Xie Zhongqiu, Babiceanu Mihaela, Kumar Shailesh, Jia Yuemeng, Qin Fujun, Barr Frederic G, Li Hui
Department of Pathology, University of Virginia, Charlottesville, VA 22908.
Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20892.
Proc Natl Acad Sci U S A. 2016 Nov 15;113(46):13126-13131. doi: 10.1073/pnas.1612734113. Epub 2016 Oct 31.
Gene fusions and fusion products were thought to be unique features of neoplasia. However, more and more studies have identified fusion RNAs in normal physiology. Through RNA sequencing of 27 human noncancer tissues, a large number of fusion RNAs were found. By analyzing fusion transcriptome, we observed close clusterings between samples of same or similar tissues, supporting the feasibility of using fusion RNA profiling to reveal connections between biological samples. To put the concept into use, we selected alveolar rhabdomyosarcoma (ARMS), a myogenic pediatric cancer whose exact cell of origin is not clear. PAX3-FOXO1 (paired box gene 3 fused with forkhead box O1) fusion RNA, which is considered a hallmark of ARMS, was recently found during normal muscle cell differentiation. We performed and analyzed RNA sequencing from various time points during myogenesis and uncovered many chimeric fusion RNAs. Interestingly, we found that the fusion RNA profile of RH30, an ARMS cell line, is most similar to the myogenesis time point when PAX3-FOXO1 is expressed. In contrast, full transcriptome clustering analysis failed to uncover this connection. Strikingly, all of the 18 chimeric RNAs in RH30 cells could be detected at the same myogenic time point(s). In addition, the seven chimeric RNAs that follow the exact transient expression pattern as PAX3-FOXO1 are specific to rhabdomyosarcoma cells. Further testing with clinical samples also confirmed their specificity to rhabdomyosarcoma. These results provide further support for the link between at least some ARMSs and the PAX3-FOXO1-expressing myogenic cells and demonstrate that fusion RNA profiling can be used to investigate the etiology of fusion-gene-associated cancers.
基因融合及融合产物曾被认为是肿瘤形成的独特特征。然而，越来越多的研究在正常生理过程中发现了融合RNA。通过对27种人类非癌组织进行RNA测序，发现了大量融合RNA。通过分析融合转录组，我们观察到相同或相似组织样本之间紧密聚类，这支持了利用融合RNA谱揭示生物样本间联系的可行性。为将这一概念付诸实践，我们选择了肺泡横纹肌肉瘤（ARMS），这是一种起源细胞尚不明确的儿童肌源性癌症。PAX3 - FOXO1（配对盒基因3与叉头框O1融合）融合RNA，被认为是ARMS的一个标志，最近在正常肌肉细胞分化过程中被发现。我们对成肌过程中不同时间点进行了RNA测序并分析，发现了许多嵌合融合RNA。有趣的是，我们发现ARMS细胞系RH30的融合RNA谱与PAX3 - FOXO1表达时的成肌时间点最为相似。相比之下，全转录组聚类分析未能揭示这种联系。引人注目的是，RH30细胞中的18种嵌合RNA在相同的成肌时间点均能被检测到。此外，7种与PAX3 - FOXO1具有相同瞬时表达模式的嵌合RNA是横纹肌肉瘤细胞特有的。对临床样本的进一步检测也证实了它们对横纹肌肉瘤的特异性。这些结果为至少一些ARMS与表达PAX3 - FOXO1的成肌细胞之间的联系提供了进一步支持，并表明融合RNA谱可用于研究融合基因相关癌症的病因。
