Development of 3D Tissue Reconstruction Method from Single-cell RNA-seq Data

In silico three-dimensional (3D) reconstruction of tissues/organs based on single-cell profiles is required to comprehensively understand how individual cells are organized in actual tissues/organs. Although several tissue reconstruction methods have been developed, they are still insufficient to map cells on the original tissues in terms of both scale and quality. In this study, we aim to develop a novel informatics approach which can reconstruct whole and various tissues/organs in silico. As the first step of this project, we conducted single-cell transcriptome analysis of 38 individual cells obtained from two mouse blastocysts (E3.5d) and tried to reconstruct blastocyst structures in 3D. In reconstruction step, each cell position is estimated by 3D principal component analysis and expression profiles of cell adhesion genes as well as other marker genes. In addition, we also proposed a reconstruction method without using marker gene information. The resulting reconstructed blastocyst structures implied an indirect relationship between the genes of Myh9 and Oct4.