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| 2023-10-25 08:33:23 | onclick： | Tsinghua Team Reveals How Genetic Information Utilizes Cells to Form Tissue Space Morphology |
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Tsinghua News Network, Oct. 24 (Xinhua) - An international team of scientists from Tsinghua University's Brain and Intelligence Laboratory and Peking University's Frontier Cross-disciplinary Research Institute has developed a new computational method.Studies have shown that this method, called De Novo Coalescent Embedding (D-CE), outperforms existing techniques in mapping individual cells back to their original locations in tissues.
The single cell transcriptome (scRNA-seq) technique can depict gene expression in a single cell, but it loses the spatial location information of the cell.Therefore, we need a computational method to reconstruct the spatial relationship between cells based on the characteristics of the transcriptome of cells.The proposed D-CE method can construct spatial mapping of cells from the head without prior knowledge.
The researchers first tested D-CE on baseline datasets with known spatial markers.The results show that it can accurately reconstruct the position of cells in mouse and human embryonic tissue samples.Compared with the previous methods NovoSpaRc and CSOMap, D-CE has the best performance and the best separation of cells from different spatial domains.
A key innovation of D-CE is that it can extract marker genes that express specific spatial patterns without prior knowledge.The researchers showed that using these D-CE marker genes further improved the accuracy of spatial reconstruction.
Through further testing on the single-cell transcript dataset of Drosophila and zebrafish embryos, the team demonstrated that the D-CE method has flexibility and versatility in different species.Overall, D-CE achieves at least four times more accuracy than existing methods in 14 datasets and nearly 500 reconstruction experiments.
D-CE also reveals new regulatory factors that influence the formation of tissue spatial features, such as oxygen, extracellular matrix and tight junction gradient, by reconstructing spatial relationships between cells.The scientists involved in the study point out that D-CE's accuracy and versatility will make it a new tool for capturing biological insights from spatial patterns of single-cell transcriptome data.
The results were published in the journal Advanced Science under the title "Spatial Reconstruction of Oligo and Single Cells by De Novo Coalescent Embedded of Transcriptomic Networks".
The research was funded by the Ministry of Science and Technology of China, China National Natural Science Foundation and Shanghai Science and Technology Major Projects.Professor Carlo Vittorio Cannistracih, lead researcher at Tsinghua University's Brain and Intelligence Laboratory, and Professor Han Jingdong, Peking University's Frontier Interdisciplinary Research Institute, are co-authors of the paper.Zhao Yuxuan, Ph. D. student at Peking University's Center for Quantitative Biology, and Zhang Shijiang, Ph. D. student at Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, are co-author
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