Unsupervised cell interaction profiling based on multiplet RNA sequencing reveals major architectural differences between small intestinal and colonic epithelium.

Cellular identity in complex multicellular organisms is strictly maintained over the course of life. This control is achieved in part by the organ structure itself, such that neighboring cells influence each other’s identity. However, large-scale investigation of the cellular interactome has been technically challenging. Here, we develop CIM-seq, an unsupervised and high-throughput method to analyze direct physical cell interactions between every cell type in a given tissue. CIM-seq is based on RNA sequencing of incompletely dissociated cells, followed by computational deconvolution of these into their constituent cell types using particle swarm optimization. We use CIM-seq to define the cell interaction landscape of the mouse small intestinal and colonic epithelium uncovering both known and novel interactions. Specifically, we find that the general architecture of the stem cell niche is radically different between the two tissues. In small intestine, the stem-paneth cell interaction forms an exceptionally strong and exclusive niche, in which paneth cells provide Wnt ligands1. In colonic epithelium, no similar compartment exists to support stem cells, and Wnt signaling is provided by a mesenchymal cell layer. However, colonic stem cells are associated with a subset of goblet cells expressing the wound healing marker Plet1, suggesting an additional level of structural control in the colon. These results identify novel cellular interactions specific for the colonic stem cell niche and shed light on a previously unappreciated complexity of the tissue organization and biology of the colon. CIM-seq is broadly applicable to studies that aim to simultaneously investigate the constituent cell types and the global interaction profile in a specific tissue.复杂多细胞生物的细胞身份在整个生命进程中受到严格维持。这种调控在一定程度上由器官自身结构实现，即相邻细胞可相互影响彼此的细胞身份。然而，对细胞互作组（cellular interactome）进行大规模研究曾在技术上颇具挑战。本研究开发了CIM-seq技术，这是一种无监督、高通量的方法，可用于分析特定组织内所有细胞类型间的直接物理细胞互作。CIM-seq基于未完全解离细胞的RNA测序技术，随后通过粒子群优化（particle swarm optimization）算法对这些细胞进行计算反卷积，以解析其组成细胞类型。我们利用CIM-seq绘制了小鼠小肠及结肠上皮的细胞互作图谱，同时揭示了已知与全新的细胞互作关系。具体而言，我们发现这两种组织中干细胞微环境（stem cell niche）的整体架构存在显著差异。在小肠中，干细胞-潘氏细胞（Paneth cell）互作构成了一个极强且排他的微环境，潘氏细胞在此提供Wnt配体（Wnt ligands）¹。在结肠上皮中，不存在类似的结构域来支持干细胞，Wnt信号由间充质细胞层提供。但结肠干细胞与一群表达创伤愈合标志物Plet1的杯状细胞（goblet cell）亚群相关，这表明结肠中存在另一层级的结构调控。本研究结果鉴定了结肠干细胞微环境特有的全新细胞互作关系，并揭示了此前未被认知的结肠组织架构与生物学的复杂性。CIM-seq技术可广泛应用于旨在同时解析特定组织的组成细胞类型与全局互作特征的研究。