Transcriptomic analysis of patient-derived ex vivo models of pancreatic cancer

The aim of this study is to compare the transcriptomic profiles of various ex vivo models of pancreatic cancer. First, primary tumours and their corresponding xenografts in nude mice were analysed by RNA-seq. Monocultures of pancreatic cancer cells derived from the xenografts were then prepared as 2D monolayers, Matrigel-embedded organoids, spheres in suspension and 3D cultures in self-assembling peptide amphiphile (PA) hydrogels. Seven-day cultures were then analysed by RNA-seq. The results suggest that all ex vivo monocultures retain patient-specific transcriptional profiles, especially cancer stem cell signatures, while being deficient in the expression of stromal components such as the core matrisome. Correlations with the primary tumours were generally higher in PA hydrogels than organoids. Biased gene expression signatures were identified in certain models. This is the first study to explore the transcriptomic signatures of four different ex vivo models matched to their primary tumours of origin. Overall design: 29 patient-matched pancreatic adenocarcinoma (PDAC) samples were analysed: three primary PDAC tumour samples, six PDAC monocultures in PA (3 patients, duplicates), six PDAC organoid monocultures in Matrigel (3 patients, duplicates), six PDAC monocultures in 2D (3 patients, duplicates), six PDAC monocultures in suspension (3 patients, duplicates), and two primary patient-derived xenografts in grown in nude mice.

本研究旨在对比多种胰腺癌体外模型的转录组谱。首先，采用RNA测序（RNA-seq）技术对原代肿瘤及其在裸鼠中的对应异种移植瘤进行转录组分析。随后，将源自异种移植瘤的胰腺癌细胞制备为四类单培养体系：二维单层培养、基质胶（Matrigel）包埋类器官培养、悬浮球体培养，以及自组装两亲性肽（peptide amphiphile, PA）水凝胶三维培养。对培养7天的各模型样本实施RNA测序分析。研究结果表明，所有体外单培养模型均保留了患者特异性的转录组特征，尤以癌症干细胞特征显著，但普遍缺乏基质成分（如核心基质组）的表达。各模型与原发肿瘤的转录组相关性以PA水凝胶培养模型为最高，普遍高于类器官模型。部分单培养模型存在偏倚的基因表达特征。本研究为首次探索四类与原发肿瘤匹配的不同体外模型转录组特征的相关工作。实验总体设计：本研究共纳入29例患者匹配的胰腺腺癌（PDAC）样本进行分析，具体包括：3例原发胰腺腺癌肿瘤样本；6例PA水凝胶三维单培养样本（来自3例患者，各设生物学重复）；6例基质胶包埋类器官单培养样本（来自3例患者，各设生物学重复）；6例二维单层单培养样本（来自3例患者，各设生物学重复）；6例悬浮球体单培养样本（来自3例患者，各设生物学重复）；以及2例在裸鼠体内构建的患者来源异种移植瘤样本。