Detection of Glioma and Prognostic Subtypes by Noninvasive Circulating Cell-Free DNA Methylation Markers

INTRODUCTION Genome-wide DNA methylation profiling has shown that epigenetic abnormalities are biologically important in glioma and can be used to classify these tumors into distinct prognostic groups. Thus far, DNA profiling has required surgically resected glioma tissue; however, gliomas release tumoral material into biofluids providing an opportunity for a minimally invasive testing. While prior studies have shown that molecular markers can be detected in liquid biopsy (LB), there has been low sensitivity for tumor-specific markers. We hypothesize that the low sensitivity is due to the targeted assay methods. METHODS Genome-wide CpG methylation levels in DNA of tumor tissue and cell-free DNA serum of glioma patients. RESULTS We defined glioma-specific and IDH-specific epigenetic LB (eLB) signatures (Glioma-eLB and IDH-eLB, respectively) from serum cell-free DNA from patients diagnosed with glioma (N = 15 IDH mutant and N = 7 IDH wildtype) and with epilepsy (N = 3). The epigenetic profiles of the matched tissue demonstrate that these eLB signatures reflected the signature of the tumor. Through cross-validation we show that Glioma-eLB can accurately predict a patient's glioma from those with other neoplasias (N = 6 Colon; N = 14 Pituitary; N = 3 Breast; N = 4 Lung), non-neoplastic immunological conditions (N = 22 sepsis; N = 9 pancreatic islet transplantation), and from healthy individuals (sensitivity: 98%; specificity: 99%). Finally, IDH-eLB includes promoter methylated markers associated with genes known to be involved in glioma tumorigenesis (PVT1 and CXCR6). CONCLUSION The application of the noninvasive eLB signature discovered in this study has the potential to complement the standard of care for patients harboring glioma.