三大杂志同时揭示胃肠癌中的跳跃基因

  近日刊登在Nature Medicine、Genome Research及PNAS上的三篇研究论文中，来自约翰霍普金斯大学等处的科学家们通过对人类癌症组织进行活检均发现了在许多胃肠癌发生期间患者机体所谓的LINE-1跳跃基因处于激活的状态；研究者指出，目前并没有证据表明，人类基因组常规元件中跳跃基因的插入可以引发人类患癌，但研究结果却表明这些转座子（跳跃基因）或许可以帮助作为早期癌症诊断的生物标志物。
  研究者重点关注LINE-1转座子的插入研究，该转座子自我复制并且将复制体插入到基因组中干扰正常的DNA序列。人类基因组中的转座子跳跃基因大约有17%都是由LINE-1拷贝组成的；此前研究者报道发现新型LINE-1的插入会促进抵御癌症的基因失活，但研究者并不清楚这种跳跃基因有多普遍，而且不知道其在癌症发生过程中的作用。
  Haig Kazazian博士说道，目前我们要克服的困难就是回答如何检测人类基因组中的新型LINE-1转座子。文章中研究者设计了一种新方法，可以利用强大的遗传测序工具来帮助寻找LINE-1，研究者分析了多种类型以及多个阶段的胃肠癌组织活检样本的转座子插入情况，同时结肠癌、胰腺癌及胃癌中发现的DNA插入情况同健康组织相比较，结果显示，在癌症发生阶段，依然处于移动状态的LINE-1转座子更趋于进行基因组的插入过程，比如研究者在结肠息肉中发现了29个新的插入位点，在来自7位胰腺癌患者的样本中发现了24个插入位点，在原发性癌症及转移性癌细胞中发现了13个插入位点，这就表明，在癌症发生转移之前LINE-1的插入现象就已经是发生了的。
  刊登在Nature Medicine的研究论文中，研究者重点对胰腺癌中的LINE-1的插入进行了研究，利用22份胰腺癌组织样本，研究者将正常组织、原发性肿瘤及转移性肿瘤样本进行了对比，结果发现在22份胰腺癌组织样本中就有21份样本中存在LINE-1的插入现象，而在健康组织中则没有LINE-1的插入，而且相比原发性肿瘤而言，转移性肿瘤或许存在更多的LINE-1插入情况，即转座子LINE-1的插入往往会随着癌症进展而频发。
  另外研究者还对食管癌中的LINE-1的插入进行了研究，结果发现在部分癌症样本中存在LINE-1的插入，但并不是所有barrett食管患者都会在15年以后发生癌症转移；研究者Kazazian说道，关键的问题就是是否LINE-1的插入会驱动癌症的发证或这是否其是癌症的产物，当然我们要回答这些问题就需要进行更多的研究，我们希望后期可以对个体细胞的基因组进行分析来解释是否癌细胞中LINE-1的插入在正常细胞中也会出现。
  跳跃基因LINE-1在癌症生物学中的角色渐渐凸现出来，相比健康细胞而言，胃肠癌细胞中LINE-1转座子处于活性状态，这获将帮助我们后期开发新型的检测手段来检测早期胃肠癌的发生。（转化医学网360zhyx.com）
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Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma
Nat Med    doi:10.1038/nm.3919
Nemanja Rodić, Jared P Steranka, Alvin Makohon-Moore, Allison Moyer, Peilin Shen, Reema Sharma, Zachary A Kohutek, Cheng Ran Huang, Daniel Ahn, Paolo Mita, Martin S Taylor, Norman J Barker, Ralph H Hruban, Christine A Iacobuzio-Donahue, Jef D Boeke & Kathleen H Burns
Pancreatic ductal adenocarcinoma (PDAC) is typically diagnosed after the disease has metastasized; it is among the most lethal forms of cancer. We recently described aberrant expression of an open reading frame 1 protein, ORF1p, encoded by long interspersed element-1 (LINE-1; L1) retrotransposon, in PDAC1. To test whether LINE-1 expression leads to somatic insertions of this mobile DNA, we used a targeted method to sequence LINE-1 insertion sites in matched PDAC and normal samples. We found evidence of 465 somatic LINE-1 insertions in 20 PDAC genomes, which were absent from corresponding normal samples. In cases in which matched normal tissue, primary PDAC and metastatic disease sites were available, insertions were found in primary and metastatic tissues in differing proportions. Two adenocarcinomas secondarily involving the pancreas, but originating in the stomach and duodenum, acquired insertions with a similar discordance between primary and metastatic sites. Together, our findings show that LINE-1 contributes to the genetic evolution of PDAC and suggest that somatic insertions are acquired discontinuously in gastrointestinal neoplasms.

