Figure 5 from Single-Cell Atlas of Lineage States, Tumor Microenvironment, and Subtype-Specific Expression Programs in Gastric Cancer

Abstract

<p>Comparative analysis of primary and organoid samples. <b>A,</b> UMAP representation of approximately 200,000 cells (∼48,000 cells from tumor PDOs with matched normal PDOs, combined with primary samples; ∼152,000 cells) recapitulating the major five metaclusters color-coded by their cell types. Each dot in the UMAP represents a single cell. <b>B,</b> Violin plot showing the expression of gastric cancer gene module scores in tumor PDOs compared with matched normal samples. <b>C,</b> Trajectory plot analysis of epithelial cells from tumor and normal PDOs demonstrating the expression of cellular differentiation gene programs in tumor PDOs depicted by long multiple branches. <b>D,</b> Density plot of UMAP representation comparing PDO and primary gastric samples demonstrating enrichment of lymphoid and plasma metaclusters in primary samples compared with PDOs. <b>E,</b> Graph showing the number of upregulated and downregulated genes in PDOs versus primary samples in the five metaclusters. The plasma meta-cluster shows the highest number of differentially expressed genes as compared with other metaclusters. <b>F,</b> Volcano plot of upregulated and downregulated genes in the plasma metacluster between PDOs and primary samples, showing significant downregulation of antibody-mediated complement factor genes in PDOs. <i>x</i>-axis shows the −log<sub>10</sub> adjusted <i>P</i> value and <i>y</i>-axis log<sub>2</sub> fold change in gene expression. <b>G,</b> Top common upregulated pathways in PDOs versus primary samples across all metaclusters.</p>

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