ICGC Pancreas: Genomic analysis reveals roles for chromatin modification and axonguidance in pancreatic cancer

Pancreatic cancer (PC) is the fourth leading cause of cancer death with an overall 5-year survival rate of < 5%, a statistic that has changed little in almost 50 years. A deeper understanding of the underlying molecular pathophysiology is expected to advance the urgent need to develop novel therapeutic and early detection strategies for this disease. Genomic characterisation of PC has previously relied on targeted PCR based exome sequencing of small cohorts of mixed primary and metastatic lesions propagated as xenografts or cell lines (Jones et al, Science 321:1801-1806), leaving the true mutational spectrum of the clinical disease largely unresolved. Here we use exome sequencing (https://www.ebi.ac.uk/ega/studies/EGAS00001000154) and copy number analysis (not submitted) to define genomic aberrations in a prospectively accrued clinical cohort (n = 142) of early (Stage I and II) pancreatic adenocarcinoma. Detailed analysis of 99 informative tumours identified 1982 non-silent mutations and 1628 significant CNV events, and defined 439 significantly mutated genes based on stringent Significant Mutated Gene or GISTIC analysis. Integration with functional data from in vitro shRNA and in vivo Sleeping Beauty-mediated somatic mutagenesis screens provided supportive evidence for 184 of these as candidate driver mutations. Pathway based analysis recapitulated clustering of mutations in core signalling pathways in PC, and identified multiple new components in each, particularly in DNA damage repair mechanisms (ATM, TOP2A, TLM, RPA1). We also identified frequent somatic aberrations in genes involved in novel mechanisms including chromatin modification (SWI/SNF complex members, SETD2, EPC1), and axon guidance (Semaphorin, Slit, Netrin and Ephrin signalling), extending the number of core perturbed pathways in PC. Aberrant expression of axon guidance genes co- segregated with poor patient survival, and in animal models was associated with disease development and progression, further implicating perturbation of the axon guidance pathway as a novel mechanism important in PC. This dataset includes gene expression data from 90 primary tumour samples, 88 of which were used in this manuscript for survival analysis. Much of this data is also available through the International Cancer Genome Consortium (ICGC) Data Portal (http://dcc/icgc.org), under the project code: "Pancreatic Cancer (QCMG, AU)". Access to the strictly restricted clinical data must be made through the ICGC Data Access Compliance Office (http://www.icgc.org/daco). This dataset contains expression array data from 90 primary pancreatic ductal adenocarcinoma samples. One sample is present with two biological replicates, all others have 1 biological replicate.

胰腺癌（Pancreatic cancer, PC）是第四大癌症致死病因，总体5年生存率低于5%，这一数据在近50年间几乎无明显变化。深入解析其潜在的分子病理生理学机制，有望推动该疾病新型治疗与早期检测策略的研发，满足该领域的迫切需求。此前胰腺癌的基因组表征研究，多依赖针对混合原发与转移性病灶、经异种移植瘤或细胞系传代培养的小队列的基于靶向PCR的外显子测序（exome sequencing）（Jones等，《Science》321:1801-1806），使得临床疾病的真实突变谱在很大程度上尚未明确。本研究通过外显子测序（https://www.ebi.ac.uk/ega/studies/EGAS00001000154）与拷贝数分析（copy number analysis，未提交数据），对142例前瞻性招募的早期（Ⅰ、Ⅱ期）胰腺腺癌临床队列（n=142）进行基因组畸变分析。对99例信息完整的肿瘤样本开展详细分析，共鉴定出1982个非同义突变与1628个显著拷贝数变异事件，并基于严格的显著突变基因（Significant Mutated Gene）或GISTIC分析，确定了439个显著突变基因。结合体外短发夹RNA（short hairpin RNA, shRNA）功能数据与体内睡美人（Sleeping Beauty）介导的体细胞诱变筛选结果，为其中184个候选驱动突变提供了佐证。基于通路的分析重现了胰腺癌核心信号通路的突变聚集特征，并在每条通路中鉴定出多个新组分，尤其是在DNA损伤修复机制（ATM、TOP2A、TLM、RPA1）中。本研究还发现了涉及新型调控机制的高频体细胞畸变，包括染色质修饰相关基因（SWI/SNF复合体成员、SETD2、EPC1）以及轴突导向相关基因（Semaphorin、Slit、Netrin和Ephrin信号通路），拓展了胰腺癌核心失调通路的数量。轴突导向基因的异常表达与患者不良预后显著相关，且在动物模型中与疾病发生发展密切相关，进一步证实轴突导向通路失调是胰腺癌发生发展中的重要新型机制。本数据集包含90例原发肿瘤样本的基因表达数据，其中88例被用于本文的生存分析。该数据集的大部分数据可通过国际癌症基因组联盟（International Cancer Genome Consortium, ICGC）数据门户（http://dcc/icgc.org）获取，项目代码为"Pancreatic Cancer (QCMG, AU)"。严格受限的临床数据需通过ICGC数据访问合规办公室（http://www.icgc.org/daco）申请获取。本数据集包含90例原发性胰腺导管腺癌样本的表达芯片数据，其中1例样本带有2份生物学重复，其余样本均为1份生物学重复。