Transcriptomic analyses of the radiation response in head and neck squamous cell carcinoma subclones with different radiation sensitivity: time-course gene expression profiles and gene association networks.
Transcriptomic analyses of the radiation response in head and neck squamous cell carcinoma subclones with different radiation sensitivity: time-course gene expression profiles and gene association networks.
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DOI：
10.1186/s13014-016-0672-0
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发表时间：
2016-07-26
期刊：
影响因子：
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通讯作者：
Hess J
中科院分区：
文献类型：
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作者：
Michna A;Schötz U;Selmansberger M;Zitzelsberger H;Lauber K;Unger K;Hess J
肿瘤细胞的获得性和固有的放射抗性与肿瘤复发和不良预后有关——不仅在头颈鳞状细胞癌（HNSCC）中。潜在的分子机制很大程度上是未知的。因此，需要系统深入的分析来确定辐射抗性的关键调节因子。在本研究中，分析了具有不同放射敏感性的 CAL-33 HNSCC 细胞系的亚克隆，以确定与不同表型相关的信号通路。通过对亲本 CAL-33 细胞进行分级照射，产生放射敏感性改变的亚克隆。放射敏感性的差异在集落形成测定中得到证实。通过 SKY、阵列 CGH 和 mRNA 微阵列分析在基因组和转录组水平上对选定的亚克隆进行表征。使用自然三次样条回归模型对辐射进行时程基因表达分析，识别出时间上差异表达的基因。此外，还鉴定了早期和晚期反应基因。使用偏相关重建基因关联网络。利用 Reactome 通路数据库进行通路富集分析。与亲本细胞相比，具有增强的辐射抗性（RP）和增强的辐射敏感性（SP）的两个亚克隆的特征揭示了明显的基因组和转录组变化。两个亚克隆共有的辐射后差异表达基因指出了早期和晚期辐射反应的重要途径，包括衰老、细胞凋亡、DNA 修复、Wnt、PI3K/AKT 和 Rho GTPase 信号传导。对基因关联网络最重要节点的分析揭示了不同放射敏感性表型中放射反应的特异性途径。例如，对于 RP 亚克隆，衰老相关分泌表型 (SASP) 与 GPCR 配体结合被认为是至关重要的。此外，还观察到内源性逆转录病毒ERV3-1在辐射反应中的表达，并确定了相关的基因关联网络。我们的研究提供了具有不同辐射敏感性的 CAL-33 亚克隆的全面基因表达数据。由此产生的与抗性表型相关的网络和途径特别令人感兴趣，其中包括 SASP。 ERV3-1 的辐射相关表达对于进一步研究获得性放射抗性的分子机制似乎也非常有吸引力。已确定的途径可能代表放射抗性的关键参与者，可以作为分子设计治疗干预的潜在目标。本文的在线版本 (doi:10.1186/s13014-016-0672-0) 包含补充材料，可供授权用户使用。
Acquired and inherent radioresistance of tumor cells is related to tumor relapse and poor prognosis – not only in head and neck squamous cell carcinoma (HNSCC). The underlying molecular mechanisms are largely unknown. Therefore, systemic in-depth analyses are needed to identify key regulators of radioresistance. In the present study, subclones of the CAL-33 HNSCC cell line with different radiosensitivity were analyzed to identify signaling pathways related to the different phenotypes. Subclones with altered radiosensitivity were generated by fractionated irradiation of the parental CAL-33 cells. Differences in radiosensitivity were confirmed in colony formation assays. Selected subclones were characterized at the genomic and transcriptomic level by SKY, array CGH, and mRNA-microarray analyses. Time-course gene expression analyses upon irradiation using a natural cubic spline regression model identified temporally differentially expressed genes. Moreover, early and late responding genes were identified. Gene association networks were reconstructed using partial correlation. The Reactome pathway database was employed to conduct pathway enrichment analyses. The characterization of two subclones with enhanced radiation resistance (RP) and enhanced radiosensitivity (SP) revealed distinct genomic and transcriptomic changes compared to the parental cells. Differentially expressed genes after irradiation shared by both subclones pointed to important pathways of the early and late radiation response, including senescence, apoptosis, DNA repair, Wnt, PI3K/AKT, and Rho GTPase signaling. The analysis of the most important nodes of the gene association networks revealed pathways specific to the radiation response in different phenotypes of radiosensitivity. Exemplarily, for the RP subclone the senescence-associated secretory phenotype (SASP) together with GPCR ligand binding were considered as crucial. Also, the expression of endogenous retrovirus ERV3-1in response to irradiation has been observed, and the related gene association networks have been identified. Our study presents comprehensive gene expression data of CAL-33 subclones with different radiation sensitivity. The resulting networks and pathways associated with the resistant phenotype are of special interest and include the SASP. The radiation-associated expression of ERV3-1 also appears highly attractive for further studies of the molecular mechanisms underlying acquired radioresistance. The identified pathways may represent key players of radioresistance, which could serve as potential targets for molecularly designed, therapeutical intervention. The online version of this article (doi:10.1186/s13014-016-0672-0) contains supplementary material, which is available to authorized users.