The functional polymorphisms of ARID5B and IKZF1 are associated with acute myeloid leukemia risk in a Han Chinese population

Whole genome, exon mutation and transcriptomic profiling of acute myeloid leukemia: A case report

The present study aimed to observe previously unidentified gene mutation and expression profiles associated with acute myeloid leukemia (AML) at the individual level, based on the blood samples of a father-son pair. Genomic DNA and RNA samples from blood serum were collected. Whole-genome sequencing (WGS) and whole-exome sequencing (WES), as well as mRNA sequencing of the son, were performed. For the father's sample, a total of 3,897,164 single nucleotide polymorphisms (SNPs) and 780,834 insertion and deletions (indels) were identified. Regarding amino acid translation, there were 11,316 non-synonymous, 12 stop-loss, 12,033 synonymous, 92 stop-gain SNPs, 63 frameshift insertions, 73 frameshift deletions, 242 non-frameshift insertions, 248 non-frameshift deletions, four stop-gains and two stop-loss for indel variants. Among the AML-related genes that had been previously identified, 14 genes were found in the father's exon region. For WES of the son's DNA, 96,639 SNPs were identified, including 10,504 non-synonymous SNPs. Seven mutant genes were found in sons' exon region compared with 121 AML-related genes. Based on the transcriptomic sequencing, there were 54 differentially expressed mRNAs, including 31 upregulated and 23 downregulated mRNAs. In the exon region, 10,072 SNPs were detected, and different types of alternative splicing in the son's sample were observed. Overall, whole genome, exon mutation and transcriptomic profiling of the present two patients with AML may provide a new insight into the molecular events governing the development of AML.

IKZF1 rs4132601 and rs11978267 Gene Polymorphisms and Acute Lymphoblastic Leukemia: Relation to Disease Susceptibility and Outcome

(IKZF1) rs4132601 and rs11978267 are common gene polymorphisms and have been associated with the risk of acute lymphoblastic leukemia. However, these associations are less evident in races and/or ethnicities other than European and Hispanic. Therefore, we investigated the association between these single-nucleotide polymorphisms and acute lymphoblastic leukemia susceptibility and disease outcome. Real-time polymerase chain reaction typing was performed for IKZF1 rs4132601 and rs11978267 for 128 pediatric acute lymphoblastic leukemia (pALL), 45 adult acute lymphoblastic leukemia (aALL), and 436 healthy controls. The G allele-containing and G-containing genotypes (GG+GT) of rs4132601 were significantly higher in pALL (P=0.003, odds ratio [OR]=1.65, 0.009, OR=1.42, respectively) and aALL (P=0.016, OR=1.81 and 0.011, OR=1.61, respectively). However, the GG haplotype was associated with the risk of pALL (P=0.044), the GA haplotype was associated with the risk of aALL (P=0.007). In aALL, the GG genotype of rs4132601 was associated with absence of remission and poor overall survival (P=0.003 and 0.041, respectively). The IKZF1 rs4132601 single-nucleotide polymorphism can be considered a susceptibility risk factor for the development of pALL and aALL in the studied cohort of Egyptian patients. The GG genotype of IKZF1 rs4132601 may be a risk factor for poor outcome in aALL patients.

ARID5B Genetic Polymorphisms Contribute to the Susceptibility and Prognosis of Male Acute Promyelocytic Leukemia

This study was conducted using TagSNPs to systematically explore the relationship between ARID5B polymorphisms and the occurrence, clinical characterization, and prognosis of acute myeloid leukemia (AML). A total of 569 unrelated AML patients and 410 healthy individuals from West China were recruited, and ARID5B TagSNPs were genotyped using iMLDR^® (improved multiplex ligation detection reaction). It was found that the association of ARID5B polymorphisms with AML was most significant in acute promyelocytic leukemia (APL), and exclusively in males, the mutant alleles of rs6415872, rs2393726, rs7073837, rs10821936, and rs7089424 were found to increase the risk of developing APL in men, the odds ratio (OR) were 1.36, 1.74, 1.45, 1.53, and 1.56 (all p < 0.05), respectively. Haplotype analysis revealed that haplotype [AACCG] increased the risk of male APL with an OR of 1.53 (95% confidence interval: 1.10-2.14, p = 0.012). Besides, there was a strong positive additive interaction between rs6415872 and rs10821936, rs7089424, respectively, and cases attributed to the interaction of rs6415872, rs10821936, and rs7089424 accounted for 100%. Furthermore, ARID5B single nucleotide polymorphisms were found associated with clinical features of AML, and rs6415872 was shown to be an independent prognosis factor in APL patients. Besides, dual luciferase report assay showed that rs6415872 may affect the binding activity of PPARG with ARID5B. ARID5B polymorphisms contribute to male APL risk, clinical feature, and prognosis, suggesting the importance of ARDI5B in AML pathogenesis and development, and the gender and subtype preference may prompt some specific mechanisms of ARID5B. Besides, ARID5B polymorphisms might be a potential prognosis biomarker.

Genetic variants of glutathione S-transferase and the risk of acute myeloid leukemia in a Saudi population

Objective

This study aims to investigate the genetic association of acute myeloid leukemia and glutathione S-transferase (GST) gene polymorphisms in a Saudi population.

Method

100 AML cases and 100 healthy controls were recruited from the Riyadh regional hospital. In the GST gene, GSTM1 and GSTT1 variants were genotyped by multiplex PCR, and GSTP1 variants were genotyped by PCR-RFLP analysis. Statistical analysis between AML cases and controls included anthropometric measurements and evaluation of the genotypic and allelic frequencies.

Result

The null genotypes of GSTM1 and GSTT1 showed no association with AML [OR 0.56 (0.26–1.19); p = 0.31 and OR 0.65 (0.37–1.16); p = 0.14]. Similarly, the GSTP1 genotype and allele frequencies did not indicate any association with AML [GG + AG vs. AA: OR 0.75 (0.43–1.31) and p = 0.32; GG vs. AA: OR 1.73 (0.55–5.44) and p = 0.34; G vs. A: OR 0.95 (0.61–1.46) and p = 0.82]. Further, a haplotype analysis between AML cases and controls did not show any positive association (p < 0.05).

Conclusion

In conclusion, there was no statistical association of the genotypes and alleles in GSTM1, GSTT1, and GSTP1 with AML. Our results confirm the negative association of the investigated genetic markers with susceptibility to AML. Further association studies would be required in different ethnic populations to facilitate a meta-analysis in the future. Our findings suggest that the GST gene has no role in the pathogenesis of AML in patients from Saudi Arabia.