RNAseq analysis on metastatic Colorectal Cancer

In this study we want present a bank of metastatic colorectal cancer (mCRC) Patient Derived Organoids (PDOs) obtained from Patient Derived Xenografts (PDXs). These models are annotated with different omics to advance our understanding of CRC. We wanted to create a resource for the scientific community to assess the predictive reliability of these preclinical models. We performed comparative analyses between PDOs and matched PDXs to assess the similarities of these two platforms regarding molecular profiles and transcriptional classification. Moreover, we analyzed how these models respond to Cetuximab, a chimeric monoclonal antibody, normally given to patients after chemotherapy, that inhibits EGFR. After having assessed models’ reliability with Cetuximab, we aimed at identifying potential synergistic drugs to individuate new possible therapeutic prospects. Transcriptional profiles were obtained with RNA sequencing – we aligned reads with STAR on a hybrid human-mouse genome, in order to remove the mouse derived reads without requiring a pre-filtering step. Reads were assigned to human genes with FeatureCounts, then we used DESeq2 to obtain normalized expression values and perform differential expression analyses. All analytical pipelines have been implemented with Snakemake as a workflow management system, to ensure portability and reproducibility. ---------------------------------------------- Authors state the following "Raw data with reads from our samples need controlled access, since they derive from human tumors." ---------------------------------------------- Clarification for columns “cell type”, “cell line” and “treatment”. The column “cell type” defines the type of samples LM: liver metastasis PR: primary (from colon) The column “cell line” defines the origin of samples H: patients X: xenografts O: organoids The column “treatment” describes the experiments done with cetuximab cetuxi: treated samples (72h (written as h) or 6w for xenografts) NT: non-treated control The word “basale” indicates xenografts or organoids grown in normal conditions. They are not the non-treated control of the cetuximab experiments.

本研究旨在构建一套源自患者来源异种移植模型（Patient Derived Xenografts, PDXs）的转移性结直肠癌（metastatic colorectal cancer, mCRC）患者来源类器官（Patient Derived Organoids, PDOs）资源库。本研究对这些模型进行多组学注释，以加深对结直肠癌（colorectal cancer, CRC）的认知。我们旨在为科研群体提供一套可用于评估此类临床前模型预测可靠性的研究资源。我们对类器官（PDOs）与配对异种移植模型（PDXs）开展比较分析，以评估这两类模型平台在分子谱特征与转录组分类方面的相似性。此外，我们分析了这些模型对西妥昔单抗（Cetuximab）的应答情况：西妥昔单抗是一种嵌合单克隆抗体，通常用于化疗后患者，可抑制表皮生长因子受体（epidermal growth factor receptor, EGFR）。在通过西妥昔单抗评估模型可靠性后，本研究旨在筛选潜在协同药物，以发掘全新的治疗方向。
转录组谱通过RNA测序获取：我们将测序读段（reads）与STAR工具比对至人-鼠混合基因组，以此在无需预过滤步骤的前提下去除小鼠来源的读段。我们使用FeatureCounts工具将读段注释至人类基因，随后借助DESeq2工具获取标准化表达量并开展差异表达分析。所有分析流程均以Snakemake作为工作流管理系统构建，以确保分析的可移植性与可重复性。
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作者作出如下声明："本研究样本的测序读段原始数据需受控访问，因其源自人类肿瘤组织。"
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以下对"细胞类型""细胞系"与"处理方式"三列进行说明：
"细胞类型"列用于定义样本类型：LM为肝转移灶（liver metastasis），PR为原发结直肠癌灶（源自结肠，primary (from colon)）；
"细胞系"列用于定义样本来源：H为患者样本，X为异种移植模型，O为类器官模型；
"处理方式"列用于说明西妥昔单抗相关实验分组：cetuxi为经西妥昔单抗处理的样本（对于异种移植模型，处理时长为72小时即标注为h，或6周）；NT为未处理对照组；
"basale"（基础组）指在正常培养条件下生长的异种移植模型或类器官模型，其并非西妥昔单抗实验中的未处理对照组。