一种新型肿瘤组织起源分子标志物的建立与评价

摘要

Background and purpose:Cancer of unknown primary (CUP) represents approximately 5%~10%of malignant neoplasms. For CUP patients, identiifcation of tumor origin allows for more speciifc therapeutic regimens and improves outcomes.Methods:By retrieving the gene expression data from ArrayExpress and Gene Expression Omnibus data repositories, we established a comprehensive gene expression database of 5 800 tumor samples encom-passing 22 main tumor types. The support vector machine-recursive feature elimination algorithm was used for feature selection and classiifcation modelling. We further optimized the RNA isolation and real-time quantitative polymerase chain reaction (RTQ-PCR) methods for candidate gene expression proifling and applied the RTQ-PCR assays to a set of formalin-fixed, paraffin-embedded tumor samples.Results:Based on the pan-cancer transcriptome database, we identiifed a list of 96-tumor speciifc genes, including common tumor markers, such as cadherin 1 (CDH1), kallikrein-re-lated peptidase 3 (KLK3), and epidermal growth factor receptor (EGFR). Furthermore, we successfully translated the microarray-based gene expression signature to the RTQ-PCR assays, which allowed an overall success rate of 88.4% (95%CI: 83.2%-92.4%) in classifying 22 different tumor types of 206 formalin-fixed, paraffin-embedded samples. Conclusion:The 96-gene RTQ-PCR assay represents a useful tool for accurately identifying tumor origins. The assay uses RTQ-PCR and routine formalin-ifxed, paraffn-embedded samples, making it suitable for rapid clinical adoption.%背景与目的：原发灶不明恶性肿瘤是一类转移性肿瘤的统称，在诊断时无法找到原发位点，约占所有恶性肿瘤的5%~10%。明确肿瘤的组织起源对于患者的诊断和治疗具有重要意义。方法：整合ArrayEx-press和Gene Expression Omnibus数据库中肿瘤类型明确的样本数据，构建涵盖22种常见肿瘤类型、5800例样本的基因表达谱数据库；通过支持向量机递归特征消除算法筛选组织特异性基因，建立肿瘤分类模型；采用实时定量聚合酶链反应(real-time quantitative polymerase chain reaction，RTQ-PCR)检测石蜡包埋肿瘤组织中基因的表达水平，并将基因分型结果与病理诊断结果进行比较。结果：基于肿瘤基因表达谱大数据，筛选出96个组织特异性基因，其中包含常见的肿瘤相关基因，如钙黏蛋白1(cadherin 1，CDH1)、激肽释放酶相关酶3(kallikrein-related peptidase 3，KLK3)和表皮生长因子受体(epidermal growth factor receptor，EGFR)等。在206例石蜡包埋组织样本中，182例的基因分型结果与病理诊断结果一致，准确率达到88.4%(95%CI：83.2%~92.4%)。结论：96基因RTQ-PCR检测对22种常见肿瘤类型具有较好的分类性能，可作为临床和病理诊断的辅助工具。