Insertional mutagenesis and deep profiling reveals gene hierarchies and a Myc/p53-dependent bottleneck in lymphomagenesis.
Insertional mutagenesis and deep profiling reveals gene hierarchies and a Myc/p53-dependent bottleneck in lymphomagenesis.
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DOI：
10.1371/journal.pgen.1004167
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发表时间：
2014-02
期刊：
影响因子：
4.5
通讯作者：
Neil JC
中科院分区：
文献类型：
--
作者：
Huser CA;Gilroy KL;de Ridder J;Kilbey A;Borland G;Mackay N;Jenkins A;Bell M;Herzyk P;van der Weyden L;Adams DJ;Rust AG;Cameron E;Neil JC
逆转录病毒插入突变（RIM）是癌症基因组学的有力工具，本研究将其与深度测序（RIM/DS）相结合，以促进对淋巴瘤进展的全面分析。在生殖系中表达两种有效协作癌基因的转基因小鼠（CD 2-MYC，-Runx 2）发展出快速发病的肿瘤，其可以通过新生儿莫洛尼鼠白血病病毒（MoMLV）感染加速并呈现多克隆。28个多克隆淋巴瘤的RIM/DS分析确定了771个共同插入位点（CIS），定义了一个“进展网络”，包括一个非常大的部分已知的MoMLV靶基因，进一步强烈的致癌选择的迹象高于背景的MoMLV整合偏好。由RIM驱动的进展被表征为克隆竞争的达尔文过程，其参与细胞因子和T细胞受体信号传导下游的增殖控制网络。增强子模式激活占最有效地选择CIS靶基因，包括Ccr 7作为驱动旁分泌生长刺激和淋巴瘤传播的一组趋化因子受体中最突出的。另一个大的靶基因子集，包括候选肿瘤抑制基因被基因内插入破坏。比较野生型和亲本转基因淋巴瘤的第二个RIM/DS筛选显示，CD 2-MYC肿瘤实际上依赖于Runx家族基因的激活，强烈优先于其他有效的Myc协作基因（Gfi 1，Notch 1）。Ikzf 1被鉴定为Runx 2的一个新的协作基因，并阐明了整合偏好和致癌选择之间的界面。MoMLV的淋巴瘤靶基因可分为（a）一小组赋予自我更新的主调节因子;克服p53和其他故障安全途径;和（B）一大组控制转化细胞中自主增殖的进展基因。这些发现为逆转录病毒生物学，人类癌症遗传学和载体介导的基因治疗的安全性提供了见解。已知癌症是由一系列突变和非突变（表观遗传）事件引起的，但癌症基因组测序的出现突出了将重要（驱动）突变与不相关（乘客）突变分开的日益增长的挑战。逆转录病毒通过插入宿主DNA从而改变关键基因来诱发癌症，这是一种有价值的工具，因为它们可以作为“标签”来识别关键靶点。在这项研究中，我们结合逆转录病毒标记与下一代测序，以实现一个全面的描述淋巴瘤的发展和进展的转基因小鼠模型系统。我们的研究表明，三个事件可能足以淋巴瘤的发展，并确定了一个小的基因集，调节肿瘤细胞自我更新，包括Myc癌基因和p53肿瘤抑制基因的遗传瓶颈。相反，许多基因可以提供淋巴瘤细胞获得独立于外部刺激分裂的能力的最后一步。由于许多靶基因是保守的，并在非病毒起源的癌症中发挥作用，这项研究可能为癌症生物学基础的基因相互作用提供一个范例。它还阐明了在最近使用的逆转录病毒为基础的人类基因治疗载体所带来的风险。
Retroviral insertional mutagenesis (RIM) is a powerful tool for cancer genomics that was combined in this study with deep sequencing (RIM/DS) to facilitate a comprehensive analysis of lymphoma progression. Transgenic mice expressing two potent collaborating oncogenes in the germ line (CD2-MYC, -Runx2) develop rapid onset tumours that can be accelerated and rendered polyclonal by neonatal Moloney murine leukaemia virus (MoMLV) infection. RIM/DS analysis of 28 polyclonal lymphomas identified 771 common insertion sites (CISs) defining a ‘progression network’ that encompassed a remarkably large fraction of known MoMLV target genes, with further strong indications of oncogenic selection above the background of MoMLV integration preference. Progression driven by RIM was characterised as a Darwinian process of clonal competition engaging proliferation control networks downstream of cytokine and T-cell receptor signalling. Enhancer mode activation accounted for the most efficiently selected CIS target genes, including Ccr7 as the most prominent of a set of chemokine receptors driving paracrine growth stimulation and lymphoma dissemination. Another large target gene subset including candidate tumour suppressors was disrupted by intragenic insertions. A second RIM/DS screen comparing lymphomas of wild-type and parental transgenics showed that CD2-MYC tumours are virtually dependent on activation of Runx family genes in strong preference to other potent Myc collaborating genes (Gfi1, Notch1). Ikzf1 was identified as a novel collaborating gene for Runx2 and illustrated the interface between integration preference and oncogenic selection. Lymphoma target genes for MoMLV can be classified into (a) a small set of master regulators that confer self-renewal; overcoming p53 and other failsafe pathways and (b) a large group of progression genes that control autonomous proliferation in transformed cells. These findings provide insights into retroviral biology, human cancer genetics and the safety of vector-mediated gene therapy. Cancers are known to arise by a series of mutational and non-mutational (epigenetic) events but the advent of cancer genome sequencing highlights the growing challenge of separating important (driver) from irrelevant (passenger) mutations. Retroviruses that induce cancer by inserting into host DNA and thereby altering key genes are valuable tools because they act as ‘tags’ to identify the critical targets. In this study we combined retroviral tagging with next generation sequencing to achieve a comprehensive description of lymphoma development and progression in transgenic mouse model systems. Our study suggests that three events may be sufficient for lymphoma development and identifies a genetic bottleneck at a small gene set that regulates tumour cell self-renewal, including the Myc oncogene and the p53 tumour suppressor. In contrast, many genes can provide the final step where the lymphoma cell acquires the ability to divide independently of external stimuli. As many of the target genes are conserved and play roles in cancers of non-viral origin, this study may provide a paradigm for the gene interactions that underlie cancer biology. It also elucidates the risks entailed in the recent use of retrovirus-based vectors for human gene therapy.
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影响因子：
5.4
作者：
Hanlon, L;Barr, NI;Neil, JC
通讯作者：
Neil, JC
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作者：
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作者：
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通讯作者：
Wessels LF