在人类乳腺癌中可移植元素的替代拼接
Alex Nesta1,2, Diogo F T Veiga3, Jacques Banchereau1,4
1The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA.
bioRxiv : the preprint server for biology
|October 10, 2024
概括
可移植元素 (TE) 通过创造新的拼接事件和改变基因表达,显著影响乳腺癌转录组. 长读测序揭示了TE驱动的异型,这些异型可能作为新的治疗点或生物标志物.
科学领域:
- 基因组学就是基因组学.
- 分子生物学分子生物学
- 癌症研究 癌症研究
背景情况:
- 可转移元素 (TE) 是移动DNA序列,影响基因组进化和基因调节.
- 癌症中TE的失调会导致异常的基因表达和转录基因变异.
- 乳腺癌转录组是复杂的,受到各种遗传和表观遗传因素的影响.
研究的目的:
- 通过长读RNA测序 (LR-seq) 研究可移植元素对乳腺癌转录组的影响.
- 识别和描述TE驱动的异型及其对乳腺癌中新型拼接事件的贡献.
- 探索TE媒介拼接事件与乳腺癌亚型,患者存活率和RNA编辑的关联.
主要方法:
- 利用长读RNA测序 (LR-seq) 来分析30个乳腺样本中的142514个全长异型.
- 在1,135个乳腺瘤 (TCGA) 和1,329个健康组织 (GTEx) 中,TE重叠异型的量化拼接事件.
- 确定了TE驱动的转录起点,TE介导的剪接事件和RNA编辑签名在全长异型中.
主要成果:
- 大约50%的分析异构体含有TE序列,导致一半的新拼接连接.
- 发现了300个TE重叠的瘤特异拼接事件,其中一些丰富于特定的乳腺癌亚型 (例如,HER2+瘤).
- 确定了与患者存活率和不良预后相关的TE媒介拼接事件,以及数千种具有RNA编辑特征的异构体,包括一种新的RHOA异构体.
结论:
- 失调的可转移元素对乳腺癌转录组有广泛的影响.
- 长时间读取的异型序列测序对于理解TE生物学及其在癌症中的作用是有利的.
- TE衍生异型代表潜在的新型,疾病特异性治疗点或乳腺癌的生物标志物.
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