ABL1 methylation is a distinct molecular event associated with clonal evolution of chronic myeloid leukemia

Methylation of the proximal promoter of the ABL1 oncogene is a common epige netic alteration associated with clinical progression of chron ic myeloid l eukemia (CML). In this study we queried whether both the Ph'-associated and normal ABL 1 alleles undergo methylation; what may be the proportion of he matopoietic progenitors bearing methylated ABL I promoters in chronic versu s acute phase disease; whether methylation affects the promoter uniformly o r in patches with discrete clinical relevance; and, finally, whether methyl ation of ABL1 reflects a generalized process or is gene-specific. To addres s these issues, we adapted the techniques of methylation-specific PCR and b isulfite-sequencing to study the regulatory regions of ABL1 and other genes with a role in DNA repair or genotoxic stress response. In cell lines esta blished from CML blast crisis, which only carry a single ABL1 allele nested within the BCR-ABL fusion gene, ABL1 promoters were universally methylated . By contrast, in clinical samples from patients at advanced stages of dise ase, both methylated and unmethylated promoter alleles were detectable. To distinguish between allele-specific methylation and a mixed cell population pattern, we studied the methylation status of ABL 1 in colonies derived fr om single hematopoietic progenitors. Our results showed that both methylate d and unmethylated promoter alleles coexisted in the same colony Furthermor e, ABL I methylation was noted in the vast majority of colonies from blast crisis, but not chronic-phase CML. Both cell lines and clinical samples fro m acute-phase CML showed nearly uniform hypermethylation along the promoter region. Finally, we showed that ABL1 methylation does not reflect a genera lized process and may be unique among DNA repair/genotoxic stress response genes. Our data suggest that specific methylation of the Ph'-associated ABL I allele accompanies clonal evolution in CML. (C) 1999 by The American Soc iety of Hematology.