3.1.FSIP2-MT is associated with a good ICI prognosis
We divided the somatic mutation and survival data (OS) from the clinical ICI treatment cohort(Miao et al. 2018) (n = 120) and TCGA-SKCM cohort (n = 467) into two groups based on the FSIP2 mutation status. In this way, the ICI treatment cohort was divided into FSIP2-MT (n = 15) and FSIP2-WT (n = 105) groups, and the TCGA-SKCM cohort was also divided into FSIP2-MT (n = 58) and FSIP2-WT (n = 409) groups. Survival analysis of these data showed that among the patients receiving ICIs, those in the FSIP2-MT group were more sensitive to ICI treatment (p = 0.038; hazard ratio (95% confidence interval (CI)): 0.43 (0.23–0.82); Fig. 1a). In contrast, traditional SKCM treatment options are generally surgical resection or chemotherapy(Coit et al. 2019). The survival analysis results for the TCGA-SKCM cohort showed that when receiving conventional treatment, OS was not significantly different between the FSIP2-MT and FSIP2-WT groups (p = 0.978; hazard ratio (95% CI): 1.01 (0.68–1.49); Fig. 1b).
3.2.Relationship among clinical characteristics, gene mutations and FSIP2 gene mutations in patients
Based on the mutation status of FSIP2, we compared differences in clinical characteristics between the FSIP2-MT and FSIP2-WT groups. Figure 2a shows that in the immunotherapy cohort from the literature, there were no significant differences in sex, treatment response or OS; however, patients with FSIP2 gene mutations tended to have an older age (p = 0.047). As shown in Fig. 2b, in the TCGA-SKCM cohort, excluding the influencing factor of receiving ICI treatment, there were no significant differences in age, stage, race or ethnicity between the two groups, but there were more men in the FSIP2-MT group (p = 0.043).
In addition, in Fig. 2, we also show the gene mutation panoramas of the ICI treatment cohort and the TCGA-SKCM cohort. As shown in Fig. 2a, among the top 20 mutated genes in the ICI treatment cohort, except for the higher mutation frequencies of the MUC16, USH2A, DNAH7 and PKHD1L1 genes in the FSIP2-MT group, there were no significant differences in other gene mutations between the two groups. The main FSIP2 mutation types in the ICI-treated cohort were missense (84.2%) and nonsense (15.8%). Figure 2b shows that among the top 20 mutated genes in the TCGA-SKCM cohort, except for the BRAF gene, the other genes had a higher mutation frequency in the FSIP2-MT group, and the main mutation type was missense (89.6%); other mutation types, including splice site (1.3%), frameshift (3.9%), inframe ins/del (1.3%) and nonsense (3.9%) mutations, accounted for small percentages of the total mutation rate.
3.3.patients With Fsip2-mt Have An Elevated Tmb And Nal
As shown in Fig. 3a, we analyzed the TMB in the ICI-treated cohort and TCGA-SKCM cohort according to the FSIP2 gene mutation status. The results showed that the FSIP2-MT group had a higher TMB than the FSIP2-WT group, and there was a significant difference. The SKCM cell line data including WES data downloaded from GDSC (n = 52) were also divided into two groups according to the FSIP2 gene mutation status: FSIP2-MT (n = 3) and FSIP2-WT (n = 49). The TMB levels of the two groups were analyzed, and the results also suggested that the FSIP2-MT group had a higher TMB. The accumulation of mutations in the cancer genome may lead to tumor-specific production of “neoantigens” that are not affected by central T cell tolerance. Therefore, we analyzed the NAL of the TCGA-SKCM cohort, and the results showed that the FSIP2-MT group had a higher NAL. The higher TMB and NAL in patients with FSIP2-MT may be related to their better response to ICIs.
