颜林林 (2022-08-26 23:18):
#paper doi:10.1101/2022.08.24.505159 bioRxiv, 2022, A genome-wide atlas of recurrent repeat expansions in human cancer. 这篇来自斯坦福大学的Michael Snyder团队。通过重分析来自ICGC和TCGA的2622个癌症全基因组测序数据,涉及29个癌种,从中鉴定出160个重复序列扩张(recurrent repeat expansions, rRE)事件,且这些事件绝大多数都与特定癌症亚型相关。这些重复序列所处基因组区域,也富集在某些基因的调控元件附近,提示了它们在基因调控方面可能发挥作用。其中一个GAAA重复发生在UGT2B7基因的内含子中,在34%的肾细胞癌样本中都能观察到,于是通过斯坦福癌症中心入组了12例肾癌病例,对其样本开展了二代测序(Illumina NovaSeq)和三代测序(PacBio),验证了该rRE事件的发生。
A genome-wide atlas of recurrent repeat expansions in human cancer
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Abstract:
Expansion of a single repetitive DNA sequence, termed a tandem repeat (TR), is known to cause more than 50 diseases. However, repeat expansions are often not explored beyond neurological and neurodegenerative disorders. In some cancers, mutations accumulate in short tracts of TRs (STRs), a phenomenon termed microsatellite instability (MSI); however larger repeat expansions have not been systematically analyzed in cancer. Here, we identified TR expansions in 2,622 cancer genomes, spanning 29 cancer types. In 7 cancer types, we found 160 recurrent repeat expansions (rREs); most of these (155/160) were subtype specific. We found that rREs were non-uniformly distributed in the genome with an enrichment near candidate cis-regulatory elements, suggesting a role in gene regulation. One rRE located near a regulatory element in the first intron of UGT2B7 was detected in 34% of renal cell carcinoma samples and was validated by long-read DNA sequencing. Moreover, targeting cells harboring this rRE with a rationally designed, sequence-specific DNA binder led to a dose-dependent decrease in cell proliferation. Overall, our results demonstrate that rREs are an important but unexplored source of genetic variation in human cancers, and we provide a comprehensive catalog for further study.
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