Medical Oncology Department, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium; Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium.
Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, Paris, France.
Gastroenterology. 2018 Dec;155(6):1999-2013.e3. doi: 10.1053/j.gastro.2018.08.033. Epub 2018 Aug 27.
BACKGROUND & AIMS: Genomic studies have revealed subtypes of pancreatic ductal adenocarcinoma (PDA) based on their molecular features, but different studies have reported different classification systems. It is a challenge to obtain high-quality, freshly frozen tissue for clinical analysis and determination of PDA subtypes. We aimed to redefine subtypes of PDA using a large number of formalin-fixed and paraffin-embedded PDA samples, which are more amenable to routine clinical evaluation.
We collected PDA samples from 309 consecutive patients who underwent surgery from September 1996 through December 2010 at 4 academic hospitals in Europe; nontumor tissue samples were not included. Samples were formalin fixed and paraffin embedded. DNA and RNA were isolated; gene expression, targeted DNA sequencing, and immunohistochemical analyses were performed. We used independent component analysis to deconvolute normal, tumor, and microenvironment transcriptome patterns in samples. We devised classification systems from an unsupervised analysis using a consensus clustering approach of our data set after removing normal contamination components. We associated subtypes with overall survival and disease-free survival of patients using Cox proportional hazards regression with estimation of hazard ratios and 95% confidence interval. We used The Cancer Genome Consortium and International Cancer Genome Consortium PDA data sets as validation cohorts.
We validated the previously reported basal-like and classical tumor-specific subtypes of PDAs. We identified features of the PDA, including microenvironment gene expression patterns, that allowed tumors to be categorized into 5 subtypes, called pure basal like, stroma activated, desmoplastic, pure classical, and immune classical. These PDA subtypes have features of cancer cells and immune cells that could be targeted by pharmacologic agents. Tumor subtypes were associated with patient outcomes, based on analysis of our data set and the International Cancer Genome Consortium and The Cancer Genome Consortium PDA data sets. We also observed an exocrine signal associated with acinar cell contamination (from pancreatic tissue).
We identified a classification system based on gene expression analysis of formalin-fixed PDA samples. We identified 5 PDA subtypes, based on features of cancer cells and the tumor microenvironment. This system might be used to select therapies and predict patient outcomes. We found evidence that the previously reported exocrine-like (called ADEX) tumor subtype resulted from contamination with pancreatic acinar cells. ArrayExpress accession number: E-MTAB-6134.
基于分子特征，基因组研究已经揭示了胰腺导管腺癌（PDA）的亚型，但不同的研究报告了不同的分类系统。获得高质量、新鲜冷冻的组织进行临床分析和确定 PDA 亚型是一项挑战。我们旨在使用大量的福尔马林固定和石蜡包埋的 PDA 样本重新定义 PDA 的亚型，这些样本更适合常规临床评估。
我们收集了 1996 年 9 月至 2010 年 12 月在欧洲 4 家学术医院接受手术的 309 例连续患者的 PDA 样本；未包括非肿瘤组织样本。样本经过福尔马林固定和石蜡包埋。提取 DNA 和 RNA；进行基因表达、靶向 DNA 测序和免疫组织化学分析。我们使用独立成分分析来解卷积样本中的正常、肿瘤和微环境转录组模式。我们使用无监督分析，通过一致聚类方法对我们的数据进行分类，并在去除正常污染成分后设计分类系统。我们使用 Cox 比例风险回归和危险比及 95%置信区间的估计值，将亚型与患者的总生存率和无病生存率相关联。我们使用癌症基因组联合会和国际癌症基因组联合会 PDA 数据集作为验证队列。
我们验证了先前报道的基底样和经典肿瘤特异性 PDA 亚型。我们确定了 PDA 的特征，包括微环境基因表达模式，这些特征使肿瘤能够分为 5 种亚型，称为纯基底样、基质激活、纤维组织增生、纯经典和免疫经典。这些 PDA 亚型具有可被药物靶向的癌细胞和免疫细胞的特征。基于我们的数据集中的分析以及国际癌症基因组联合会和癌症基因组联合会 PDA 数据集，肿瘤亚型与患者的预后相关。我们还观察到与胰腺腺泡细胞污染（来自胰腺组织）相关的外分泌信号。
我们基于福尔马林固定 PDA 样本的基因表达分析确定了一种分类系统。我们根据癌细胞和肿瘤微环境的特征确定了 5 种 PDA 亚型。该系统可用于选择治疗方法并预测患者预后。我们发现证据表明，先前报道的外分泌样（称为 ADEX）肿瘤亚型是由胰腺腺泡细胞污染引起的。ArrayExpress 注册号：E-MTAB-6134。