LINE-1 expression and retrotransposition in Barrett’s esophagus and esophageal carcinoma
PNAS    doi: 10.1073/pnas.1502474112
Tara T. Doucet-O'Harea,b, Nemanja Rodićc, Reema Sharmac, Isha Darbaria, Gabriela Abrila, Jungbin A. Choia, Ji Young Ahna, Yulan Chengd, Robert A. Andersc, Kathleen H. Burnsa,c, Stephen J. Meltzerd,1, and Haig H. Kazazian, Jr.a,1
Barrett’s esophagus (BE) is a common disease in which the lining of the esophagus transitions from stratified squamous epithelium to metaplastic columnar epithelium that predisposes individuals to developing esophageal adenocarcinoma (EAC). We hypothesized that BE provides a unique environment for increased long-interspersed element 1 (LINE-1 or L1) retrotransposition. To this end, we evaluated 5 patients with benign BE, 5 patients with BE and concomitant EAC, and 10 additional patients with EAC to determine L1 activity in this progressive disease. After L1-seq, we confirmed 118 somatic insertions by PCR in 10 of 20 individuals. We observed clonal amplification of several insertions which appeared to originate in normal esophagus (NE) or BE and were later clonally expanded in BE or in EAC. Additionally, we observed evidence of clonality within the EAC cases; specifically, 22 of 25 EAC-only insertions were present identically in distinct regions available from the same tumor, suggesting that these insertions occurred in the founding tumor cell of these lesions. L1 proteins must be expressed for retrotransposition to occur; therefore, we evaluated the expression of open reading frame 1 protein (ORF1p), a protein encoded by L1, in eight of the EAC cases for which formalin-fixed paraffin embedded tissue was available. With immunohistochemistry, we detected ORF1p in all tumors evaluated. Interestingly, we also observed dim ORF1p immunoreactivity in histologically NE of all patients. In summary, our data show that somatic retrotransposition occurs early in many patients with BE and EAC and indicate that early events occurring even in histologically NE cells may be clonally expanded in esophageal adenocarcinogenesis.

Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution
Genome  Research    doi:10.1101/gr.196238.115
Adam D. Ewing1, Anthony Gacita2, Laura D. Wood3, Florence Ma2, Dongmei Xing3, Min-Sik Kim2, Srikanth S. Manda2, Gabriela Abril2, Gavin Pereira2, Alvin Makohon-Moore3, Leendert H. J. Looijenga4, Ad J. M. Gillis4, Ralph H. Hruban3, Robert A. Anders3, Katharine E. Romans2, Akhilesh Pandey2, Christine A. Iacobuzio-Donahue3, Bert Vogelstein5, Kenneth W. Kinzler5, Haig H. Kazazian2 and Szilvia Solyom2,6
Somatic L1 retrotransposition events have been shown to occur in epithelial cancers. Here, we attempted to determine how early somatic L1 insertions occurred during the development of gastrointestinal (GI) cancers. Using L1-targeted resequencing (L1-seq), we studied different stages of four colorectal cancers arising from colonic polyps, seven pancreatic carcinomas, as well as seven gastric cancers. Surprisingly, we found somatic L1 insertions not only in all cancer types and metastases, but also in colonic adenomas, well-known cancer precursors. Some insertions were also present in low quantities in normal GI tissues, occasionally caught in the act of being clonally fixed in the adjacent tumors. Insertions in adenomas and cancers numbered in the hundreds and many were present in multiple tumor sections implying clonal distribution. Our results demonstrate that extensive somatic insertional mutagenesis occurs very early during the development of GI tumors, probably before dysplastic growth.