背景：胰腺癌(PDAC)是全世界最致命的恶性肿瘤之一，超过90%的胰腺肿瘤是起源于胰腺导管上皮的腺癌。结构变异(SVs)是基因组变异的最大来源，可导致肿瘤的发生。然而，由于技术上的限制，深入了解胰腺癌中的SVs变异图谱及其在胰腺癌发生发展中发挥的作用，仍在很大程度上有待探索。

方法：HPDE6-C7和人胰腺癌细胞系PANC1和BxPC3均取自ATCC，采用长读单分子实时测序技术(SMRT)系统研究并分析了胰腺癌细胞SVs的特征，并确定了直接影响人类胰腺癌中癌症相关基因的致病SVs。利用转录组测序技术（RNA-seq）表征了胰腺癌细胞系的转录谱。从公共数据库（cBioportal TCGA、the Cancer Genome Atlas、GEO等）中获取胰腺癌增强子活性、基因表达水平和临床预后数据集，以验证上述调控的相关性或生物学意义。统计分析方法应用秩和检验和fisher检验来确定转录组和SVs数据之间的关系。基因表达比较，数据以四分位范围(IQR)与中位数表示，p值采用Wilcoxon秩和检验或Kruskal-Wallis检验。构成比的比较采用卡方检验或fisher精确检验。在生物过程富集分析中，P值是用富化r进行Fisher精确检验得到的。Kaplan-Meier生存分析采用R(版本3.6.3)中的Cox回归获得P值，认为p < 0.05时差异显著。

结果：本研究首次揭示了人类胰腺癌的整体结构变异谱，这将为全面研究胰腺癌中SVs的发病机制提供有价值的资源。分析3D基因组中SVs的分布情况发现，在A/B compartment或CD水平上，SVs的发生与肿瘤中的3D染色体结构存在一定的相关性。此外，SVs在3D基因组中的分布模式具有高度的细胞类型特异性。同时，本研究还重点分析并研究了关键驱动基因CDKN2A纯合缺失对胰腺癌3D基因组结构和基因表达的影响，详细阐述了CDKN2A在胰腺癌发生发展中所发挥的作用，表明CDKN2A纯合缺失与胰腺癌中MIR31HG表达上调有关，这可能与CDKN2A纯合缺失的相邻基因组区域的扩增和CD融合有关，并从线性和3D角度分别阐明了CDKN2A对癌症相关基因表达的影响，为理解CDKN2A的失活从而驱动胰腺癌的发生和发展提供了新的见解。

结论：这项工作较为全面的提供了胰腺癌全基因组水平上的研究资源，突出了SVs与3D基因组之间相互作用的影响、复杂性和动态性，并进一步拓展了对SVs在人类胰腺癌发病机制中的理解。

Background: Structural variations (SVs) are the greatest source of variation in the genome and can lead to oncogenesis. However, the identification and interpretation of SVs in human pancreatic cancer remain largely undefined due to technological limitations.

Methods: The signatures of SVs in pancreatic cancer cell were first investigated by long-read single-molecule real-time (SMRT) sequencing technology and the pathogenetic SVs that directly affect cancer-related genes in human pancreatic cancer were identified. Transcription profile were characterized using transcriptome sequencing techniques. Enhancer activity, expressional level and clinical prognosis datasets were acquired from public databases to validate above regulatory correlation or biological significance.

Results: The global structural variation spectrum in human pancreatic cancer were first revealed. Meanwhile, the 3D chromatin architecture was also depicted and undergone widespread remodeling accompanied with gene expressional changes. The distributions of SVs among 3D genome architectures presented a strong cell type specificity. The study identified and further explored the impacts of cross-boundary SVs and found that the bulk remodeling effect observed in the 3D genome partly depends on intercellular genomic heterogeneity resulting from discrepancy of SV frequency. Moreover, the data also demonstrated complex genomic rearrangements involved in key driver genes CDKN2A, and elucidated its influence on cancer-related gene expression from both linear view and 3D perspective.

Conclusion: Overall, this study highlights the impact, complexity and dynamicity of the interplay between SVs and 3D genome organization and further expands our understanding of pathogenesis of SVs in human pancreatic cancer.