SSBP1 high expression in LUAD
Compared with the adjacent normal tissues detected by the Oncomine database, the expression of SSBP1 in various tumors increased or decreased (Fig. 1A). And, TIMER online database analysis showed that compared with adjacent tissues or normal lung tissues, the expression of SSBP1 in LUAD was significantly up-regulated (Fig. 1B; * p <0.05, ** p <0.01, *** p <0.001). In addition, to explore the gene and protein expression of LUAD patients, we used UALCAN to analyze SSBP1 expression in LUAD patients from the TCGA database (Fig. 1C, D; P <0.01). Furthermore, we also used the HPA database to analyze the expression of SSBP1 in tumor tissues (Fig. 1E).
Clinical characteristics and poor prognosis of LUAD with high expression of SSBP1
UALCAN was used to detect the relationship between SSBP1 and the clinical characteristics of patients with LUAD. As shown in Fig 2A,2B, and 2C, SSBP1 expression in LUAD tissues was significantly higher than that in normal tissues. In addition, SSBP1 expression is also closely related to the clinical characteristics of patients, such as tumor stage, lymph node metastasis, and TP53 mutation. Moreover, compared with normal tissues, regardless of race, gender, or age, the expression of SSBP1 increased(Fig S1). GEPIA, UALCAN, and KM were used to analyze the prognostic value of SSBP1 expression on LUAD. The results showed that OS and SSBP1 expression in LUAD patients were significantly negatively correlated. (HR= 2, log-rank p = 1.2e-05) (Fig. 2D). However, the correlation between DFS and SSBP1 expression was not significant (HR = 1.3, log-rank p = 0.065) (Fig. 2E). The UALCAN database showed that high SSBP1 expression was also associated with poorer OS in LUAD patients (p = 0.037), and the Kaplan-Meier plotter database showed the prognosis of LUAD patients with worsened OS (HR = 1.38, log-rank p = 1e-07) (Fig. 2F).
Relationship between SSBP1 expression and tumor-infiltrating immune cells
A positive correlation was detected by Spearman’s correlation analysis between the expression of SSBP1 and TMB (P = 5.9E-6) (Fig. 3A).TISIDB database was used to comprehensively analyze the relationship between the expression of SSBP1 and chemokines to further elucidate the underlying mechanism of SSBP1 in immune cells migration. Meanwhile, based on the TISIDB database, we analyzed the relationship of SSBP1 expression and 28 TILs in multiple cancer types (Fig. S2), and most tumor infiltrating cells in LUAD are negatively correlated with the expression of SSBP1 (Fig. 3B). Furthermore, in order to explore the relationship between SSBP1 expression and immune score, we used the ESTIMATE algorithm in the SangerBox tool showed that the expression of SSBP1 had a significantly negatively correlation with StromalScore(r = -0.191, P =1.29e-05), ESTIMATEScore (r = -0.205, P = 2.81 e-06) and ImmuneScore (r = -0.179, P =4.69e-05) (Fig. 3C). TIMER database was used to analysis of the correlation between the expression of SSBP1 and the level of immune cells infiltrating showed that SSBP1 had a negatively correlation with B cells (r = -0.32, P =1.24e-13), CD4+T (r = -0.321, P = 1.02E-13), Neutrophil (r = -0.101, P = 0.024), Macrophages (r = -0.145, P = 0.00104) and Dendritic (r = -0.166, P = 0.00016). However, the expression of SSBP1 has no statistically significant correlation with CD8+ T cells (Fig. 3D).Moreover, the high expression of SSBP1 in B cells (P = 0.001), CD8+ T cells (P = 0.045) and dendritic cells (P = 0.007) was better correlated with the OS of LUAD by survival analysis (Fig. 3E).
SSBP1 interaction network
We used STRING to analyze the relationship between SSBP1 and upstream and downstream proteins. A corresponding relational network diagram can be obtained (Fig. 4A). PPI enrichment P-value is < 1.05e-5. There are 11 nodes containing INTS3, SSBP2, INIP, SSBP1, GABPA, GABPB1, TP53, TFAM, POLRMT, POLG, C10orf2.
The SSBP family (SSBP1, SSBP2, SSBP3, and SSBP4) gene interaction network was further constructed by GeneMANIA (Fig. 4B). According to GO analysis, SSBP1 is a key molecule in mitochondrial DNA synthesis, mainly involved in the replication, transcription, and post-injury repair of mitochondrial DNA. The main cellular components are Mitochondrial nucleoid, Mitochondrial matrix, SOSS complex, and Intracellular organelle lumen. (Fig. 4C)
High SSBP1 expression significantly increases cancer malignancy
The Sangerbox tool was used to perform GSEA on KEGG and HALLMARK to explore the biological pathways of the two groups. We found that the top 3 significantly enriched KEGG pathways in the high expression group of SSBP1 were pyrimidine metabolism, purine metabolism, and Huntington’s disease (Fig. 5A). While, in the low expression group of SSBP1, the top 4 significantly enriched KEGGs pathways are related to hematopoietic cell lineage, aldosterone-regulated sodium reabsorption, linoleic acid metabolism, and α-linoleic acid metabolism (Fig. 5B). In addition, the GSEA of the HALLMARK pathway showed that the top 3 pathways related to the high expression of SSBP1 were glycolysis, DNA repair, and mTORC. And, the top 4 pathways related to the low expression of SSBP1 were the IL-6 JAK STAT3 signaling pathway, KRAS signaling pathway, myogenesis, and hedgehog signaling pathway (Fig. 5C, D). Moreover, CancerSEA database22 was used to explore the single-cell RNA (scRNA) analysis of LUAD showed that the expression of SSBP1 had significantly positive correlation with tumor malignant features including DNA damage(r = 0.48, P =0.000), DNArepair (r =0.47, P =0.000), invasion (r = 0.45, P =0.000), cell-cycle (r =0.40, P =0.000), and metastasis (r = 0.36, P =0.000) (Fig. 6 A, B, C, D and E). These findings implied that high SSBP1 expression is significantly related to the malignancy of LUAD. The t-SNE plot shows siRNA analysis of SSBP1 expression (Fig. 6 F).
High expression of SSBP1 is associated with anti-angiogenesis response
From the Cancer Cell Line Encyclopedia (CCLE), Genomics of Drug Sensitivity in Cancer (GDSC, previously named CGP), and The Cancer Therapeutics Response Portal (CTRP) cohorts’ analysis, Analysis from the Cancer Cell Line Encyclopedia (CCLE), The Cancer Therapeutics Response Portal (CTRP), and Genomics of Drug Sensitivity in Cancer (GDSC) cohorts showed that among the top5 chemical components, the expression of SSBP1 had a positive correlation with the CARE score, which was mainly including Tacrolimus, Dabrafenib, Elocalcitol, CHEMBL3186197, and GSK525762A. At the same time, it was found that these drugs act on anti-angiogenesis and other malignant biological processes, indicating the treatment strategy for LUAD patients based on the high expression of SSBP1 could add anti-angiogenesis drugs.(Fig. 7, and Table 1)