Transfer learning of multicellular organization via single-cell and spatial transcriptomics
Fig 5
In-silico gene knockout experiments on DLPFC dataset and analysis of the human artery dataset.
(a) Reconstruction of DLPFC by iSORT without gene knockout. (b) Reconstruction of DLPFC with the top-20 SOGs knocked out. Knocking out the first 20 SOGs disrupts the structure of the cerebral cortex. (c) Reconstruction of DLPFC with the top-300 SOGs knocked out. The structural disruption in the cerebral cortex is intensified, with increased mixing of cells across cortical layers. (d) Curve of the mean squared error (MSE) in reconstruction with increasing SOGs knocked out. The more genes that are knocked out, the worse the reconstruction is in the sense of MSE. (e) Reconstruction of DLPFC with the top-20 Moran’s I SVGs knocked out. (f) Reconstruction of DLPFC with the top-20 SpatialDE SVGs knocked out. (g) Schematic diagram of artery structure illustrating layered composition: the innermost layer is lined with endothelial cells (ECs), followed by smooth muscle cells (SMCs), and the outermost layer composed of fibroblasts. (h) Hematoxylin and Eosin staining and the reconstruction results of the normal artery and the diseased artery with atherosclerosis (AS): Panel I: Histology image of a normal artery. Panel II: Histology image of an artery with AS. Panel III: Reconstruction result for a normal artery, showcasing ECs, SMCs, and fibroblasts. Panel IV: Reconstruction result for a diseased artery with AS, showcasing ECs, SMCs, and fibroblasts. The reconstruction results by iSORT distinguish the hierarchical structure of the three cell types.