Additional file 1 of Development and validation of a novel stem cell subtype for bladder cancer based on stem genomic profiling

Additional file 1 : Table S1. The 26 stem gene sets used for identification of BLCA subtype. BLCA: Bladder cancer. Figure S1. Clustering heat map of stem cell subtype in (A) E-MTAB-4321, (B) GSE13507, (C) GSE31684, (D) GSE32548, and (E) GSE32894. Figure S2. Evaluation of immune cell infiltration level, tumor purity, and stromal content in BLCA. (A–F) Immune score, (G–L) stromal score (stromal content), and (M–R) tumor purity in all six datasets. *P < 0.05, **P < 0.01, ***P < 0.001; ns means not significant. BLCA: bladder cancer. Figure S3. Comparisons of the expression levels of immune-related genes between BLCA subtypes. (A–C) Expression levels of HLA genes between BLCA subtypes in TCGA, E-MTAB-4321 and GSE32894. (D–E) Expression levels of immune cell subgroup marker genes between BLCA subtypes. Kruskal–Wallis test, *P < 0.05, **P < 0.01, ***P < 0.001; ns means not significant. BLCA: bladder cancer. Figure S4. Difference analysis of 22 human immune cell subgroups of BLCA stem cell subtypes in CIBERSORT. Immune cell subgroups with significant differences in BLCA stem cell subtypes in (A) TCGA, (B) GSE32894, (C) GSE31684, (D) E-MTAB-4321, (E) GSE13507, and (F) GSE32548 cohort with CIBERSORT. Fraction of different immune cell subgroups among the four subtypes evaluated using Kruskal–Wallis tests, * P < 0.05, ** P < 0.01, *** P < 0.001. Kaplan–Meier survival curve based on median ssGSEA score for (G) TCGA, (H) GSE13507, (I) GSE32548, and (J) GSE32894, and best cut-off for (K) E-MTAB-4321 cohort in OS for macrophage M0, together with median ssGSEA score for (L) TCGA in OS for macrophage M2. BLCA: bladder cancer; TCGA: The Cancer Genome Atlas. Table S2. Univariate Cox analysis for all six datasets. Table S3. GSEA for BLCA stem cell subtypes.

附加文件1：表S1。用于膀胱癌（Bladder cancer, BLCA）亚型鉴定的26个干细胞基因集。BLCA：膀胱癌。
图S1。（A）E-MTAB-4321、（B）GSE13507、（C）GSE31684、（D）GSE32548及（E）GSE32894数据集中的干细胞亚型聚类热图。
图S2。膀胱癌（BLCA）中免疫细胞浸润水平、肿瘤纯度及基质成分的评估。（A~F）所有6个数据集的免疫评分，（G~L）基质评分（基质成分）及（M~R）肿瘤纯度。*P<0.05，**P<0.01，***P<0.001；ns表示无显著性差异。BLCA：膀胱癌。
图S3。膀胱癌亚型间免疫相关基因表达水平的比较。（A~C）癌症基因组图谱（The Cancer Genome Atlas, TCGA）、E-MTAB-4321及GSE32894数据集中膀胱癌亚型间人类白细胞抗原（Human Leukocyte Antigen, HLA）基因的表达水平；（D~E）膀胱癌亚型间免疫细胞亚群标记基因的表达水平。采用Kruskal-Wallis检验，*P<0.05，**P<0.01，***P<0.001；ns表示无显著性差异。BLCA：膀胱癌。
图S4。膀胱癌干细胞亚型在CIBERSORT算法下的22个人类免疫细胞亚群差异分析。（A）TCGA、（B）GSE32894、（C）GSE31684、（D）E-MTAB-4321、（E）GSE13507及（F）GSE32548队列中膀胱癌干细胞亚型间存在显著性差异的免疫细胞亚群。采用Kruskal-Wallis检验评估4种亚型间不同免疫细胞亚群的占比，*P<0.05，**P<0.01，***P<0.001。基于单样本基因集富集分析（single-sample Gene Set Enrichment Analysis, ssGSEA）中位数评分的Kaplan-Meier生存曲线：（G）TCGA、（H）GSE13507、（I）GSE32548及（J）GSE32894数据集，以及（K）E-MTAB-4321队列中巨噬细胞M0的总生存期（Overall Survival, OS）最佳截断值，同时（L）TCGA数据集中巨噬细胞M2的总生存期ssGSEA中位数评分。BLCA：膀胱癌；TCGA：癌症基因组图谱。
表S2。所有6个数据集的单因素Cox回归分析。
表S3。膀胱癌干细胞亚型的基因集富集分析（Gene Set Enrichment Analysis, GSEA）。