Baseline Clinical Characteristics
One hundred and fifty-seven patients with bladder cancer were enrolled in this study. Eighteen patients had pTa, 49 had pT1, 51 had pT2, 21 had pT3, and 18 had pT4. The detailed clinical characteristics are shown in Additional file 1: Table S1. Four hundred and eight patients with bladder cancer in the TCGA dataset were included in this study. The detailed clinical characteristics of these patients (including age, sex, race, AJCC stage and subgroups based on mRNA clusters) are listed in Additional file 2: Table S2.
Associations Between SNF5 Expression And Clinical Characteristics
First, we plotted a receiver operating characteristic (ROC) curve to study the clinical value of SNF5. It showed promising power to predict bladder cancer, as the area under the curve (AUC) was 0.781 (Fig. 1a). To investigate the relationships between SNF5 and clinical factors, Cox analysis was applied (Table 1). Univariate Cox analysis revealed that age, SNF5 level, tumor size, lymph node status, metastasis status and AJCC stage were significantly related to survival. Multivariate analysis indicated that age and SNF5 level were independent prognostic factors for survival in bladder cancer. Next, Kaplan-Meier survival analysis of the TCGA cohort data was plotted to evaluate the correlation between the SNF5 expression level and survival time of patients with bladder cancer. A clear separation between the patients with higher SNF5 expression and those with lower expression was observed, and low expression of SNF5 conferred a poor prognosis in bladder cancer (Fig. 1b). Similar results were also obtained for the 88 patients with bladder cancer. The patients whose tumor sections showed high expression had a more favorable prognosis than their counterparts (Fig. 1c and Fig. 1d). These findings indicate that low SNF5 expression is associated with a poor prognosis.
Table 1
Univariate and multivariate Cox analyses in TCGA datasets
Variables | Univariate Cox analysis | | | Multivariate Cox analysis | |
| Hazard ratio (95%CI) | P | | Hazard ratio (95%CI) | P |
Age | 1.03 (1.02–1.05) | < 0.001 | | 1.09 (0.75–1.60) | < 0.001 |
Gender | 0.92 (0.73–1.16) | 0.471 | | | |
Race | 0.99 (0.74–1.31) | 0.921 | | | |
SNF5 | 0.88 (0.76–1.02) | 0.029 | | 0.91 (0.77–1.07) | 0.024 |
Tumor size | 1.70 (1.30–2.21) | < 0.001 | | 1.46 (0.65–3.28) | 0.355 |
Lymph node | 1.77 (1.42–2.21) | < 0.001 | | 1.25 (0.82–1.93) | 0.301 |
Metastasis | 0.85 (1.38–3.92) | < 0.001 | | 1.01 (0.50–2.03) | 0.977 |
AJCC stage | 1.64 (1.35–2.01) | < 0.001 | | 1.12 (0.91–1.37) | 0.696 |
CI confidence interval |
SNF5 Is Involved In The Immune Response
To explore the role of SNF5 in bladder cancer, we extracted the upper third and lower third of samples sorted in decreasing order according to the SNF5 expression level and identified the DEGs between the two groups. In total, we obtained 781 significant DEGs in the low-expression group, with 481 upregulated and 301 downregulated genes (| log (fold change) | >1, P < 0.05). The expression profiles of the DEGs in both groups are shown in Fig. 2a. To further investigate the biological functions of the DEGs, we conducted GO analysis after gene annotation. A total of 266 GO terms were identified. Many inflammation-related gene sets, such as leukocyte chemotaxis and cytokine secretion, and immune cell-related gene sets, such as neutrophil-mediated immunity, neutrophil activation, T cell activation and T cell proliferation, were upregulated in the low SNF5 expression group (Fig. 2b). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis implied that the altered genes were mainly involved in cytokine-cytokine receptor interactions, chemokine signaling pathways, IL-17 signaling pathways and T cell receptor signaling pathways (Fig. 2c). Taken together, these results suggest that SNF5 is associated with immune responses.
Relationships Between SNF5 Expression And Tumor-infiltrating Immune Cells
Based on the samples extracted above, we explored the potential connection between SNF5 expression and immune infiltration in bladder cancer. ImmuCellAI was used to precisely estimate the abundances of 24 types of immune cell types. As shown in Figure, SNF5 expression significantly affected the CD4 naive, CD8 naive, Tc, nTreg, Th1, Th2, Tfh, NKT, MAIT, macrophage, NK, neutrophil, Tgd, CD4T, and CD8T fractions. Among the fractions, the Tc, Th1, Th2, Tfh, NKT, MAIT, macrophage, NK, CD4T, Tgd and CD8T fractions were increased in the low-expression group, while the nTreg, CD4 naive, CD8 naive and neutrophil fractions exhibited higher proportions in the high SNF5 expression group (Fig. 2d). The correlations among the tumor-infiltrating immune cell types are shown in Fig. 3a. A heatmap revealed that different subpopulations of tumor-infiltrating immune cells were weakly to strongly correlated. Two points were particularly noteworthy. The Th1, Tex, Tc, Tfh, NK, iTreg, Th2, CD8T, Tfh and CD4T fractions were positively correlated with each other. The CD4 naive, CD8 naive and neutrophil fractions displayed positive relationships with each other but negatively correlated with the other TIIC fractions. As in previous work, we calculated the immune infiltration score (IIS) based on TIICs [13]. The IIS in the low-expression group was remarkably higher than that in the high-expression group (Fig. 3b). The results of the analyses corroborated each other and indicated that patients with bladder cancer with low SNF5 expression have elevated immune cell infiltration.
Low SNF5 expression is correlated with the antitumor response and immune checkpoints
Antigen processing and presentation are fundamental processes in the antitumor response. Here, we first used GSVA to calculate an antigen processing and presentation machinery score (APPMS) in light of a signature defined in previous studies [14, 15]. The APPMS of the low-expression group was significantly higher than that of the high-expression group (Fig. 3b). Next, to guide our exploration of immune pathways crucial for SNF5 function, GSEA was applied using gene sets from the MSigDB v7.0. Consistent with the GSVA findings, the GSEA results revealed that pathways related to antigen processing and presentation, such as the MHC pathway and T cell receptor activation pathway, were enriched in the low-expression group (Fig. 3c and Fig. 3d). Additionally, antitumor response gene sets, such as the cytotoxic T lymphocyte (CTL)-mediated immune response and NO2-dependent IL-12 pathway in NK cells, were overrepresented in tumor tissue samples with low SNF5 expression (Fig. 4a and Fig. 4b). Considering that the antitumor response of T cells is also influenced by immune checkpoints, we tested whether there was a significant difference in immune checkpoint expression between the two groups. CTLA4 expression was observed to be significantly elevated in the low-expression group, whereas PD-1 expression and PD-L1 presented nonsignificant differences between the groups (Fig. 4c). Additionally, the low-expression group had a significantly lower TIDE score (Fig. 4d). A gene set representing CTLA-4 pathway was enriched in BC patients with low SNF5 expression (Fig. 4e). Collectively, these findings indicated that low SNF5 expression enhanced antigen processing and presentation and the antitumor response. On the other hand, the CTLA4-mediated immune checkpoint mechanism was activated to suppress the CTL-mediated antitumor response. Hence, compared with the high-expression group, the low-expression group would potentially derive more benefits from anti-CTLA4 immunotherapy.