Microarray data analysis to identify crucial genes regulated by CEBPB in human SNB19 glioma cells

Glioma, which is known as one of the most common primary malignancies in the brain or spine, accounts for nearly 30 % of all brain and central nervous system tumors and 80 % of all malignant brain tumors [1, 2]. Previous researches have shown that the most important hallmarks of malignant glioma are its invasion and angiogenesis [3]. So far, researchers have indicated that glioma can be induced by neurofibromatoses and tuberous sclerosis complex [4], electromagnetic radiation [5], DNA repair genes (such as excision repair cross-complementing 1, ERCC1, and X-ray repair cross-complementing group 1, XRCC1) [6]. However, the exact molecular mechanisms of glioma were still unclear.

In the central nervous system, the neoplastic transformation can convert the neural cells into cells of mesenchymal phenotype which possess the ability of invasion and promoting angiogenesis [7, 8]. What is more, it has been identified that mesenchymal stem cells (MSC)-like properties may play a role in the tumorigenesis, invasion, and recurrence of primary glioblastoma tumors [8]. The transcription factor (TF) CCAAT/enhancer binding protein beta (CEBPB) is associated with the mesenchymal state of primary glioblastoma, and its expression in glioma is important for maintaining the tumor initiating capacity and invasion ability [9, 10]. Moreover, the transforming growth factor beta 1/SMAD family member 3 (TGFB1/SMAD3) plays a key role in the extracellular matrix (ECM) production which can lead to glioblastoma aggression [11, 12]. It has been revealed that CEBPB can regulate the synthesis of ECM [13]. However, the regulation mechanism of CEBPB on TGFB1/SMAD3 in glioma was seldom studied.

In our study, in order to gain a better understanding of the regulation mechanisms of CEBPB and investigate whether CEBPB could regulate the production of ECM via the TGFB1/SMAD3 signaling pathway in glioma, the microarray data deposited by Carro et al. were further analyzed with bioinformatics methods. Firstly, the differentially expressed genes (DEGs) between SNB19 human glioma cells transduced with non-target control small hairpin RNA (shRNA) lentiviral vectors for 72 h and SNB19 human glioma cells transduced with CEBPB shRNA lentiviral vectors for 72 h were identified and annotated. Subsequently, their potential functions were predicted by enrichment analysis. Finally, protein-protein interaction (PPI) network and transcriptional regulatory network were constructed to screen key genes.

In this study, a total of 529 DEGs were obtained, including 336 up-regulated genes and 193 down-regulated genes. Enrichment analysis indicated that the up-regulated CCL2 was significantly enriched in the chemokine signaling pathway. Reports have found that chemokine expressed by stromal cells or endogenously produced in glioma cells may play key roles in tumor cell migration, invasion, proliferation, angiogenesis and immune cell infiltration in the tumor mass [26]. The chemokine CCL2 can promote glioma tumor aggressiveness by promoting attraction of T regulatory cells (which suppress the lymphocyte anti-tumor effector function) and microglial cells (which can reduce the anti-tumor functions and secrete pro-invasive metalloproteinases) [27, 28]. Meanwhile, metalloproteinases can promote the glioma invasion through the detachment of ECM [29]. Besides, results of DEGs annotation showed that CCL2 was screened out as a TAG. Therefore, we speculated that the increased expression of CCL2 could promote glioma aggressiveness through the pathway of chemokine signaling.

In addition, some up-regulated genes (such as THBS1, THBS2, SMAD5, and SMAD6) were significantly enriched in the TGF-beta signaling pathway in our study. Recently, it has been reported that the TGFB is a key factor in controlling migration, invasion and angiogenesis in glioblastoma and induces profound immunosuppression [30]. Besides, the THBS1 (belonging to thrombospondin family), which is referred as a TGFB activating protein, induces the glioma invasion [31]. THBS1 is a powerful anti-angiogenesis protein in glioblastoma [32]. These suggested that THBS1 might play a key role in regulating the angiogenesis in glioma. As another member of thrombospondin family, THBS2 may be a potential inhibitor of tumor growth and angiogenesis [33]. Moreover, it has been shown that THBS2 can function as an endogenous inhibitor of angiogenesis through directly affecting endothelial cell migration, proliferation, survival, and apoptosis [34]. In our study, we also found that THBS1 and THBS2 were significantly involved in the pathway of focal adhesion. Previous study reported that focal adhesion can suppress the migration and metastasis of tumor cells [35]. Therefore, we speculated that THBS1 and THBS2 could regulate angiogenesis and invasion in glioma via TGF-beta signaling pathway and focal adhesion pathway. Former researches have shown that SMAD6 is an inhibitor of TGFB signaling and blocked the phosphorylation of receptor-regulated SMADs (such as SMAD5) in the cytoplasm [36]. As a result, we assumed that SMAD5 and SMAD6 might affect glioma by regulating the TGFB signaling. In the PPI network, THBS1 could interact with CCL2, to some extent, indicating that THBS1 might play key roles in glioma through regulating CCL2. Consequently, THBS1, THBS2, SAMD5 and SMAD6 could be key factors involved in the CEBPB-silenced glioma.

Moreover, CCND1, as a member of the cyclin family, possessed the highest degree in the PPI network. Cyclins can modulate tumor cell cycle through alterations in cyclin-dependent kinase activity [37]. What’s more, researchers have discovered that overexpression of CCND1 can elevate the proliferation and invasion potential of human glioblastoma cells [38]. In the PPI network, we also found that CCND1 had interaction with THBS1, suggesting that CCND1 could be involved in regulating proliferation and invasion of glioma via interacting with THBS1.

TGFBR2 plays a key role in TGFB signal propagation via activating TGFBR1 and the phosphorylation of SMAD proteins [39]. Moreover, silencing of TGFBR2 can abolish TGFB-induced invasion and migratory responses of glioblastoma in vitro [40]. In our study, we also discovered that the up-regulated TCF12 could regulate TGFB1 and SMAD3, indicating that CEBPB might regulate TGFB1 and SMAD3 through TCF12. Previous studies have shown that TGFB1/SMAD3 can promote tumor cell migration, invasion and metastasis through inducing epithelial-mesenchymal transition [41, 42]. What is more, TCF12 has been found to suppress the expression of E-cadherin, which can lead to the metastasis of tumor cells [43]. Therefore, we assumed that CEBPB might regulate TGFBR2 and SMAD3 through TGF-β1/SMAD3 signaling pathway in glioma, and CEBPB could also affect metastasis of glioma by regulating TCF12. However, in our study, TGFB1 and SMAD3 were not significantly expressed, which might due to the relatively short time for CEBPB silencing. In our further research, the regulation of CEBPB on TGFB1/SMAD3 will be studied with CEBPB-silenced for a relatively long time.

We conducted a comprehensive bioinformatics analysis to identify genes which may be correlated with CEBPB-silenced glioma. A total of 529 DEGs were identified in the normal glioma cells compared with the CEBPB-silenced glioma cells. Besides, The identified DEGs, such as TCF12, TGFBR2, CCL2, THBS1, THBS2, SMAD5, SMAD6, and CCND1, might play important roles in the progression of glioma via the regulation of CEBPB. However, further researches are still needed to unravel their action mechanisms in glioma.