Monitoring of lung malignant epithelial cells by gene methylation analysis in the conditionally reprogrammed cell cultures

Conditionally reprogrammed cell (CRC) technology is an effective method for culturing primary malignant cells and non-malignant epithelial cells in vitro. This can be useful for precision medicine applications, such as drug sensitivity assays. However, this approach is commonly hindered by the non-specific growth of non-malignant epithelial cells in CRC cultures and the lack of effective biomarkers/assays to distinguish them from primary tumor cells. In this study, we developed a DNA methylation-based, real-time PCR assay to investigate SHOX2 and PTGER4 gene promoters as sensitive markers for human lung cancer. We first found that in formalin-fixed, paraffin-embedded (FFPE) malignant lung samples, 90% (28/31) had increased SHOX2 and/or PTGER4 promoter methylation as compared with their adjacent non-malignant samples. We then applied this assay to fresh surgical tumors and found increased SHOX2 and/or PTGER4 promoter methylation in 80% (20/25) of tumor samples as compared with their corresponding adjacent non-malignant tissues. Increased methylation of SHOX2 or PTGER4 promoter regions was also detected in 52% (13/25) of CRC cultures. The presence of malignant cells was confirmed by growth in soft agar cultures, a hallmark of malignant transformation, as well by EGFR mutation analysis. These results demonstrate that SHOX2 and PTGER4 promoter methylation levels can be used to detect malignant lung epithelial cells in CRC cultures.