Exploring the key genes and pathways of side population cells in human osteosarcoma using gene expression array analysis

Osteosarcoma (OS), which is produced by mesenchymal cells, is the most common primary malignant tumor originating from bone tissues. OS occurs mainly in children and adolescents and accounts for 8.9% of cancer-related diseases which lead to death [1, 2]. Although new therapies of neoadjuvant chemotherapy and surgery have contributed greatly to OS treatment, the 5-year survival rate of OS is difficult to exceed 60–65% [3, 4]. To sum up, the early diagnosis and effective treatment of OS are the breakthrough point of OS research and clinical application, and exploring the pathogenesis, development, and metastasis of OS is the key. Although a large number of studies have been made on OS at molecular and cellular levels, the mechanisms of OS formation and metastasis have not been fully elucidated.

Side population (SP) cells are a group of special cells, which were found when Hoechst and flow cytometry are used to separate hematopoietic stem cells and progenitor cells. SP cells are widely distributed in a variety of adult tissues, embryos, and some tumor cell lines [5]. They not only have self-renewal and multipotential differentiation potential, but also have unique phenotypic markers and biological characteristics of stem cells, whose characteristics are very similar to those of tumor stem cells [6, 7]. SP cells help maintain the tumorigenic potential of some tumor cell lines [8‐10]. Ho et al. reported that SP cells were enriched in tumor-initiating capability compared with non-SP cells by nonobese diabetic/severe combined immunodeficiency xenograft experiments. Matrigel invasion assay showed that SP cells also have higher potential for invasiveness. Human telomerase reverse transcriptase expression was higher in the SP cells, suggesting that this fraction may represent a reservoir with unlimited proliferative potential for generating cancer cells [11]. Chiba et al. hold that a minority population of SP cells detected in hepatocellular carcinoma cells possessed extreme tumorigenic potential and provided heterogeneity to the cancer stem cell system characterized by distinct hierarchy [12]. Wang et al. observed a strong tumorigenesis ability of SP cells from HeLa cell line following in vivo transplantation into 5- to 6-week-old female Balb/c mice [13]. These findings indicate that SP cells is an enriched source of tumor-initiating cells with stem cell properties and may be an important target for effective therapy and a useful tool to investigate the tumorigenic process.

Interestingly, SP cells are present in primary mesenchymal neoplasms, including primary OS [14]. Here, we downloaded the gene expression profile GSE63390 from the Gene Expression Omnibus (GEO) database and made bioinformatics analysis to investigate differentially expressed genes (DEGs) that regulated between the SP cells and the non-SP cells from primary human OS. By doing this, we hope that the key target genes and pathways involved in the carcinogenesis and progression of human OS could be identified and existing molecular mechanisms could be revealed.

OS is the most common primary bone sarcoma [15‐19]. Previous studies discovered that sarcomas contain a small subpopulation of tumor-propagating cells (TPCs) such as SP cells, characterized by enhanced tumorigenicity and self-renewal capacity [20‐22]. Self-renewal is a defining characteristic of these cells and is associated with tumor recurrence [23, 24]. The inhibition of self-renewal in OS SP cells may offer valuable targets of therapy and tumorigenesis mechanisms. In the present study, the gene expression profile of GSE63390 was downloaded and a bioinformatics analysis was performed. The results showed that there were 141 DEGs in SP cells compared with non-SP cells of human OS. Furthermore, GO and KEGG pathway and gene–gene interaction network analysis were performed to obtain the biomarkers or the major genes related to cytogenetic pathways to OS tumorigenesis.

In order to disclose the underlying molecular mechanisms between SP cells and human OS, we characterized the possible GO functional terms and signaling pathways of DEGs. Considering the results of GO function analysis, we linked the DEGs with mRNA catabolic process and cellular modified amino acid metabolic process, which are probably very important for the development process of human OS. As previous articles reported, our KEGG pathway analysis showed that hippo signaling pathway, mTOR signaling pathway, hedgehog signaling pathway, and others were among the most relevant pathways for OS. Zhou et al. found that the correlation between the mTOR/p70S6K signal transduction pathway in human OS and patients’ prognosis, and the overexpression of mTOR and p70S6K, is well correlated with tumor metastasis pattern, which might be an important mechanism responsible for the survival and proliferation of OS cells [25]. Wang et al. identified that hippo/YAP signaling pathway not only is involved in tumorigenesis, but also hippo/YAP signaling pathway induces OS chemoresistance [26]. Chai et al. deemed that the oncogenic activities in OS are mediated by TED1 through hippo–YAP1 signaling [27]. Cheng et al. highlighted a new discovery that CNOT1–LMNA–Hedgehog signaling pathway axis exerts an oncogenic role in OS progression, which could be a potential target for gene therapy [28]. Emerging data suggested that interference with hedgehog signaling signal transduction by inhibitors may reduce OS cell proliferation and tumor growth, thereby preventing osteosarcomagenesis [29]. All these signaling pathways may play important roles in molecular mechanism of development process between SP cells and human OS.

