Additional file 1 of The potential crosstalk between tumor and plasma cells and its association with clinical outcome and immunotherapy response in bladder cancer
Creators: name: Long, Fei
name: Wang, Wei
name: Li, Shuo
name: Wang, Bicheng
name: Hu, Xin
name: Wang, Jun
name: Xu, Yaqi
name: Liu, Min
name: Zhou, Junting
name: Si, Huaqi
name: Xi, Xiaodan
name: Meng, Xiang-yu
name: Yuan, Chunhui
name: Wang, Fubing
Publisher: name: figshare
Year: 2024
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Plant Biology

description: Additional file 1: Figure S1. Immune cells associated with patient overall survival risk in the TCGA-BLCA (A) and IMvigor210 cohorts (B) based on Cox regression analysis. Figure S2. Expression of antibody-related genes in PCs. (A) Box plot showing the expression of IgG-, IgA-, IgM-, and IgD-associated genes in PCs (Kruskal‒Wallis test). (B) UMAP plot of antibody-related gene expression showing that IgG1 and IgA1 PCs are the dominant PCs based on dimension reduction and PCA with selected genes. Figure S3. PCs were classified into four types based on the median expression of IGHG1 and IGHA1. Figure S4. Branch point analysis based on the pseudotime trajectory. Figure S5. Association of IgG1 and IgA1 PCs with different subtypes of bladder cancer. (A) Heterogeneous relationship of IgG1 and IgA1 PCs with survival in patients with different bladder cancer subtypes. (B) Abundance of IgG1 and IgA1 PCs inferred by ssGSEA in different subtypes of bladder cancer samples. Wilcoxon test; *, P &lt; 0.05; **, P &lt; 0.01; ***, P &lt; 0.001; ****, P &lt; 0.0001. Figure S6. Tumor cell states associated with patient overall survival risk in the TCGA-BLCA (A) and IMvigor210 cohorts (B) based on Cox regression analysis. Figure S7. Cell communication analysis for all cell types. (A) The marker gene expression of T cells, myeloid-derived cells (MDCs), and mast cells. (B) Dot plot showing the incoming and outgoing signal strength in different cell types. (C) Crosstalk networks showing that PCs tended to send signals to T cells and MDCs but receive signals from stromal cells. Figure S8. Signaling pathways enriched in plasma cell-tumor cell communication. (A&amp;B) Heatmap showing the signaling pathways enriched for each cell type in both incoming and outgoing signaling patterns. (C-E) Dot plots showing the strengths of incoming and outgoing interactions of each cell type in the MK/MIF signaling and all signaling pathways. Figure S9. Comparison of PC and tumor cell crosstalk between low- and high-grade bladder cancer samples. Figure S10. Survival analysis based on ligands and receptors. (A) Overall survival analysis based on selected L/R pairs between tumor cells and PCs in the anti-PD-L1 treatment IMvigor210 cohort. (B) Overall survival analysis based on selected L/R pairs between tumor cells and IgG1 PCs in the anti-PD-L1 treatment IMvigor210 cohort. Figure S11. Spatial transcriptome cell clustering and assessment of selected gene expression based on sample GSM5224027. Figure S12. Spatial transcriptome cell clustering and assessment of selected gene expression based on the validation sample GSM5224029.