Fig. 1

A single-cell and spatially resolved atlas of human osteosarcomas. A Workflow of this study. B UMAP plot displaying 49,356 single cells from osteosarcoma tissues, annotated by major cell types in NCC sc-RNA seq data. (osteosarcoma cells (n = 10,467), myeloid cells (n = 13,966), mesenchymal stromal cells (MSCs; n = 3,240), endothelial cells (ECs; n = 2,084), osteoclast cells (OCs; n = 2,555), B cells (n = 462), plasma cells (n = 206), mast cells (n = 184), myocytes (n = 1,790) and TNK cells (n = 14,402)). C UMAP plot displaying 194,083 single cells from osteosarcoma tissues, annotated by major cell types in integrated sc-RNA seq data. (osteosarcoma cells (n = 87,256), myeloid cells (n = 51,894), MSCs (n = 9,867), ECs (n = 6,960), OCs (n = 12,910), B cells (n = 1,094), plasma cells (n = 874), mast cells (n = 592), myocytes (n = 2,050) and TNK cells (n = 21,306)). D Pie chart depicting the proportion of major cell types within the sample in NCC sc-RNA seq data. E Pie chart depicting the proportion of major cell types within the sample in integrated sc-RNA seq data. F Spearman correlation analysis showing relationships between proportions of major cell types; MSC and endothelium demonstrate the correlation in NCC sc-RNA seq data. G. Spearman correlation analysis showing relationships between proportions of major cell types; MSC and endothelium demonstrate the correlation in integrated sc-RNA seq data. H MRI images of the BS3 sample before and after three chemotherapy cycles, indicating no significant tumor reduction, suggestive of potential chemotherapy resistance. I H&E staining of a BS3 tissue slice reveals less than 50% necrosis, indicating potential chemotherapy resistance. Spatial transcriptomics show a low number of detected genes in the necrotic areas of BS3. J Cell2location deconvolution analysis estimates the proportions and spatial distribution of primary cell types (OS, MSC, endothelium, myeloid, osteoclasts, and TNK cells) in SP_BS3. K Analysis by Scanpy identifies six spatial niches within SP_BS3, with cluster_6 located at the tumor necrosis front, highly expressing genes such as COL4A1, suggesting a potential link to chemotherapy resistance