Detection of DNA methylation in the calcitonin gene in human leukemias using differential polymerase chain reaction

One of the earliest events in the multistep process of malignant transformation is a change in the methylation pattern of certain genes. DNA methylation is usually detected by Southern blotting after restriction digest with methylation-sensitive endonucleases. Calcitonin gene hypermethylation has been described in a variety of human malignancies including lymphomas and leukemias. Here we report a technique based on the semi-quantitative differential polymerase chain reaction (PCR) which is capable of detecting subtle changes in the methylation pattern of the human calcitonin gene. This technique is based on two principles: (i) simultaneous coamplification of the target gene (5'-region of the calcitonin gene) and a reference gene for quantitative purposes; and (ii) simultaneous coamplification of a competitor with identical primer-binding sites as the target gene to control for proper restriction digest. Using this technique, we investigated calcitonin gene methylation in a variety of human cell lines, primary leukemias and normal human blood donors. The data revealed good correlation with standard Southern blotting. Weak calcitonin gene methylation was found in all normal blood donors tested (n = 14). In contrast, strong calcitonin gene methylation was detected in most acute leukemias (five of 10 acute myeloid leukemias (AML); six of seven acute lymphoblastic leukemias (ALL)). These data show that this technique can reliably be used to quantitate gene methylation and indicate that there exists heterogeneity with regard to methylation status in different leukemias, suggesting that hypermethylation of the calcitonin gene may play a role in the transformation process of some, but not all, human leukemias. Furthermore, differential PCR may facilitate determination of calcitonin gene methylation in clinical or archival tumor samples.