On Jul.30, Professor Xiaohui Fan, College of Pharmaceutic Science Zhejiang University, Professor Xiao Xu Affiliated Hangzhou First People's Hospital Zhejiang University, Professor Huajun Chen College of Computer Science and Technology Zhejiang University published the newest research entitled Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk in Nature Communications.

Spatially resolved transcriptomics provides genetic information in space toward elucidation of the spatial architecture in intact organs and the spatially resolved cell-cell communications mediating tissue homeostasis, development, and disease. To facilitate inference of spatially resolved cell-cell communications, we here present SpaTalk, which relies on a graph network and knowledge graph to model and score the ligand-receptor-target signaling network between spatially proximal cells by dissecting cell-type composition through a non-negative linear model and spatial mapping between single-cell transcriptomic and spatially resolved transcriptomic data. The benchmarked performance of SpaTalk on public single-cell spatial transcriptomic datasets is superior to that of existing inference methods. Then we apply SpaTalk to STARmap, Slide-seq, and 10X Visium data, revealing the in-depth communicative mechanisms underlying normal and disease tissues with spatial structure. SpaTalk can uncover spatially resolved cell-cell communications for single-cell and spot-based spatially resolved transcriptomic data universally, providing valuable insights into spatial inter-cellular tissue dynamics.

This work was supported by the National Natural Science Foundation of China, the Key Program, National Natural Science Foundation of China, the Natural Science Foundation of Zhejiang Province. This work was carried out by Postdoctor Xin Shao, Ph.D student Chengyu Li and Ph.D student Haihong Yang under the supervision of Professor Xiaohui Fan, Professor Xiao Xu and Professor Huajun Chen.

Link: https://doi.org/10.1038/s41467-022-32111-8