PO.BCS01.03 · 生物信息与计算

利用vmwhere分析长读长测序数据揭示尤文肉瘤中微卫星长度和染色质状态的变异

Analysis of long-read sequencing data with vmwhere reveals variation in microsatellite length and chromatin state in Ewing sarcoma

编号 2685 展板 10 时间 4/20 02:00–05:00 区域 Section 1 主讲 Sara Peterson, BS;M Eng

分会场 Application of Bioinformatics to Cancer Biology 3

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作者与单位 Authors & Affiliations

Sara K. Peterson¹, A. McCauley Massie², Alex Rubinsteyn³, Jeremy R. Wang³, Ian J. Davis⁴

¹Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC,²Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC,³Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC,⁴Departments of Pediatrics and Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC

摘要 Abstract

中文摘要

微卫星（mSats），或短串联重复序列（STRs），是重复的1-6 bp DNA基序，在人类基因组中广泛分布。STR长度的变异有助于遗传多样性和结构变异，而超出致病阈值的扩增是近60种遗传疾病的基础。mSat重复还可作为转录调控因子的非经典增强子，包括通过结合尤文肉瘤的EWS::FLI1融合癌蛋白发挥作用。由于短读长测序的限制（包括读长和比对模糊性），mSats的全基因组分析一直受限。长读长测序改善了对这些区域的分析，但需要专门的算法。我们开发了一个计算流程，利用长读长纳米孔全基因组测序对四聚体mSats进行全基因组参考序列检测、长度基因分型、序列分解和可视化。我们将该方法应用于五个尤文肉瘤细胞系和100个不同的正常人群基因组中的GGAA mSats。我们发现EWS::FLI1与GGAA mSats的结合以及染色质可及性均与重复长度相关。比较分析揭示了一部分mSats（2-3%）在尤文肉瘤中相对于正常基因组发生了选择性扩增或收缩。尽管我们假设这种mSat长度变异会趋向于相似的重复长度，但我们发现扩增位点倾向于落在11至13之间，而收缩位点通常在4至6之间。此外，与相同和收缩的位点相比，扩增的mSats表现出最高比例的具有EWS::FLI1占据和可及染色质的mSats。最后，我们展示了表现出细胞系特异性染色质可及性获得或丧失的mSats分别与这些细胞中的扩增和收缩相关。这些结果揭示了尤文肉瘤中染色质可及mSats的选择性扩增，并为利用长读长测序解析人类疾病中mSats的遗传和结构复杂性提供了一个可推广的框架。

查看英文原文 English abstract

Microsatellites (mSats), or short tandem repeats (STRs), are repeated 1-6 bp DNA motifs that are abundantly distributed across the human genome. Variation in STR length contributes to genetic diversity and structural variation, and expansions beyond a pathogenic threshold underlie nearly 60 genetic disorders. mSat repeats can also serve as non-canonical enhancers for transcriptional regulators, including through binding the EWS::FLI1 fusion oncoprotein of Ewing sarcoma. Genome-wide analysis of mSats has been limited by short-read sequencing constraints, including read length and mapping ambiguity. Long-read sequencing has improved analyses of these regions but requires specialized algorithms. We developed a computational pipeline for genome-wide reference-based detection, length genotyping, sequence decomposition, and visualization of tetrameric mSats using long-read nanopore whole-genome sequencing. We applied this approach to GGAA mSats in five Ewing sarcoma cell lines and 100 diverse normal population genomes. We find both EWS::FLI1 binding to GGAA mSats and chromatin accessibility correlated with repeat length. Comparative analysis revealed a subset of mSats (2 - 3%) that were selectively expanded or contracted in Ewing sarcoma relative to normal genomes. Although we hypothesized that this variation in mSat length would converge towards a similar repeat length, we found that expanded loci tend to fall between 11 and 13 whereas contracted loci are commonly between 4 and 6. Further, expanded mSats demonstrated the highest proportion of mSats with EWS::FLI1 occupancy and accessible chromatin, compared to same and contracted. Finally, we show mSats demonstrating cell line-specific gained or lost chromatin accessibility was associated with expansion and contraction, respectively, in those cells. These results reveal a selective expansion of chromatin accessible mSats in Ewing sarcoma and provide a generalizable framework for resolving the genetic and structural complexity of mSats in human disease using long-read sequencing.

利益披露 Disclosure

S. K. Peterson, None.. A. M. Massie, None. A. Rubinsteyn, Pathfinder Oncology Other, Consulting. Decade Bio Other, Consulting. J. R. Wang, Oxford Nanopore Technologies Travel. I. J. Davis, Triangle Biotechnology Stock Option.

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