Background:Circulating cell-free DNA (cfDNA) has been widely used as a prognostic marker for different cancers.Objective: In this study, we used 30 cfDNA samples from oral squamous cell carcinoma (OSCC), 199 public OSCC samples, and 192 normal samples to study various correlation factors that could improve the early-stage diagnostics and/or prognosis of OSCC.Methods: The statistical correlation between healthy and OSCC patients was done and deep sequencing analyses was performed to study various genomic alterations likes copy number variation (CNV), and single nucleotide variants (SNVs), gene fusion and genomic integration of viruses.Results: We found that the 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 CNVs, fusion genes, and viral integrations. The CNV analysis suggested a correlation with amplification and deletion in chromosomes at loci 1q, 2q, 3p, 3q, and chromosome 8 at loci q22. Moreover, at these loci, amplification ofTP53,PIK3CA, and other genes related to keratinization in OSCC patients was observed. In addition, we identified a novel abundant fusion gene,TRMO-TRNT1 ‘chimera’, in seven high-grade tumor samples. The parental genes of this chimera,TRMOandTRNT1, are known to play roles in tRNA modification and DNA repair, respectively. We have identified SNVs in our OSCC cohort. Some of these SNVs, likeKMT2C,MUC3A, andMUC6, have been identified as common cases in different cancer populations. Finally, we detected contigs integrations of human papillomavirus, simian virus, and enterovirus in the OSCC samples, which may point to the potential causes of OSCC.Conclusions: Our results indicate that the liquid biopsy technique may thus serve as a sensitive tool to study OSCC patient genomic alterations by exploring cfDNA circulating in the plasma, providing an easy-to-use blood test in the future.
背景：循环游离DNA（cfDNA）已被广泛用作多种癌症的预后标志物。目的：本研究通过30例口腔鳞状细胞癌（OSCC）患者cfDNA样本、199例公共OSCC样本及192例正常样本，探究可改善OSCC早期诊断和/或预后的多种相关因素。方法：通过统计学分析健康人群与OSCC患者的相关性，并采用深度测序技术研究基因组变异，包括拷贝数变异（CNV）、单核苷酸变异（SNV）、基因融合及病毒基因组整合。结果：研究发现OSCC患者cfDNA浓度可作为肿瘤分期、恶性程度及生存预后的指标。cfDNA深度基因组测序揭示了CNV、融合基因及病毒整合等基因组改变。CNV分析显示1q、2q、3p、3q染色体位点及8号染色体q22位点存在扩增和缺失相关性，并在这些位点观察到OSCC患者中TP53、PIK3CA等与角化相关基因的扩增。此外，在7例高级别肿瘤样本中发现新型高丰度融合基因TRMO-TRNT1嵌合体，其亲本基因TRMO和TRNT1分别参与tRNA修饰和DNA修复过程。在OSCC队列中鉴定出多个SNV，其中KMT2C、MUC3A、MUC6等变异已在不同癌症群体中被确认为常见突变。最后，在OSCC样本中检测到人乳头瘤病毒、猿病毒和肠道病毒的序列整合，这可能提示OSCC的潜在致病因素。结论：本研究结果表明，通过检测血浆中循环cfDNA，液体活检技术可作为研究OSCC患者基因组变异的灵敏工具，为未来提供便捷的血液检测方法。
肿瘤(癌症)患者之家