Circulating cell-free DNA in oral squamous cell carcinoma patients allows for non-invasive prognosis and identification of structural variants, novel chimeras and oncoviruses

Circulating cell-free DNA (cfDNA) has been widely used as a prognostic marker of different cancers. In this study, we used cfDNA from oral squamous cell carcinoma (OSCC) patients to study various correlation factors that could improve early-stage diagnostics and prognosis. We found that OSCC patient cfDNA concentration can serve as an indicator of tumor stage, malignancy, and survival prognosis. Deep genome sequencing of cfDNA revealed genomic alterations, such as copy number variation, fusion gene identification, and viral integration. Copy number variation analysis suggested correlation with amplification and deletions in chromosome 1 at loci 1q, 2q, 3p, 3q and 8q22. Moreover, at these loci, amplification of TP53, PIK3CA and other genes related to keratinization in relapsed OSCC was observed. In addition, we identified a novel fusion gene, TRMO-TRNT1, in seven high-grade tumor samples. The parent genes of this chimera, TRMO and TRNT1, are known to play roles in tRNA modification and DNA repair. Liquid biopsy may thus serve as a sensitive tool to study OSCC patient genomic alterations by addressing cfDNA circulating in the plasma, using an easy-to-use blood test. Finally, we detected integrations of human papilloma virus, simian virus and enterovirus that may point to the origins of OSCC. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study was funded by Bar-Ilan university's seed funding ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Blood samples of 30 OSCC patients were collected in a cfDNA preservation tube at Rabin Medical Center following Helsinki committee approval. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Available Upon request