Exome sequencing of oral squamous cell carcinoma in users of Arabian snuff reveals novel candidates for driver genes

Abstract

The study sought to identify genetic aberrations driving oral squamous cell carcinoma (OSCC) development among users of shammah, an Arabian preparation of smokeless tobacco. Twenty archival OSCC samples, 15 of which with a history of shammah exposure, were whole-exome sequenced at an average depth of 127×. Somatic mutations were identified using a novel, matched controls-independent filtration algorithm. CODEX and Exomedepth coupled with a novel, Database of Genomic Variant-based filter were employed to call somatic gene-copy number variations. Significantly mutated genes were identified with Oncodrive FM and the Youn and Simon’s method. Candidate driver genes were nominated based on Gene Set Enrichment Analysis. The observed mutational spectrum was similar to that reported by the TCGA project. In addition to confirming known genes of OSCC (TP53, CDKNA2, CASP8, PIK3CA, HRAS, FAT1, TP63, CCND1 and FADD) the analysis identified several candidate novel driver events including mutations of NOTCH3, CSMD3, CRB1, CLTCL1, OSMR and TRPM2, amplification of the proto-oncogenes FOSL1, RELA, TRAF6, MDM2, FRS2 and BAG1, and deletion of the recently described tumor suppressor SMARCC1. Analysis also revealed significantly altered pathways not previously implicated in OSCC including Oncostatin-M signalling pathway, AP-1 and C-MYB transcription networks and endocytosis. There was a trend for higher number of mutations, amplifications and driver events in samples with history of shammah exposure particularly those that tested EBV positive, suggesting an interaction between tobacco exposure and EBV. The work provides further evidence for the genetic heterogeneity of oral cancer and suggests shammah-associated OSCC is characterized by extensive amplification of oncogenes.

Multiomic analysis of oral keratinocytes chronically exposed to shisha

“…10,11 We observed 10 mutations per MB in cells treated with shisha extract with similar mutation spectrum as reported in whole-exome sequence analysis study of 15 OSCC patients with history of Shamma exposure. 25 In addition, missense variant(s) were identified in SAM and SH3 domain containing 1 (SASH1), Filamin C (FLNC), and Adenylate Cyclase 8 (ADCY8) with >30% allele frequency supported by at least 10 reads and predicted to be deleterious by ≥3…”

Profiling cancer-related gene mutations in oral squamous cell carcinoma from Japanese patients by targeted amplicon sequencing

“…The India Project Team of the International Cancer Genome Consortium published an exome sequencing study of 50 Indian patients with OSCC [ 9 ]. Recent analysis of smokeless tobacco-associated OSCC in Arabian patients revealed altered pathways not previously implicated in OSCC, such as Oncostatin-M signaling and AP-1 and C-MYB transcription networks [ 10 ]. However, these molecular alterations do not fully recapitulate the pathogenesis of OSCC.…”

Possible interaction between tobacco use and EBV in oral squamous cell carcinoma

“…In a very recent study that involved whole-exome sequencing of 20 OSCC DNA extracts, we realized consistent trends in the numbers of identified genetic aberrations by use of shammah, a form of dipping snuff used in the South of the Arabian Peninsula, and EBV infection status [9]. The shammah users/EBV-positive group had the highest number of somatic mutations, copy number variations, as well as driver events.…”