PNAS:融合基因组学揭示横纹肌肉瘤细胞起源

　　基因融合一直被认为是肿瘤独有的特征。基因融合是指染色体上两个异位的基因嵌合在一起，由于染色体发生易位、缺失或者倒置造成的，通常在癌症的发生发展扮演着重要的角色，并且可以作为诊断和治疗癌症的靶标。基因融合现象最早在慢性粒细胞白血病中发现 BCR-ABL基因融合（费城染色体）。除血液系统肿瘤外，在实体瘤中也存在着基因融合，例如前列腺癌中的TMPRSS2-ERG、小细胞肺癌中的EML4-ALK、结直肠癌中的VTI1A-TCF7L2，横纹肌肉瘤PAX3-FOXO1等融合基因。

　　横纹肌肉瘤（Rhabdomyosarcoma，RMS）是罕见的一种恶性肿瘤，在小儿实体瘤中发病率较高，其临床亚型有胚胎型横纹肌肉瘤（ERMS），腺泡型横纹肌肉瘤( ARMS)，在85%左右的ARMS中可检测到特异性染色体易位，两种易位分别形成相应的融合基因PAX3-FOXO1或PAX7-FOXO1。

　　基因融合一直被认为是肿瘤独有的特征。本研究从间充质干细胞MSCsg骨骼肌分化发生的融合基因事件入手，采用生物信息学和分子生物学等研究手段，提供了横纹肌肉瘤细胞起源的线索。这项研究发表在PNAS《美国科学院院刊》。文章第一作者(ZhongqiuXie)谢仲秋博士，通讯作者是美国佛吉尼亚大学医学院（Hui Li）李辉。

　　本研究首次从融合基因的角度来研究肿瘤细胞的起源。在MSCs干细胞骨骼肌分化样品中发现这些时间点样品和横纹肌肉瘤细胞RH30类似的融合基因组，这些肿瘤标志性融合基因如PAX3-FOXO1等都在干细胞分化过程中瞬时表达。而且至少有18种融合基因几乎在同一时间点发生。这种瞬时的融合基因组发生事件提供了肿瘤细胞起源的新线索。(Hui Li)李辉实验室近几年在融合基因领域取得了很大进展：最先证明了RNA反式剪切（trans-splicing）会产生嵌合融合RNA（chimeric fusion RNAs）； 除了反式剪接外，相邻基因之间的顺式剪接（cis-SAGe）是产生基因间剪接的嵌合RNA的另一种机制；发现正常细胞以及几乎所有器官和组织都会产生融合基因，而且具有很重要的生理功能；在间充质干细胞骨骼肌分化过程中发现可以瞬时产生横纹肌肉瘤肿瘤标志性融合RNA和蛋白质（PAX3-FOXO1）， 使用这些肿瘤标志物来追踪复杂癌症的细胞起源； 首次提出了"融合基因组学"概念。

　　http：//www.pnas.org/content/arly/2016/10/25/1612734113.abstract

　　doi： 10.1073/pnas.1612734113

　　Fusion transcriptome profiling provides insights into alveolar rhabdomyosarcoma

　　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.