Novel principles of gamma-retroviral insertional transcription activation in murine leukemia virus-induced end-stage tumors.
Novel principles of gamma-retroviral insertional transcription activation in murine leukemia virus-induced end-stage tumors.
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DOI：
10.1186/1742-4690-11-36
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发表时间：
2014-05-19
期刊：
影响因子：
3.3
通讯作者：
Pedersen FS
中科院分区：
文献类型：
--
作者：
Sokol M;Wabl M;Ruiz IR;Pedersen FS
逆转录病毒诱导的小鼠肿瘤的插入突变筛选已被证明在人类癌症研究和了解基于逆转录病毒的基因治疗的不良影响方面有价值。在以前的研究中，将小鼠的基因分配到单个逆转录病毒整合位点是基于基因组中目标位置的注释基因的紧密接近和表达模式。在这里，我们使用下一代RNA测序来绘制全基因组范围的逆转录病毒-小鼠嵌合连接图，并确定由小鼠白血病伽马逆转录病毒SL3-3诱导的T淋巴瘤中转录激活的局部模式。此外，为了确定逆转录病毒远程激活基因的表观遗传整合偏好，我们检测了来自2,000多只小鼠的终末期肿瘤的6,117个整合基因与常见的表观遗传增强子标记(H3K4me1和H3K27Ac)的共存倾向。我们发现了几种新的逆转录病毒插入突变机制：双向激活小鼠在前病毒相反侧的转录，包括未注释的小鼠序列的转录；位于相反DNA链上的基因的正/反义型激活；邻近同一DNA链上的远端基因的串联激活；非直接整合靶标的基因的激活；组合型插入突变，其中增强子激活、选择性嵌合剪接和逆转录病毒启动子插入由单一逆转录病毒诱导。我们还表明，无论到转录起始点的距离有多远，终末期肿瘤中的绝大多数逆转录病毒都与小鼠淋巴组织中的H3K4me1和H3K27Ac富集区共存。我们揭示了新的逆转录病毒诱导的宿主转录激活模式，这些模式超出了单个和最近的注释基因靶点。意识到这一先前未被描述的复杂性对于阐明基于逆转录病毒的基因治疗的不良反应可能被证明是重要的。我们还发现野生型伽马逆转录病毒经常定位在增强子上，这表明整合到调节区是特异的，也受到阳性选择的影响，以维持终末期肿瘤的远程基因激活。总之，这项研究应该被证明有助于推断逆转录病毒载体疗法的不良结果，并有助于理解基本的细胞调节原理和逆转录病毒生物学。
Insertional mutagenesis screens of retrovirus-induced mouse tumors have proven valuable in human cancer research and for understanding adverse effects of retroviral-based gene therapies. In previous studies, the assignment of mouse genes to individual retroviral integration sites has been based on close proximity and expression patterns of annotated genes at target positions in the genome. We here employed next-generation RNA sequencing to map retroviral-mouse chimeric junctions genome-wide, and to identify local patterns of transcription activation in T-lymphomas induced by the murine leukemia gamma-retrovirus SL3-3. Moreover, to determine epigenetic integration preferences underlying long-range gene activation by retroviruses, the colocalization propensity with common epigenetic enhancer markers (H3K4Me1 and H3K27Ac) of 6,117 integrations derived from end-stage tumors of more than 2,000 mice was examined. We detected several novel mechanisms of retroviral insertional mutagenesis: bidirectional activation of mouse transcripts on opposite sides of a provirus including transcription of unannotated mouse sequence; sense/antisense-type activation of genes located on opposite DNA strands; tandem-type activation of distal genes that are positioned adjacently on the same DNA strand; activation of genes that are not the direct integration targets; combination-type insertional mutagenesis, in which enhancer activation, alternative chimeric splicing and retroviral promoter insertion are induced by a single retrovirus. We also show that irrespective of the distance to transcription start sites, the far majority of retroviruses in end-stage tumors colocalize with H3K4Me1 and H3K27Ac-enriched regions in murine lymphoid tissues. We expose novel retrovirus-induced host transcription activation patterns that reach beyond a single and nearest annotated gene target. Awareness of this previously undescribed layer of complexity may prove important for elucidation of adverse effects in retroviral-based gene therapies. We also show that wild-type gamma-retroviruses are frequently positioned at enhancers, suggesting that integration into regulatory regions is specific and also subject to positive selection for sustaining long-range gene activation in end-stage tumors. Altogether, this study should prove useful for extrapolating adverse outcomes of retroviral vector therapies, and for understanding fundamental cellular regulatory principles and retroviral biology.
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影响因子：
3.7
作者：
Abel U;Deichmann A;Nowrouzi A;Gabriel R;Bartholomae CC;Glimm H;von Kalle C;Schmidt M
通讯作者：
Schmidt M
影响因子：
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作者：
Dong H;Luo L;Hong S;Siu H;Xiao Y;Jin L;Chen R;Xiong M
通讯作者：
Xiong M
影响因子：
5.4
作者：
Dabrowska, Magdalena Julia;Dybkaer, Karen;Pedersen, Finn Skou
通讯作者：
Pedersen, Finn Skou
影响因子：
6.4
作者：
Chang ST;Sova P;Peng X;Weiss J;Law GL;Palermo RE;Katze MG
通讯作者：
Katze MG
影响因子：
14.9
作者：
Eun B;Sampley ML;Good AL;Gebert CM;Pfeifer K
通讯作者：
Pfeifer K