Gnai1+ stromal cells regulate intestinal goblet and Paneth cell differentiation through c-Jun signaling

Combining single-cell and spatial transcriptomics for mapping different intestinal segments is still relatively absented, and the subtypes of intestinal stromal cells and their downstream signling also remain obscure. Our study provides a comprehensive view of 18 identified cell types across five mouse intestinal segments using single-cell RNA sequencing (scRNA-seq). Integrating scRNA-seq with spatial transcriptomics reveals gene profiles along both segmental and crypt-villus spatial dimensions, including cell characteristics, interactions, signaling networks, extracellular matrix contributions, and functional coordination. Not only the different subtypes of intestinal immune cells were analyzed, but also a subtype of Pdgfra-high stromal cells, Gnai1+ stromal cells, was identified. These cells can support intestinal morphology and regulate the activities of goblet cells, Paneth cells, and intestinal stem cells via the activation of c-Jun and Wnt signaling. Thus, we have compiled a publicly available single-cell and spatial transcriptomics resource covering five intestinal segments to facilitate further research, particularly on stromal cell populations and intestinal microenvironment homeostasis. Single-cell RNA sequencing libraries were constructed to profile cellular heterogeneity and gene expression across the duodenum, jejunum, ileum, colon, and rectum segments of the mouse intestine目前针对不同肠道节段的单细胞与空间转录组学（spatial transcriptomics）联合分析研究仍较为匮乏，肠道基质细胞的亚型及其下游信号通路也尚未完全明晰。本研究依托单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）技术，对小鼠5个肠道节段内的18种已鉴定细胞类型展开了系统性解析。通过将单细胞RNA测序与空间转录组学联合分析，本研究揭示了沿肠道节段及隐窝-绒毛空间轴的基因表达特征，涵盖细胞特性、细胞互作、信号网络、细胞外基质调控作用以及功能协同模式。本研究不仅分析了肠道免疫细胞的多种亚型，还鉴定出一类高表达Pdgfra的基质细胞亚群——Gnai1+基质细胞。该细胞亚群可通过激活c-Jun与Wnt信号通路，维持肠道形态稳态，并调控杯状细胞、潘氏细胞以及肠道干细胞的功能活性。综上，本研究构建了一套覆盖5个肠道节段的公开单细胞与空间转录组学数据集，旨在为后续研究提供支撑，特别是针对基质细胞群体及肠道微环境稳态的相关研究。本研究构建了单细胞RNA测序文库，以解析小鼠十二指肠、空肠、回肠、结肠及直肠各肠道节段的细胞异质性与基因表达谱。