Also of note is that there were numerous evidences for our DEGs of SP cells, which have proven to play important roles during OS tumorigenesis. The STRING database revealed top 20 high-degree hub nodes of DEGs including GAPDH, GART, FAU, HSPA8, EEF1A1, RPS3A, EIF4E, MAPK3, IL6, RPL6, eukaryotic translation initiation factor 3 beta (EIF3b), DEAD-box helicase 5 (DDX5), heat shock protein family D member 1 (HSPD1), ribosomal protein S29 (RPS29), ribosomal protein L18a (RPL18A), ribosomal protein L18 (RPL18), calmodulin 3 (CALM3), actin gamma 1 (ACTG1), ribosomal protein S27 (RPS27), and ribosomal protein L32 (RPL32). Furthermore, we analyzed the gene interaction network and top 10 modules using MCODE and found that ACTG1, eukaryotic translation initiation factor 3 subunit E (EIF3E), EIF4E, FAU, HSPD1, IL-6, KiSS-1 metastasis-suppressor (KISS1), PRIM1, pituitary tumor-transforming 1 (PTTG1), PRL32, S100 calcium-binding protein A8 (S100A8), S100 calcium-binding protein A9 (S100A9), serine hydroxymethyltransferase 1 (SHMT1), and TNF receptor-associated protein 1 (TRAP1) were the core interaction genes, which may be potential therapeutic targets for OS. Parts of them were in accord with STRING database results. Ajiro et al. found that serine/arginine-rich splicing factor 3 (SRSF3) regulates the expression of DDX5 in human OS U2OS cells [30]. By participating in the transcriptional regulation of ribosomal protein L34 (RPL34) which plays an important role in the proliferation of OS cells, MYC interacts with the subunits of EIF3 and probably involves the translational control of growth-promoting proteins [31]. EIF3, a multi-subunit complex, plays a critical role in translation initiation. Expression levels of EIF3 subunits are elevated or decreased in various cancers, suggesting a role for EIF3 in tumorigenesis [32]. Choi et al. confirmed that EIF3b silencing could completely suppress cell growth in multiple OS cell lines [33]. Osborne et al. also discovered that EIF4E is uniformly expressed in OS patient samples and it could be a relevant protein biomarker in OS [34]. Rossman et al. found that overexpressing FAU itself is able to transform human osteogenic sarcoma cells to anchorage independence and make them easy to proliferate [35]. Liang et al. proved that the expression of HSPD1 was high in OS tissues and cells; moreover, targeted inhibition of this gene could inhibit the proliferation of the tumor [36]. Zhang et al. indicated that the decreased expression of KISS1 is correlated with distant metastasis of OS, and KISS1 may function as a tumor suppressor in OS cells through inhibition of the MAPK pathway [37]. EEF1A1 is overexpressed in OS cell lines, and siRNA treatment against EEF1A1 produces a chemosensitization toward methotrexate, which showed that this gene is a potential therapeutic target of OS [38]. Through ASK1/p38/AP-1 signal pathway, IL-6 occurs, which in turn results in the activations of vascular endothelial growth factor (VEGF) expression and contributing the angiogenesis of human OS cells [39]. In addition, the ILK/Akt/AP-1 pathway is activated after IL-6 treatment, and IL-6 induces expression of ICAM-1 and migration activity of human OS cells [40]. Yotov et al. proposed that PRIM1 is a major target of 12q13 amplifications, playing an essential role in tumorigenesis of human OS [41]. PTTG1 siRNA markedly downregulates the expression of PTTGl protein in OS cells, leading to obvious inhibition of cell proliferation, alters cell cycle distribution, and reduces ability of invasion of OS cells [42]. Tsai et al. deemed that expression stability of RPL32 is high in OS samples, and this gene could be a potential target [43]. In Montesano’s study, the anti-apoptotic role of TRAP1 is confirmed in Saos-2 OS cells, which suggested that increased expression of this gene could make diethylmaleate-adapted and chemoresistant cells evade toxic effects of oxidants and anticancer drugs [44]. Endo-Munoz et al. proved downregulation of S100A8 between chemo-naive OS biopsies and non-malignant bone biopsies, highlighting their potential as therapeutic targets for OS [45]. Cheng et al. confirmed that through inactivating MAPK and NF-κB signaling pathways, downregulation of S100A9 could inhibit OS cell growth [46]. Besides, Both et al. concluded that some genes, including SHMT1, are candidate oncogenes in 17p11.2–p12 of importance in OS tumorigenesis [47]. Taken together, all these core genes discovered in OS SP cells by bioinformatics enrichment analysis and gene interaction network analysis may increase or decrease tumorigenicity and self-renewal capacity of OS SP cells; further, these changed SP cells could result in development process of human OS.

Some gene and pathway interaction relationship predicted in our study has been reported in previous researches. Oncogenic activation of mTOR signaling significantly contributes to the progression of different types of cancers including OS. EIF4E is one of the downstream effectors of mTOR. Activated mTOR contributes to OS cellular transformation and poor cancer prognosis via targeting the downstream effectors such as EIF4E [48]. In addition, our results of core pathways and their associated genes found also confirmed the relationship of EIF4E and mTOR signaling pathway. Therefore, EIF4E/mTOR signaling pathway could be a potential research target for therapy and tumorigenesis of OS.

Lastly, there are several limitations of this study. It is acknowledged that predicting key genes merely by means of bioinformatics is not sufficient, and further molecular biological experiments such as the use of gene transfection/knockdown and quantitative real-time polymerase chain reaction are needed to confirm these results.

In summary, 141 DEGs were identified including 72 upregulated DEGs and 69 downregulated DEGs screened in SP cells compared with non-SP cells. GO and KEGG pathway analysis provided a series of related key genes and pathways to contribute to the understanding of the molecular mechanisms between SP cells and human OS, thus yielding clues to speculate the EIF4E/mTOR signaling pathway is highly correlated with the development process of OS. Furthermore, these predictions need further experimental validation in future studies.