3.4.fsip2-mt Results In A Relatively Low Cnv
We analyzed the downloaded TCGA-SKCM queue data by GISTIC2.0 after grouping according to the mutation status of FSIP2. As shown in Fig. 3b, compared with normal samples, the TCGA-SKCM cohort samples showed significant amplifications on chromosomes 1, 3 to 8, 11 to 12, 15 to 17 and 22, while deletions were found on chromosomes 1 to 6, 8 to 12, 14 to 16 and 19. For the FSIP2-MT group, the amplified regions were mainly located on chromosomes 1, 6, 12 and 15, and the deleted regions were located on chromosomes 1, 3, 9 and 15. However, the amplification regions in the FSIP2-WT group were mainly located on chromosomes 1, 3 to 9, 11 to 13, 15 to 17, and 22, and the deleted regions were located on chromosomes 1, 3 to 9, 11 to 13, 15 to 17, 19, 22 and X. Compared with those of the FSIP2-MT group, the distribution and peak value of the amplified/deleted regions in the FSIP2-WT group were significantly higher, and the results were similar to those of the TCGA-SKCM cohort.
3.5.relationship Between Fsip2 And The Tumor Immune Status
The effect of ICI therapy depends not only on the immunogenicity of the tumor itself but also on the immune status of the tumor. The infiltration of immune cells, such as CD8 + T cells, Tregs, NK cells and macrophages (M0, M1, and M2), also affects the efficacy of ICI treatment. As shown in Fig. 4a and Fig. 4b, we analyzed the statuses of infiltrating immune cells and immune genes between the FSIP2-WT group and the FSIP2-MT group in the TCGA-SKCM cohort and marked the cells and genes with significant differences. In addition, we also analyzed the infiltration statuses of several specific immune cell populations. As shown in Fig. 4c, CIBERSORT analysis results for the FSIP2-MT and FSIP2-WT groups in the TCGA-SKCM cohort showed that except for memory B cells, CD8 + T cells, and Tregs, which were significantly upregulated in the FSIP2-WT group, and M2 macrophages, which were significantly upregulated in the FSIP2-MT group, there were no significant differences in immune cell infiltration between the two groups.
3.6.relationship Between Fsip2 And The Expression Of Immune-related Genes
The immune status of tumors is regulated by immune-related genes, so the expression of immune-related genes also affects the prognosis of ICI therapy. According to the immune-related gene sets reported in the literature, we evaluated the expression of immune-related genes between the FSIP2-MT group and FSIP2-WT group in the TCGA-SKCM cohort. As shown in Fig. 4d, the expression levels of the CD8A and CD8B genes, which are related to immune cell activity (cytolytic activity), in the FSIP2-WT group were significantly increased, and the expression levels of the PDCD1 and TIGIT genes, which are related to immune checkpoints, were also significantly increased. In addition, there was no significant difference in the expression of chemokine genes (CCL5, CXCL10, and CXCL9), other immune cell activity-related genes (GZMA, PRF1, and GZMB) or immune checkpoint-related genes (CD274, CTLA-4, HAVCR2, IDO1, LAG3, and PDCD1LG2) between the FSIP2-MT and FSIP2-WT groups.
3.7.effect Of Fsip2 On Chemotherapy Sensitivity
As shown in Fig. 5, we analyzed SKCM cell lines drug sensitivity data obtained from GDSC. After grouping the data according to the mutation status of FSIP2, we compared the difference in the 50% inhibitory concentration (IC50) between the FSIP2-MT group and FSIP2-WT group for 18 commonly used antineoplastic drugs. The results showed that except for that of bleomycin, the IC50s of the FSIP2-MT group were significantly higher than those of the FSIP2-WT group for the other 17 antineoplastic drugs.
3.8.pathway Analysis Of Fsip2-mt And Fsip2-wt
After GSEA of the TCGA-SKCM cohort, we screened out significantly upregulated or downregulated pathways that might be related to the prognosis of ICI treatment. The results are shown in Fig. 6. The pathways related to tumor progression, such as positive regulation of the MAPK cascade and FGFR (FGFR1, FGFR2, FGFR2c, FGFR3, and FGFR3c) ligand binding and activation, were significantly downregulated in the FSIP2-MT group (ES < 0, p < 0.05), suggesting a better prognosis. In addition, we observed that the negative immune-regulation pathways, such as negative regulation of IL-2 production, negative regulation of the immune response, and negative regulation of lymphocyte-mediated immunity, were also significantly downregulated in the FSIP2-MT group.