(Cyto)genomic and epigenetic characterization of BICR 10 cell line and three new established primary human head and neck squamous cell carcinoma cultures

Background Head and neck squamous cell carcinoma cell lines are useful preclinical models to understand the molecular processes underlying the development of such tumors, and to establish targeted therapies. Objective We performed a comprehensive (cyto)genomic and epigenetic characterization of three new established primary human head and neck squamous cell carcinoma cultures and an established, yet undercharacterized cell line: BICR 10. Methods Karyotyping, multiplex fluorescence in situ hybridization, array comparative genomic hybridization and methylation-specific multiplex ligation-dependent probe amplification were applied. Results The three primary cultures turned out to be a near-triploid and BICR 10 near-diploid. Banding and molecular cytogenetic analysis revealed non-random numerical and structural aberrations. The most common rearrangements identified in BICR 10 cell line were non-complex derivatives of reciprocal translocations, in which the breakpoints often appeared in centromeric/near-centromeric regions. In the 3 primary cell cultures the most common rearrangements observed were iso- and derivatives chromosomes derived from translocations. Overall, gains of 7p, 8q and losses at 3p, 8p, 9p, 18q and Xp were present in all four studied samples. Among the analyzed genes, BICR 10 cell line exhibited enhanced methylation of gene promoter; however, in all studied samples PAX5 , WT1 and GATA5 were methylated. Conclusion The here reported comprehensive characterization of BICR 10 cell line and the new established cultures enriches the resources available for head and neck cancer research, especially for testing therapeutic agents.