Inflation-collapse dynamics drive patterning and morphogenesis in intestinal organoids. Inflation-collapse dynamics drive patterning and morphogenesis in intestinal organoids

We apply single cell RNA-sequencing (scRNA-seq) to murine intestinal organoids in two experiments: 1) Comparing the transcriptomic landscape of organoids cultured in dome and sandwich culture systems (as described in the accompanying paper for this GEO submission), and 2) Assessing the transcriptomic landscape of organoids perturbed with CFTRinh-172 to inhibit inflation events, and with Forskolin to activate inflation events in the sandwich culture system, with respective controls. We find that the dome and sandwich culture systems produce similar abundance levels of each major specialized cell type, with similar marker gene expression shared across culture types. We find in the perturbation experiments a stretch-responsive cell state, similar in gene expression to several previously reported cell states, which is significantly more abundant in the Forskolin treated organoids compared to controls, and significantly less abundant in CFTRinh-172 treated organoids compared to controls. Additionally, we find that Stem and Enterocyte cell states are respectively, significantly less abundant, and more abundant in the Forskolin treated organoids compared to controls. Overall design: Examination of transcriptomic landscapes of two murine intestinal organoid culture types: dome and sandwich culture systems; examination of transcriptomic landscape changes in murine intestinal organoids as a result of inflation perturbations.

本研究针对小鼠肠道类器官开展两项单细胞RNA测序（single cell RNA-sequencing, scRNA-seq）实验：1）比较在dome培养与sandwich培养体系中培养的类器官的转录组图谱，相关细节已见于本GEO提交的配套论文；2）在sandwich培养体系中，分别以CFTRinh-172抑制膨胀事件、佛司可林（Forskolin）激活膨胀事件处理类器官，并设置相应对照组，评估其转录组图谱。
研究发现，dome培养与sandwich培养体系所产生的各主要特化细胞类型丰度水平相近，且两类培养体系中共有的标记基因表达模式相似。在扰动实验中，我们发现了一种牵张响应性细胞状态，其基因表达特征与此前报道的多种细胞状态相似；相较于对照组，该细胞状态在佛司可林处理的类器官中丰度显著升高，而在CFTRinh-172处理的类器官中丰度显著降低。此外，相较于对照组，佛司可林处理的类器官中干细胞（Stem）与肠上皮细胞（Enterocyte）细胞状态的丰度分别显著降低与显著升高。
实验整体设计：检测两类小鼠肠道类器官培养体系（dome与sandwich培养体系）的转录组图谱；并探究膨胀扰动对小鼠肠道类器官转录组图谱的影响。