Simultaneous characterization of somatic events and HPV-18 integration in a metastatic cervical carcinoma patient using DNA and RNA sequencing.
Simultaneous characterization of somatic events and HPV-18 integration in a metastatic cervical carcinoma patient using DNA and RNA sequencing.
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DOI：
10.1097/igc.0000000000000049
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发表时间：
2014-02
期刊：
影响因子：
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通讯作者：
Monk BJ
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文献类型：
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作者：
Liang WS;Aldrich J;Nasser S;Kurdoglu A;Phillips L;Reiman R;McDonald J;Izatt T;Christoforides A;Baker A;Craig C;Egan JB;Chase DM;Farley JH;Bryce AH;Stewart AK;Borad MJ;Carpten JD;Craig DW;Monk BJ
补充数字内容可在文本中找到。致癌性人乳头瘤病毒（HPV）整合到宿主基因组中是包括宫颈癌在内的特定癌症中的重要致瘤因素。虽然在HPV诊断和预防方面取得了重大进展，但鉴定和开发宫颈癌患者的有效治疗方法仍然是一个目标，因此需要对体细胞事件和HPV整合进行额外的详细表征。鉴于这一需求，本研究的目标是使用下一代测序技术同时评估转移到肺的宫颈鳞状细胞癌病变患者的体细胞改变和表达变化，并检测和分析同一样本中的HPV感染。我们对患者的肺转移进行了肿瘤和正常外显子组、肿瘤和正常浅层全基因组测序以及RNA测序。我们产生了超过12亿个映射读数，并鉴定了130个体细胞点突变和插入缺失，21个基因易位，16个编码区显示拷贝数变化，超过36个基因显示肿瘤中的表达改变（校正P < 0.05）。测序还揭示了HPV 18型（HPV-18）在转移中的整合。使用DNA和RNA读数，我们确定了3个主要事件，表明HPV-18整合到患者肿瘤中染色体6p25.1的内含子区域中，并使用桑格测序验证了这些事件。尚未报道HPV-18的这种整合位点。我们证明，DNA和RNA测序可用于同时表征体细胞的改变和表达的变化，在活检和描绘HPV整合在宫颈癌的基础分辨率。进一步的测序将使我们更好地了解宫颈癌发病机制的分子基础。
Supplemental digital content is available in the text. Integration of carcinogenic human papillomaviruses (HPVs) into the host genome is a significant tumorigenic factor in specific cancers including cervical carcinoma. Although major strides have been made with respect to HPV diagnosis and prevention, identification and development of efficacious treatments for cervical cancer patients remains a goal and thus requires additional detailed characterization of both somatic events and HPV integration. Given this need, the goal of this study was to use the next generation sequencing to simultaneously evaluate somatic alterations and expression changes in a patient’s cervical squamous carcinoma lesion metastatic to the lung and to detect and analyze HPV infection in the same sample. We performed tumor and normal exome, tumor and normal shallow whole-genome sequencing, and RNA sequencing of the patient’s lung metastasis. We generated over 1.2 billion mapped reads and identified 130 somatic point mutations and indels, 21 genic translocations, 16 coding regions demonstrating copy number changes, and over 36 genes demonstrating altered expression in the tumor (corrected P < 0.05). Sequencing also revealed the HPV type 18 (HPV-18) integration in the metastasis. Using both DNA and RNA reads, we pinpointed 3 major events indicating HPV-18 integration into an intronic region of chromosome 6p25.1 in the patient’s tumor and validated these events with Sanger sequencing. This integration site has not been reported for HPV-18. We demonstrate that DNA and RNA sequencing can be used to concurrently characterize somatic alterations and expression changes in a biopsy and delineate HPV integration at base resolution in cervical cancer. Further sequencing will allow us to better understand the molecular basis of cervical cancer pathogenesis.