Evaluation of rs62527607 [GT] single nucleotide polymorphism located in BAALC gene in children with acute leukemia using mismatch PCR-RFLP

Acute leukemia is the most common cancer in children and involves several factors that contribute to the development of multidrug resistance and treatment failure. According to our recent studies, the BAALC gene is identified to have high mRNA expression levels in childhood acute lymphoblastic leukemia (ALL) and those with multidrug resistance. Several polymorphisms are associated with the expression of this gene. To date, there has been no study on the rs62527607 [GT] single nucleotide polymorphism (SNP) of BAALC gene and its link with childhood acute lymphoblastic and myeloid leukemia (AML). The purpose of this study is to evaluate the prevalence of this polymorphism in pediatric acute leukemia, as well as its relationship with prognosis. DNA samples were extracted from bone marrow slides of 129 children with ALL and 16 children with AML. The rs62527607 [GT] SNP was evaluated using mismatch polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP)-based analysis. The association between the SNP alleles and patient disease-free survival was then assessed. The prevalence of the T-allele of rs62527607 [GT] SNP in childhood T-ALL and pre-B-ALL was 28.3% and 11.2%, respectively. In the pre-B-ALL patients, 3 year disease free survival was associated with the GG genotype. Results showed a robust association between the rs62527607 SNP and the risk of relapse in ALL, but not AML, patients. T-ALL patients with the GT genotype had an 8.75 fold higher risk of relapse. The current study demonstrates a significant association between the genotype GT and the polymorphic allele G424T, and introduces this SNP as a negative prognostic factor in children with ALL.

Introduction

Acute lymphoblastic leukemia (ALL) is the most common malignancy diagnosed in children aged 2–5 years and represents one-third of all pediatric cancers 1, 2. Acute myeloid leukemia (AML), on the other hand, is responsible for 15% of childhood leukemia cases (2). With the development of support facilities, discovery of new drugs, and a new set of treatment protocols, 75–80% of children with ALL and 40–60% with AML can now be cured 2, 3. The choice of treatment, especially for ALL, depends on the risk factors present; patients that are determined to be at “high risk” are referred for bone marrow transplant 3, 4, whereas those who are at “standard risk” are recommended for chemotherapy. Even in standard risk cases, 20–25% of patients will experience relapse, most commonly caused by the development of multidrug resistance (MDR) 5, 6. This indicates a lack of sufficient awareness of risk factors when selecting the appropriate treatment.

The BAALC (Brain and Acute Leukemia, Cytoplasmic) gene is located on the human chromosome 8q22.3.18 (7). Although the functional role of BAALC protein remains unknown, decreased expression of this gene during the differentiation of hematopoietic cells indicates its potential role in early hematopoiesis and the impact of its altered expression in leukemogenesis 8, 9. Different studies indicate that BAALC expression is positively associated with the genes related to drug resistance, such as MDR1, that are in turn associated with poor treatment outcome through unknown mechanisms 10, 11. Recent studies by our group also show that an increase of BAALC expression in leukemic blasts is related to drug resistance (12).

Through analysis of the BAALC gene sequence, a variety of single nucleotide polymorphisms (SNPs) has been found that can affect the level of expression of this gene. G424T (rs62527607 [GT]) is one such SNP and is located downstream of exon 1. RUNX1 is a known transcriptional activator that has been implicated in normal and malignant hematopoiesis and binds preferentially to the T allele of rs62527607 [TG] to promote its transcriptional activity 13, 14.

The association between the G424T polymorphism and prognosis in adults with acute myeloid leukemia is currently described (14), but its relationship with relapse and acute pediatric leukemia remains unclear. The association between this polymorphism and MDR is an easy and low cost investigation that can provide a better definition of the “high risk” cases in childhood leukemia and improve the chances of a complete cure with proper treatment. In this study, for the first time, we evaluate the prevalence of this polymorphism in children under 15 years of age with ALL and AML and examined the relationship between this polymorphism and prognosis of acute leukemia.