Novel gene fusions in human oropharyngeal carcinoma

IF 1.4 4区医学 Q4 GENETICS & HEREDITY

Cancer Genetics Pub Date : 2024-07-01 DOI:10.1016/j.cancergen.2024.06.004

Katsuhiro Masago , Hiroaki Kuroda , Eiichi Sasaki , Yasuko Fujita , Shiro Fujita , Yoshitsugu Horio , Motoyoshi Endo , Hiromasa Ishihara , Nobuhiro Hanai , Hirokazu Matsushita

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引用次数: 0

Abstract

Few reports have analyzed the fusion genes involved in carcinogenesis in the oropharynx, where the incidence of human papillomavirus-associated tumors is relatively low. The aim of this study was to identify novel driver fusion genes in patients with oropharyngeal cancer. The study enrolled fifty-seven patients who were diagnosed with oropharyngeal carcinoma. RNA sequencing data from fresh-frozen specimens were used to identify candidate fusion genes via the JAFFA, arriba, and STAR-Fusion pipelines. Candidate fusion genes were confirmed by direct sequencing. The expression level of a candidate fusion gene was compared to that of tumors without fusion genes. Finally, filtering was performed for driver genes using the annoFuse pipeline. In addition, the VIRTUS pipeline was used to analyze the presence of human papillomavirus in the tumors. We identified 5 (8.8 %) novel potential driver in-frame fusion genes, MKNK2::MOB3A, ICMT::RPS6KA3, ATP1B3::GRK7, CSNK2A1::KIF16B, and FGFR3::MAEA, and 1 (1.8 %) known in-frame fusion gene, FGFR3::TACC3, in 57 patients with pharyngeal carcinoma. Our results suggest that sporadic fusion genes may contribute to tumorigenesis in oropharyngeal carcinomas.

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人类口咽癌中的新型基因融合

口咽部是人类乳头状瘤病毒相关肿瘤发病率相对较低的部位，很少有报告分析口咽部癌变的融合基因。本研究旨在确定口咽癌患者体内的新型驱动融合基因。研究共招募了57名确诊为口咽癌的患者。鲜冻标本的RNA测序数据通过JAFFA、arriba和STAR-Fusion管道用于鉴定候选融合基因。通过直接测序确认候选融合基因。将候选融合基因的表达水平与无融合基因的肿瘤表达水平进行比较。最后，使用 annoFuse 管道对驱动基因进行筛选。此外，我们还使用 VIRTUS 管道分析了肿瘤中是否存在人类乳头瘤病毒。我们在57名咽癌患者中发现了5个（8.8%）新的潜在驱动帧内融合基因，即MKNK2::MOB3A、ICMT::RPS6KA3、ATP1B3::GRK7、CSNK2A1::KIF16B和FGFR3::MAEA，以及1个（1.8%）已知帧内融合基因，即FGFR3::TACC3。我们的研究结果表明，散发性融合基因可能有助于口咽癌的肿瘤发生。

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来源期刊

Cancer Genetics ONCOLOGY-GENETICS & HEREDITY

CiteScore

3.20

自引率

5.30%

发文量

167

审稿时长

27 days

期刊介绍： The aim of Cancer Genetics is to publish high quality scientific papers on the cellular, genetic and molecular aspects of cancer, including cancer predisposition and clinical diagnostic applications. Specific areas of interest include descriptions of new chromosomal, molecular or epigenetic alterations in benign and malignant diseases; novel laboratory approaches for identification and characterization of chromosomal rearrangements or genomic alterations in cancer cells; correlation of genetic changes with pathology and clinical presentation; and the molecular genetics of cancer predisposition. To reach a basic science and clinical multidisciplinary audience, we welcome original full-length articles, reviews, meeting summaries, brief reports, and letters to the editor.