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在癌症中绘制集群突变显示了ecDNA的APOBEC3突变
Erik N Bergstrom1,2,3, Jens Luebeck4,5, Mia Petljak6
1Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
Nature
|February 10, 2022
概括
这项研究全面分析了2583个癌症基因组中的集群突变,揭示了多种突变过程及其与癌症驱动基因和患者生存的联系. APOBEC3在促进染色体外DNA进化方面发挥着关键作用.
科学领域:
- 基因组学
- 癌症生物学
- 突变的签名
背景情况:
- 在癌症基因组中,集群体突变,包括替代和内基因突变,很普遍.
- 之前的研究发现了像omikli和kataegis这样的特定类型,但缺乏跨不同癌症的综合性特征.
研究的目的:
- 在30种癌症类型的大群中全面描述集群替代和小插入/删除 (indels).
- 研究集群突变与驱动基因,基因表达和患者生存的关联.
- 阐明各种集群突变类型的独特突变过程,包括omikli,kataegis和新发现的kyklona.
主要方法:
- 来自30种癌症样本的2583个全基因组测序.
- 生物信息分析以识别和表征集体体突变 (替代和内基).
- 关联分析将突变模式与基因特征,基因表达,生存数据和已知的突变过程 (例如吸烟,APOBEC3) 联系起来.
主要成果:
- 聚类突变在驱动基因中显著丰富,并与差异性基因表达和改变患者存活率有关.
- 对于集群的体,已经确定了多种不同的突变过程,其中一些与吸烟和同源重组缺乏有关.
- 双基替代产生的至少12个过程,而多基替代主要与吸烟或紫外线有关.
- 尽管只有16.2%的事件与APOBEC3模式相匹配,但Omikli事件在很大程度上归因于APOBEC3.
- 卡塔吉斯事件是由多个过程引起的,其中76. 1%与AID和APOBEC3脱氨酶有关.
- 在31%的ecDNA阳性样本中发现了一种新型的APOBEC3 kataegis和异染色体DNA (ecDNA) 的同时存在.
- 携带癌症基因的ecDNA显示出阳性选择和基因突变,表明它在癌症进化中的作用.
结论:
- 人类癌症表现出各种各样的集群突变过程.
- APOBEC3活动是重复突变的重要驱动因素,并通过基克隆等过程推动了ecDNA的演变.
- 了解这些聚类突变模式可以了解癌症的发展和潜在的治疗策略.
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