3.1 Differential Expression of THOC3 in Cancers
This study meticulously analyzed THOC3 mRNA expression of the TCGA databases, revealing pronounced upregulation in 13 cancers: BLCA,BRCA, CESC, COAD, CHOL, ESCA, HNSC, LIHC, LUAD, LUSC, READ, STAD, UCEC. In contrast, it was downregulated in KICH(Fig. 1A). Due to the limited availability of normal samples in the TCGA database, we integrated data from both TCGA and GTEx databases. This allowed us to assess the variability in THOC3 expression across 34 cancer types, ensuring a comprehensive analysis(Fig. 1B). Moreover, the UALCAN database helped us determine THOC3 protein expression levels in LUAD、LUSC、OV、COAD、GBM、KIRC and LIHC, all of which showed high expression(Fig. 1C). Furthermore, we utilized the GEPIA2 database to investigate the correlation between THOC3 expression levels and disease staging, revealing significant associations in SKCM, KIRP, TGCT, and COAD (p < 0.05, Fig. 1D).
3.2 Prognostic Value of THOC3 in Cancer
This study comprehensively assessed the impact of THOC3 expression levels on the prognosis of 33 types of cancer. In the overall survival (OS) analysis, high expression of THOC3 was found to be associated with poor prognosis in GBMLGG, LGG, BRCA, KIRP, SKCM-M, SKCM, PAAD, UVM, and KICH, while low expression of THOC3 was associated with poor prognosis in KIRC and OV (p < 0.05, Fig.2A). The Progression-free interval (PFI) analysis showed that high expression of THOC3 was associated with poor prognosis in GBMLGG, KIRP, KIPAN, LIHC, MESO, UVM, and KICH (p < 0.05, Fig.2B).
3.3 Alteration of THOC3 Gene Analysis Data
Using the pan-cancer data from the cBioPortal database, amplification of the THOC3 gene was found to be the predominant form of mutation, occurring most frequently in Endometrial Carcinoma at a rate of 10%(Fig.3). Other cancer types with notable amplification rates include Pancreatic Adenocarcinoma at 9.09%, Lung Cancer at 7.89%, Renal Cell Carcinoma at 6.45%, Hepatobiliary Cancer at 5.59%, and Cervical Cancer at 5%. Notably, Head and Neck Cancer presented a elatively lower rate of deep deletions, at 3.57%. Collectively, these data indicate that amplification of the THOC3 gene is a common genetic alteration in the cancerous contexts analyzed.
3.4 The Correlation of THOC3 Expression with Immune Cell Infiltration and TME in Different Cancers
According to the results of Figure S1, the expression of THOC3 is closely related to stromal cell infiltration in 23 types of cancers. The expression of THOC3 is significantly negatively correlated with 22 types of cancer and significantly positively correlated with KIPAN. To assess anti-tumor immunity, the relationship between THOC3 and TMB, MSI, and HRD was explored in all cancers (Fig. 4). In GBM, GBMLGG, LUAD, STES, STAD, PRAD, MESO, READ, and PCPG, the expression of THOC3 is positively correlated with TMB, while in LUSC, the expression of THOC3 is negatively correlated with TMB. For STES, SARC, and STAD, the expression of THOC3 is positively correlated with MSI, while in GBMLGG, KIPAN, and PRAD, the expression of THOC3 is negatively correlated with MSI. Additionally, in GBM, LUAD, BRCA, ESCA, STES, SARC, KIRP, KIPAN, PRAD, HNSC, KIRC, LUSC, LIHC, OV, and KICH, the expression of THOC3 is positively correlated with HRD.
3.5 Association between THOC3 and immune checkpoint.
In a variety of cancer types, THOC3 expression consistently correlates positively with immune checkpoint (ICP) genes, observed in cancers including LAML, KICH, KIPAN, KIRC, OV, and PAAD; in contrast, a negative correlation is evident in LUSC and THCA. More than 90% of cases involving the ICP genes CD276, VEGFA, and HMGB1 show a correlation with THOC3 expression (Fig. 5). These observations imply that elevated THOC3 expression could predict the effectiveness of immune therapies targeting ICP genes.
3.6 Analysis of THOC3's Association with Immune Cell Profiles
The analysis of THOC3's impact on immune cells using the TIMER algorithm shows that THOC3 has varying effects on B cell, T cell CD4, T cell CD8, Neutrophil, Macrophage, and DC cell infiltration in different tumors(Figure 6). In KIRC, PRAD, LIHC, and OV, THOC3 promotes the infiltration levels of B cell, T cell CD4, T cell CD8, Neutrophil, Macrophage, and DC cell, while in LUSC, THOC3 significantly inhibits the infiltration levels of B cell, T cell CD4, T cell CD8, Neutrophil, Macrophage, and DC cells(Figure S2).
3.7 Functional Enrichment Analysis of THOC3
We utilized the GeneMANIA database to extract the top 20 genes that exhibited the strongest correlation with THOC3 (Figure 7A). Following, we performed an in-depth analysis of the potential biological functions and pathways linked to THOC3 and these 20 interacting genes utilizing the DAVID database. The enrichment analysis for biological processes (BP) demonstrated that THOC3-related genes were predominantly involved in RNA splicing, mRNA processing, mRNA nuclear export, and the export of viral mRNA from the host cell nucleus (Figure 7B). The enrichment analysis for molecular functions (MF) indicated that THOC3 was involved in protein binding, RNA binding, and mRNA binding (Figure 7B). In the enrichment analysis for cellular components (CC), THOC3-related genes were found to be enriched in the nucleoplasm, cytoplasm, and nucleolus (Figure 7B). Additionally, KEGG pathway analysis revealed the involvement of THOC3 in nucleocytoplasmic transport and spliceosome pathways (Figure 7C).
3.8 Drug Sensitivity Analysis
Using the CellMiner database, we investigated the Pearson correlation between THOC3 expression levels and drug sensitivity. The results indicate that there is no significant correlation between the sensitivity to Allopurinol, Cladribine, Fludarabine, Mithramycin, Amuvatinib, Cpd-401, Econazole Nitrate, ARTENIMOL, artesunate, WORTMANNIN, Depsipeptide, and Cediranib and the expression level of THOC3(Figure S3). However, the sensitivity to Pluripotin and RAF-265 is negatively correlated with THOC3 expression, while the sensitivity to Bisacodyl (the active ingredient of Viraplex) is positively correlated with THOC3 expression(Figure 8).
3.9 Differential Analysis of THOC3 in Lung Adenocarcinoma
Figure 9A contrasts the expression of the THOC3 gene in tumor and normal tissues from the TCGA database. The results indicate that the expression of THOC3 in lung adenocarcinoma tissues is significantly higher than in normal tissues. Through univariate COX regression analysis, we determined that THOC3 significantly impacts lymph node metastasis in LUAD patients and has a significant effect on stage II and stage III LUAD (Figure 9B), but it does not affect the prognosis of LUAD (Figure 9C). To validate the differences in THOC3 expression between tumor and normal tissues, we analyzed four sets of human lung adenocarcinoma and adjacent normal specimens provided by the Department of Thoracic Surgery at the Fourth Affiliated Hospital of Hebei Medical University. Immunoblot analysis confirmed the significant overexpression of THOC3 in lung adenocarcinoma (Figure 9D, E).