RNA-seq analysis of sporadic and Basal Cell Nevus Syndrome-associated odontogenic keratocysts (OKCs)

The aim of this study was to decode the gene expression program characterizing odontogenic keratocyst (OKC) development, by performing a comprehensive transcriptomics analysis applied on whole OKC tissue derived from sporadic and Basal Cell Nevus Syndrome (BCNS)-associated OKCs, and control samples of pericoronal tissues of impacted teeth (dental follicles, DFs) derived from healthy individuals. Overall design: Formalin-fixed and paraffin-embedded tissue samples from 6 cases of sporadic OKCs, 6 cases of BSCN-associated OKCs and 6 cases of pericoronal tissues of impacted teeth (dental follicles, DFs) were included in RNA-seq analysis. 150-bp paired-end multiplexed sequencing was implemented using an Illumina Hiseq4000 sequencer (Illumina Inc., San Diego, CA). DFs were selected as the control group, as they represent a source of dental lamina rests, proposed to be a potential tissue of origin of OKC. Transcriptomics analysis of the whole OKC tissue was perfomed, composed of the lining epithelium and the fibrous capsule, as the former harbors the pathognomonic features of OKC and the latter is thought to effect its epithelial structure and biological behavior. Validation of RNA-seq results for selected gene markers via immunohistochemistry was performed in all cases.