DNA methylation signatures in circulating cell-free DNA for the monitoring of at-risk populations progressing to lung cancer

Alteration of DNA methylation patterns at the 5′ position of cytosines, in the context of CpG dinucleotides, is one of the most promising epigenetic biomarkers for many biomedical applications and has been actively studied in many diseases and developmental questions for the last twenty years (How Kit et al., 2012). In comparison to genetic alterations such as mutations, which are usually distributed throughout the gene, DNA methylation alterations are concentrated in a defined area, often the promoter, facilitating analysis. DNA methylation can be reliably analyzed in freshly frozen and archived clinical specimens, but more importantly, also in biofluids, that were either in direct contact with the disease (e.g. stool for colorectal, urine for genitourinary or sputum, bronchoalveolar lavages or brushes for lung cancer) or in cell-free circulating DNA isolated from serum or plasma of patients (How Kit et al., 2012). Although it is currently unclear if DNA methylation changes are the cause or the consequence of the disease, it is clear that DNAmethylation changes occur early during disease pathogenesis and precede disease detection by histological and/or imaging methods. Several DNA methylation-based biomarkers are already commonly used in the clinic, such as the testing of the DNAmethylation status of theMGMT promoter for the prediction of the response to chemotherapy using alkylating agents in glioblastoma or ofMLH1 for the diagnosis of Lynch Syndrome. Commercial products such as the Epi proColon test, analyzing methylation in the SEPT9 gene (Church et al., 2014) for the population-wide screening for colorectal cancer and approved by the Chinese FDA in July 2015, and the Epi proLung (SHOX2) test (Ilse et al., 2014) are now available. Panelswithmultiple genes can further improve the specificity and sensitivity of DNAmethylation signatures as recently demonstrated in a stool-based screening test for colorectal cancer ((Imperiale et al., 2014), Cologuard, Exact Sciences), where DNA methylation alterations were combined with mutation detection and which received the first US-FDA approval for a DNA methylation-based diagnostic test in 2014. Lung cancer is the most common cancer in the world and few effective and cheap methods are available for its early detection and screening, especially in at-risk populations such as heavy smokers or patients with chronic obstructive lung disease (COPD) and fibrotic interstitial lung diseases (ILDs). Although histological and cytological examinations are currently the gold standard in lung cancer diagnosis, patients are often at late stages when diagnosis is confirmed. Therefore,