Queen Mary University of London, Centre for Neuroscience and Trauma, Blizard Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, London, United Kingdom.
Genome Res. 2011 Apr;21(4):505-14. doi: 10.1101/gr.115782.110. Epub 2011 Mar 10.
Gene fusions involving members of the RAF family of protein kinases have recently been identified as characteristic aberrations of low-grade astrocytomas, the most common tumors of the central nervous system in children. While it has been shown that these fusions cause constitutive activation of the ERK/MAPK pathway, very little is known about their formation. Here, we present a detailed analysis of RAF gene fusion breakpoints from a well-characterized cohort of 43 low-grade astrocytomas. Our findings show that the rearrangements that generate these RAF gene fusions may be simple or complex and that both inserted nucleotides and microhomology are common at the DNA breakpoints. Furthermore, we identify novel enrichment of microhomologous sequences in the regions immediately flanking the breakpoints. We thus provide evidence that the tandem duplications responsible for these fusions are generated by microhomology-mediated break-induced replication (MMBIR). Although MMBIR has previously been implicated in the pathogenesis of other diseases and the evolution of eukaryotic genomes, we demonstrate here that the proposed details of MMBIR are consistent with a recurrent rearrangement in cancer. Our analysis of repetitive elements, Z-DNA and sequence motifs in the fusion partners identified significant enrichment of the human minisatellite conserved sequence/χ-like element at one side of the breakpoint. Therefore, in addition to furthering our understanding of low-grade astrocytomas, this study provides insights into the molecular mechanistic details of MMBIR and the sequence of events that occur in the formation of genomic rearrangements.
基因融合涉及 RAF 家族蛋白激酶成员，最近被确定为低级别星形细胞瘤的特征性异常，低级别星形细胞瘤是儿童中枢神经系统最常见的肿瘤。虽然已经表明这些融合导致 ERK/MAPK 通路的组成性激活，但对于它们的形成知之甚少。在这里，我们对来自一个特征明确的 43 例低级别星形细胞瘤队列的 RAF 基因融合断点进行了详细分析。我们的研究结果表明，产生这些 RAF 基因融合的重排可能是简单的或复杂的，并且在 DNA 断点处插入的核苷酸和微同源性都很常见。此外，我们还确定了在断点侧翼区域中存在新的微同源序列富集。因此，我们提供了证据表明，这些融合所负责的串联重复是由微同源介导的断裂诱导复制（MMBIR）产生的。尽管 MMBIR 先前已被牵连到其他疾病的发病机制和真核基因组的进化中，但我们在此证明，MMBIR 的提议细节与癌症中的反复重排一致。我们对重复元件、Z-DNA 和融合伙伴中的序列基序的分析表明，在断点的一侧存在人类微卫星保守序列/χ 样元件的显著富集。因此，除了进一步了解低级别星形细胞瘤外，这项研究还深入了解了 MMBIR 的分子机制细节以及基因组重排形成过程中发生的事件序列。
