PNAS:融合基因組學揭示橫紋肌肉瘤細胞起源

　　基因融合一直被認為是腫瘤獨有的特征。基因融合是指染色體上兩個異位的基因嵌合在一起，由于染色體發生易位、缺失或者倒置造成的，通常在癌癥的發生發展扮演著重要的角色，并且可以作為診斷和治療癌癥的靶標。基因融合現象最早在慢性粒細胞白血病中發現 BCR-ABL基因融合（費城染色體）。除血液系統腫瘤外，在實體瘤中也存在著基因融合，例如前列腺癌中的TMPRSS2-ERG、小細胞肺癌中的EML4-ALK、結直腸癌中的VTI1A-TCF7L2，橫紋肌肉瘤PAX3-FOXO1等融合基因。

　　橫紋肌肉瘤（Rhabdomyosarcoma，RMS）是罕見的一種惡性腫瘤，在小兒實體瘤中發病率較高，其臨床亞型有胚胎型橫紋肌肉瘤（ERMS），腺泡型橫紋肌肉瘤( ARMS)，在85%左右的ARMS中可檢測到特異性染色體易位，兩種易位分別形成相應的融合基因PAX3-FOXO1或PAX7-FOXO1。

　　基因融合一直被認為是腫瘤獨有的特征。本研究從間充質干細胞MSCsg骨骼肌分化發生的融合基因事件入手，采用生物信息學和分子生物學等研究手段，提供了橫紋肌肉瘤細胞起源的線索。這項研究發表在PNAS《美國科學院院刊》。文章第一作者(ZhongqiuXie)謝仲秋博士，通訊作者是美國佛吉尼亞大學醫學院（Hui Li）李輝。

　　本研究首次從融合基因的角度來研究腫瘤細胞的起源。在MSCs干細胞骨骼肌分化樣品中發現這些時間點樣品和橫紋肌肉瘤細胞RH30類似的融合基因組，這些腫瘤標志性融合基因如PAX3-FOXO1等都在干細胞分化過程中瞬時表達。而且至少有18種融合基因幾乎在同一時間點發生。這種瞬時的融合基因組發生事件提供了腫瘤細胞起源的新線索。(Hui Li)李輝實驗室近幾年在融合基因領域取得了很大進展：最先證明了RNA反式剪切（trans-splicing）會產生嵌合融合RNA（chimeric fusion RNAs）； 除了反式剪接外，相鄰基因之間的順式剪接（cis-SAGe）是產生基因間剪接的嵌合RNA的另一種機制；發現正常細胞以及幾乎所有器官和組織都會產生融合基因，而且具有很重要的生理功能；在間充質干細胞骨骼肌分化過程中發現可以瞬時產生橫紋肌肉瘤腫瘤標志性融合RNA和蛋白質（PAX3-FOXO1）， 使用這些腫瘤標志物來追蹤復雜癌癥的細胞起源； 首次提出了"融合基因組學"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.