Modeling the effect of prolonged ethanol exposure on global gene expression and chromatin accessibility in normal 3D colon organoids

In this study we aimed to explore the potential biological effect of ethanol exposure on healthy colon epithelial cells using normal human colon 3D organoid “mini-gut” cultures. In numerous published studies ethanol use has been shown to be an environmental risk factor for colorectal cancer (CRC) development; however, the influence of ethanol exposure on normal colon epithelial cell biology remains poorly understood. We investigated the potential molecular effects of ethanol exposure in normal colon 3D organoids in a small pilot study (n = 3) using RNA-seq and ATAC-seq. We identify 1965 differentially expressed genes and 2217 differentially accessible regions of chromatin in response to ethanol treatment. Further, by cross-referencing our results with previously published analysis in colorectal cancer cell lines, we have not only validated a number of reported differentially expressed genes, but also identified several novel candidates for future investigation. In summary, our data highlights the potential importance for the use of normal colon 3D organoid models as a novel tool for the investigation of the relationship between the effects of environmental risk factors associated with colorectal cancer and the molecular mechanisms through which they confer this risk.本研究旨在利用正常人类结肠3D类器官（3D organoid）“迷你肠道”培养体系，探究乙醇暴露对健康结肠上皮细胞的潜在生物学效应。既往多项已发表研究已证实，乙醇摄入是结直肠癌（colorectal cancer, CRC）发生的环境危险因素；但目前学界对乙醇暴露对正常结肠上皮细胞生物学特性的影响仍知之甚少。本研究通过一项小型预实验（n=3），利用RNA测序（RNA-seq）与转座酶可及性染色质测序（ATAC-seq）技术，探究了乙醇暴露对正常结肠3D类器官的潜在分子效应。研究共鉴定出1965个差异表达基因以及2217个响应乙醇处理的染色质差异可及区域。进一步地，本研究将所得结果与既往结直肠癌细胞系的已发表分析结果进行交叉比对，不仅验证了多篇报道中提及的差异表达基因，还鉴定出若干可供后续研究的新型候选靶点。综上，本研究数据凸显了正常结肠3D类器官模型作为新型研究工具的潜在应用价值，可用于探究结直肠癌相关环境危险因素的效应与其介导该风险的分子机制之间的关联。