Background: Several studies have examined the presence of DNA methylation of CpG islands in leukemia. Methylation of SOX17 and RUNX3 genes may play a role in leukemogenesis through silencing tumor suppressor genes. We investigated the methylation status of SOX17 and RUNX3 genes in patients with acute leukemia.   
Methods: In this case-control study, peripheral blood samples from 100 AML and 100 ALL patients and 100 healthy controls were collected. Isolated DNA was treated with sodium bisulfite and methylation status was examined by methylation specific PCR (MS-PCR) with primers specific for methylated and unmethylated sequences of SOX17 and RUNX3 genes.
Results: The frequency of hypermethylation of SOX17 and RUNX3 genes were 36% and 28%I in patients with acute myeloid leukemia (AML), and 21% and 22% in patients with acute lymphoblastic leukemia (ALL), respectively. Aberrant methylation of these genes was found in all FAB classifications of AML and ALL. Hypermethylation of SOX17 (P=0.055) and RUNX3 (P=0.003) genes were associated with FAB-M0 and M1 subtypes of AML, respectively. Also, aberrant methylation of RUNX3 gene was associated with FAB-L1 subtype of ALL (P=0.053). There was not any significant association between hypermethylation of SOX17 and RUNX3 genes and clinical parameters of patients with leukemia including sex, age, WBC, and platelet counts.
Conclusion: Hypermethylation of SOX17 and RUNX3 genes was seen in patients with acute leukemia. Moreover, no significant association was observed between hypermethylation of SOX17 and RUNX3 and induction of remission.