one of the most hematological malignancies of lymphoid origin. It has been proposed that deregulation of cytokines could be linked with pathogenesis, progression, and survival in many diseases. Genetic polymorphisms in two important cytokines like tumor necrosis factor-α (TNF-α) −308 and lymphotoxin-α (LT-α) +252 can disturb both their transcription and expression and lead to their high plasma levels. A difference in the occurrence of the polymorphisms in TNF-α −308 G/A and LT-α +252 A/G in ALL cases among several populations with different ethnicities was observed. The study investigated the occurrence and the role of polymorphisms of tumor necrosis factor genes including TNF-α −308 G>A and LT-α +252 A>G in the development of ALL in Egypt. A case-control study was done on 126 newly diagnosed ALL patients (96 pediatric and 30 adult patients); 130 healthy subjects composed the control group. Polymorphism variants of TNF-α and LT-α genes were studied by PCR-RFLP on genomic DNA of all studied individuals. TNF-α −308 G/A polymorphism was statistically significant in ALL pediatric patients (P value = 0.008) with no association with ALL adult patients. TNF AA homozygous variant genotype and the A allele both showed significant risks of the development of pediatric ALL. However, there was no association between LT-α +252 A/G polymorphism in both pediatric and adult ALL. The results show that TNF AA homozygous variant genotype and A allele showed a significant risk of development of pediatric ALL.

Abstract 2228: Folate-related genes polymorphism and risk of pediatric acute lymphoplastic leukemia

Abstract Background: Childhood acute lymphoblastic leukemia (ALL) is the most common malignancy affecting children, constituting about 30% of all cancers among children. It constitutes about 75% of pediatric acute leukemia with peak incidence between ages 3 and 4. The assertion that ALL may have a genetic basis has long been pursued through association studies based on candidate genes as folate metabolism. Polymorphisms in folate pathway genes may influence the susceptibility to acute lymphoblastic leukemia. Increased risk of ALL was observed in reduced folate carrier protein (RFC1) 80GA variant carriers. A 1.4-fold reduction in ALL risk was observed for carriers of the methyl tetrahydrofolate reductase (MTHFR) 677T allele. Objectives: this study was carried out to evaluate the contribution of MTHFR C677T and RFC1 80GA gene polymorphism and susciptability of childhood acute lymphoblastic leukemia. Materials &amp;Methods: DNA was isolated from 200 children, divided into 2 groups, group I included 100 pediatric ALL patients and group II included 100 healthy donors as controls. Genotyping of MTHFR C677T and RFC1 G80A was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using Hinf I and HhaI restriction endonuclease respectively. Results: MTHFR 677T allele carriers were significantly lower in ALL cases (46%) than healthy controls (56%). Reduction in ALL risk was observed for heterozygous (CT) or homozygous (TT) carriers of the MTHFR 677T allele (OR 0.8; 95% CI, 0.9-1.5; P &amp;lt; 0.002). RFC1 80A allelic carriers have an increased susceptibility to ALL. Risk was increased 2.0 times (OR 3.5; 95% CI, 1.5-4.8 ; P .02) for A-allelic carriers. Conclusion: our data suggested that the MTHFR gene variants are associated with decreased ALL rate and risk. the reduced risk associated with the MTHFR C677T polymorphisms may be the result of changed intracellular folate redistribution. the results of our study also supported the suggestion that RFC1 G80A RFC1 G80A single nucleotide polymorphism contributed to increase the susceptibility and the development of pediatric ALL. Citation Format: Nermin Raafat, Amal Gharib, Usama Elsafy, Tamer Hassan. Folate-related genes polymorphism and risk of pediatric acute lymphoplastic leukemia. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2228. doi:10.1158/1538-7445.AM2014-2228