Gene expression profiles of mouse derived esophagus and stomach epithelial stem cells 3D organoids

The gastroesophageal squamocolumnar junction (GE-SCJ) is a critical tissue interface between the esophagus and stomach, with significant relevance in the pathophysiology of gastrointestinal diseases. Despite this, the molecular mechanisms underlying GE-SCJ development remain unclear. Using single-cell transcriptomics, organoids, and spatial analysis, we examine the cellular heterogeneity and spatiotemporal dynamics of GE-SCJ development from embryonic to adult mice. We identify distinct transcriptional states and signaling pathways in the epithelial and mesenchymal compartments of the esophagus and stomach during development. Fibroblast-epithelial interactions are mediated by various signaling pathways, including WNT, BMP, TGF-β, FGF, EGF, and PDGF. Our results suggest that fibroblasts predominantly send FGF and TGF-β signals to the epithelia, while epithelial cells mainly send PDGF and EGF signals to fibroblasts. We observe differences in the ligands and receptors involved in cell-cell communication between the esophagus and stomach. Our findings provide insights into the molecular mechanisms underlying GE-SCJ development and fibroblast-epithelial crosstalk involved, paving the way to elucidate mechanisms during adaptive metaplasia development and carcinogenesis. Mouse-derived esophagus and stomach epithelial stem cells were isolated and cultured as 3D organoids as described in the accompanying manuscript (Materials and Methods). Total RNA was extracted from samples and hybridized on Agilent-8x60k Mouse custom arrays as single-color hybridizations.

胃食管鳞状柱状交界（gastroesophageal squamocolumnar junction, GE-SCJ）是食管与胃之间的关键组织界面，与胃肠道疾病的病理生理学密切相关。尽管如此，GE-SCJ发育背后的分子机制仍未明确。本研究借助单细胞转录组学（single-cell transcriptomics）、类器官（organoids）与空间分析（spatial analysis）技术，解析了小鼠从胚胎期到成年期GE-SCJ发育过程中的细胞异质性（cellular heterogeneity）与时空动态（spatiotemporal dynamics）变化。我们鉴定出发育过程中食管与胃上皮及间充质区域中独特的转录状态（transcriptional states）与信号通路（signaling pathways）。成纤维细胞-上皮细胞相互作用（fibroblast-epithelial interactions）由多种信号通路介导，包括WNT、BMP、TGF-β、FGF、EGF及PDGF通路。研究结果显示，成纤维细胞主要向上皮细胞传递FGF与TGF-β信号，而上皮细胞则主要向成纤维细胞传递PDGF与EGF信号。我们还发现，食管与胃之间参与细胞间通讯（cell-cell communication）的配体与受体存在差异。本研究结果为解析GE-SCJ发育的分子机制及相关成纤维细胞-上皮细胞串扰提供了新见解，为阐明适应性化生（adaptive metaplasia）发生与癌变（carcinogenesis）过程中的机制奠定了基础。如随附手稿（材料与方法部分）所述，我们分离并培养了源自小鼠的食管与胃上皮干细胞，并将其构建为三维类器官（3D organoids）。从样本中提取总RNA（total RNA）后，以单通道杂交（single-color hybridizations）方式在安捷伦8x60k小鼠定制基因芯片（Agilent-8x60k Mouse custom arrays）上进行杂交实验。