International Journal of Molecular Sciences Article DNA Methylome Distinguishes Head and Neck Cancer from Potentially Malignant Oral Lesions and Healthy Oral Mucosa Nina Milutin Gašperov 1,*, Ivan Sabol 1 , Ksenija Božinovi´c 1 , Emil Dediol 2, Marinka Mravak-Stipeti´c 3, Danilo Licastro 4 , Simeone Dal Monego 4 and Magdalena Grce 1,* 1 Division of Molecular Medicine, Ruder¯ Boškovi´cInstitute, 10000 Zagreb, Croatia;
[email protected] (I.S.);
[email protected] (K.B.) 2 Department of Maxillofacial Surgery, School of Medicine, Clinical Hospital Dubrava, University of Zagreb, 10000 Zagreb, Croatia;
[email protected] 3 Department of Oral Medicine, School of Dental Medicine, University of Zagreb, 10000 Zagreb, Croatia;
[email protected] 4 ARGO Open Lab Platform for Genome sequencing, AREA Science Park, Padriciano, 99, 34149 Trieste, Italy;
[email protected] (D.L.);
[email protected] (S.D.M.) * Correspondence:
[email protected] (N.M.G.);
[email protected] (M.G.) Received: 7 July 2020; Accepted: 15 September 2020; Published: 18 September 2020 Abstract: There is a strong need to find new, good biomarkers of head and neck squamous cell carcinoma (HNSCC) because of the bad prognoses and high mortality rates. The aim of this study was to identify the potential biomarkers in HNSCC that have differences in their DNA methylome and potentially premalignant oral lesions, in comparison to healthy oral mucosa. In this study, 32 oral samples were tested: nine healthy oral mucosae, 13 HNSCC, and 10 oral lesions for DNA methylation by the Infinium MethylationEPIC BeadChip. Our findings showed that a panel of genes significantly hypermethylated in their promoters or specific sites in HNSCC samples in comparison to healthy oral samples, which are mainly oncogenes, receptor, and transcription factor genes, or genes included in cell cycle, transformation, apoptosis, and autophagy.