DEGs from different cancer types
TCEAL2 was the only DEG that expressed in all 9 cancer types (Fig 2A). The other co-expressed differential genes partially showed in Additional file 1: Table S1. TCEAL2 expression was downregulated in all 9 cancer types shown in Fig 2B-J (p<0.05). We searched TCEAL2 location in the cell from THE HUMAN PROTEIN ATLAS website and found that it mainly localized on the nuclear speckles and cytosol shown in Fig 2L.
TCEAL2 expression in pan cancer
Relative TCEAL2 expressions in 22 tumor cell lines were shown in Fig 3A. The expressions in autonomic ganglia, lung and thyroid cell lines were relatively higher. The expression in all the tumor cell lines had little difference. Then we analyzed TCEAL2 expression levels in 31 normal tissues and found that the expression level was the highest in pituitary. In blood and bone marrow, TCEAL2 expression was relatively low (Fig 3B). Furthermore, we analyzed the expression in various tumors. In 33 types of cancers, brain lower grade glioma (LGG), pheochromocytoma & paraganglioma (PCPG) and glioblastoma multiforme (GBM) has the higher expression level (Fig 3C). In the last, we compared the TCEAL2 expression between various cancers and matched normal samples (Fig 3D). In addition to those which the normal tissues data were not available, 21 cancers and normal tissues were studied. The results showed that except cholangiocarcinoma (CHOL) and pancreatic adenocarcinoma (PAAD), there were significant differences in 19 cancer types (p<0.05). TCEAL2 expression was markedly decreased in tumor tissues in 18 cancer types included bladder urothelial carcinoma (BLCA), breast invasive carcinoma (BRCA), cervical & endocervical cancer (CESC), colon adenocarcinoma (COAD), esophageal carcinoma (ESCA), GBM, head & neck squamous cell carcinoma (HNSC), kidney chromophobe (KICH), kidney clear cell carcinoma (KIRC), kidney papillary cell carcinoma (KIRP), liver hepatocellular carcinoma (LIHC), lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC), prostate adenocarcinoma (PRAD), rectum adenocarcinoma (READ), stomach adenocarcinoma (STAD), thyroid carcinoma (THCA), uterine corpus endometrioid carcinoma (UCEC). In PCPG, the expression was obviously upregulated in tumor tissues.
Correlations of TCEAL2 expression with clinical stage and prognosis
We analyzed the relationships between TCEAL2 expression and clinical stage in 21 types of cancers which can acquire the stage data. We found that TCEAL2 expression was significantly related with clinical stage in BLCA, BRCA, PAAD, READ, STAD, TGCT and THCA (Fig 4, p<0.05). And the main difference was between stage I and the other stages (stage II, III and IV). The expression in stage I was higher in BRCA, PAAD and THCA, but lower in BLCA, READ, STAD and TGCT (p<0.05). In THCA, the expression in stage II and III was also higher than stage IV (p<0.05).
To investigate the prognostic value of TCEAL2, the survival analysis contained overall survival (OS), disease-specific survival (DSS) and progression-free interval (PFI) was studied. The Kaplan-Meier analysis revealed that TCEAL2 was markedly associated with OS in BLCA, BRCA, CESC, LGG, LIHC, LUAD, MESO and PAAD (Fig 5). The high expression of TCEAL2 in BRCA, CESC, LGG, LIHC, MESO and PAAD was related with relative prolonged OS. But in BLCA and LUAD, the higher expression was related with shorter OS. DSS analysis showed that patients with high expression had long survival time in BRCA, CESC, LGG and MESO (Fig 6). In BRCA, LGG and MESO, the high expression was also associated with longer PFI. However, in COAD, patients with high levels had shorter PFI (Fig 6).
Correlation of TCEAL2 expression with DNA methylation
TCEAL2 expression was markedly correlated with DNA methylation in 17 types of tumors. We presented 6 strongest relationships included 5 negative correlations in COAD, HNSC, MESO, PAAD, TGCT and 1 positive correlations in PCPG in Fig 7A. The other 11 types of tumors were shown in Additional file 2: Figure S1. Then we analyzed correlations between methylation and OS in pan cancer. In STAD, UCEC and UVM, TCEAL2 methylation prolonged the OS time. However, in MESO and PAAD, it shortened the OS time (Fig 7B). In other cancers, there was no statistically significant difference.
Relationship between TCEAL2 and immunity
TCEAL2 expression was significantly related with the levels of immune cell in mostly cancers (Additional file 3: Table S2). 10 types of cancer (BLCA, CHOL, ESCA, LAML, PAAD, PRAD, READ, SARC, STAD, and TGCT) with relative higher correlation coefficient were showed in Fig 8A. To explore which immune cells were most likely to be involved, we further calculated the sum of correlation coefficients (the absolute value) of all tumors in each immune cell. Natural Killer (NK) cells had the highest sum value and followed by Mast cells and T follicular helper cells (TFH). Then, correlation between NK cells and TCEAL2 expression in 33 cancers was further studied. Significant associations were found in 24 cancers. Among them, TCEAL2 expression was positively correlated with NK cells in 20 cancers except ACC, GBM, LGG and PCPG. 10 cancers include BLCA, CESC, COAD, ESCA, PRAD, READ, SARC, STAD, TGCT and UCS which has the strongest correlations were showed in Fig 8B.
Furthermore, we analyzed the relationships between TCEAL2 and immune-related genes in pan cancer. The related genes included 21 major histocompatibility complex (MHC), 41 chemokine, 18 chemokines receptors, 46 immune activation and 24 immunosuppressive genes. TCEAL2 were mostly related with immune-related genes in most types of cancers in addition to ACC, KICH, UCS and UVM (Fig 9). Moreover, the correlations were positive in most various cancers except LGG.
Enrichment analysis of TCEAL2
To investigate the role of TCEAL2 in tumorigenesis, we screened out relevant genes for enrichment analysis using STRING and GEPIA2 website. 50 interacted genes from STRING website (Fig 10A) and 100 top correlated genes from GEPIA2 were selected. Then we calculated the intersection of the two datasets using Venn diagram and obtained 3 related genes (BEX1, CNRIP1 and USP11, Fig 10B). Further, the correlations between TCEAL2 and 3 related genes in 32 types of cancers were explored. BEX1 was significantly and positively correlated with TCEAL2 in all various cancers (Fig 10C). CNRIP1 and USP11 had remarkable positive correlations with TCEAL2 in most types of cancers. The negative correlation was just observed between USP11 and TCEAL2 in MESO (Fig 10C). The 150 related genes (50 from STRING and 100 from GEPIA2) were used to explore the Gene Ontology (GO) and (Kyoto Encyclopedia of Genes and Genomes) KEGG enrichment analyses. The results were showed in Additional file 4: Table S3. Through GO analysis, we found that TCEAL2 was mainly localized in axon and synaptic vesicle, and the involved biological process (BP) was mainly about synaptic vesicle localization, cognition and axonal transport (Fig 10D). Two molecular functions (MF) were enriched. One is tau protein binding, and the other one is WW domain binding (Fig 10E). The related genes involved in WW domain binding were all TCEAL gene family (TCEAL 1,4,5 and 8, Fig 10E). Through KEGG analysis, 4 pathways were enriched. But only two (mRNA surveillance pathway and Ribosome biogenesis in eukaryotes) was significant (p<0.05, Fig 10F). Fig 10G displayed the related genes of each pathway.