Detection of glioma and prognostic subtypes by non-invasive circulating cell-free DNA methylation markers

Noushmehr, H.; Sabedot, T. S.; Malta, T. M.; Nelson, K.; Snyder, J.; Wells, M.; deCarvalho, A.; Makherjee, A.; Chitale, D.; Mosella, M.; Asmaro, K.; Robin, A. M.; Rosenblum, M. L.; Mikkelsen, T.; Rock, J.; Poisson, L. M.; Lee, I. Y.; Walbert, T.; Kalkanis, S.; Castro, A. V.

doi:10.1101/601245

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bioRxiv · 10.1101/601245

Detection of glioma and prognostic subtypes by non-invasive circulating cell-free DNA methylation markers

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Abstract

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, such as blood and cerebrospinal fluid, providing an opportunity for a minimally invasive testing. While prior studies have shown that genetic and epigenetic markers can be detected in blood or cerebrospinal fluid (e.g., 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. Therefore, we profiled the genome-wide CpG methylation levels in DNA of tumor tissue and cell-free DNA in serum of glioma patients, to identify non-invasive epigenetic LB (eLB) markers in the serum that reflect the characteristics of the tumor tissue. From the epigenetic profiles of serum from patients diagnosed with glioma (N=15 IDH mutant and N=7 IDH wildtype) and with epilepsy (N=3), we defined glioma-specific and IDH-specific eLB signatures (Glioma-eLB and IDH-eLB, respectively). 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 patients 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). The application of the non-invasive eLB signature discovered in this study has the potential to complement the standard of care for patients harboring glioma.

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Noushmehr, H., Sabedot, T. S., Malta, T. M., Nelson, K., Snyder, J., Wells, M., deCarvalho, A., Makherjee, A., Chitale, D., Mosella, M., Asmaro, K., Robin, A. M., Rosenblum, M. L., Mikkelsen, T., Rock, J., Poisson, L. M., Lee, I. Y., Walbert, T., Kalkanis, S., Castro, A. V.. 2019-04-08. Detection of glioma and prognostic subtypes by non-invasive circulating cell-free DNA methylation markers. https://doi.org/10.1101/601245

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