방사선의학 웹진

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Abstract
Deciphering the cellular composition in genome-wide spatially resolved transcriptomic data is a critical task to clarify the spatial context of cells in a tissue. In this study, we developed a method, CellDART, which estimates the spatial distribution of cells defined by single-cell level data using domain adaptation of neural networks and applied it to the spatial mapping of human lung tissue. The neural network that predicts the cell proportion in a pseudospot, a virtual mixture of cells from single-cell data, is translated to decompose the cell types in each spatial barcoded region. First, CellDART was applied to a mouse brain and a human dorsolateral prefrontal cortex tissue to identify cell types with a layer-specific spatial distribution. Overall, the proposed approach showed more stable and higher accuracy with short execution time compared to other computational methods to predict the spatial location of excitatory neurons. CellDART was capable of decomposing cellular proportion in mouse hippocampus Slide-seq data. Furthermore, CellDART elucidated the cell type predominance defined by the human lung cell atlas across the lung tissue compartments and it corresponded to the known prevalent cell types. CellDART is expected to help to elucidate the spatial heterogeneity of cells and their close interactions in various tissues.

Affiliations

Sungwoo Bae  1   2 , Kwon Joong Na  3   4 , Jaemoon Koh  5 , Dong Soo Lee  1   2   6 , Hongyoon Choi  2   6 , Young Tae Kim  3   4
1 Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea.
2 Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
3 Department of Thoracic and Cardiovascular Surgery, Seoul National University Hospital, Seoul, Republic of Korea.
4 Seoul National University Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
5 Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea.
6 Department of Nuclear Medicine, Seoul National University College of Medicine, Republic of Korea.