Identification of Key Genes and Pathways in Osteosarcoma by Bioinformatics Analysis

Purpose. Osteosarcoma (OS) is the most primary bone malignant tumor in adolescents. Although the treatment of OS has made great progress, patients’ prognosis remains poor due to tumor invasion and metastasis. Materials and Methods. We downloaded the expression profile GSE12865 from the Gene Expression Omnibus database. We screened differential expressed genes (DEGs) by making use of the R limma software package. Based on Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Gene Set Enrichment Analysis, we performed the function and pathway enrichment analyses. Then, we constructed a Protein-Protein Interaction network and screened hub genes through the Search Tool for the Retrieval of Interacting Genes. Result. By analyzing the gene expression profile GSE12865, we obtained 703 OS-related DEGs, which contained 166 genes upregulated and 537 genes downregulated. The DEGs were primarily abundant in ribosome, cell adhesion molecules, ubiquitin-ubiquitin ligase activity, and p53 signaling pathway. The hub genes of OS were KDR, CDH5, CD34, CDC42, RBX1, POLR2C, PPP2CA, and RPS2 through PPI network analysis. Finally, GSEA analysis showed that cell adhesion molecules, chemokine signal pathway, transendothelial migration, and focal adhesion were associated with OS. Conclusion. In this study, through analyzing microarray technology and bioinformatics analysis, the hub genes and pathways about OS are identified, and the new molecular mechanism of OS is clarified.

Long Non-Coding RNA CD27-AS1-208 Facilitates Melanoma Progression by Activating STAT3 Pathway

Melanoma is the most lethal skin cancer that originates from epidermal melanocytes. Recently, long non-coding RNAs (lncRNAs) are emerging as critical regulators of cancer pathogenesis and potential therapeutic targets. However, the expression profile of lncRNAs and their role in melanoma progression have not been thoroughly investigated. Herein, we firstly obtained the expression profile of lncRNAs in primary melanomas using microarray analysis and unveiled the differentially-expressed lncRNAs compared with nevus. Subsequently, a series of bioinformatics analysis showed the great involvement of dysregulated lncRNAs in melanoma biology and immune response. Further, we identified lncRNA CD27-AS1-208 as a novel nuclear-localized factor with prominent facilitative role in melanoma cell proliferation, invasion and migration. Mechanistically, CD27-AS1-208 could directly interact with STAT3 and contribute to melanoma progression in a STAT3-dependent manner. Ultimately, the role of CD27-AS1-208 in melanoma progression in vivo was also investigated. Collectively, the present study offers us a new horizon to better understand the role of lncRNAs in melanoma pathogenesis and demonstrates that CD27-AS1-208 up-regulation contributes to melanoma progression by activating STAT3 pathway. Targeting CD27-AS1-208 in melanoma cells can be exploited as a potential therapeutic approach that needs forward validation in clinical trials in the future.

C-kit+VEGFR-2+ Mesenchymal Stem Cells Differentiate into Cardiovascular Cells and Repair Infarcted Myocardium after Transplantation

Background: Resent preclinical studies and clinical trails prove that transplantation of mesenchymal stem cells (MSCs) is a promised therapy for ischemic diseases. However, the properties of c-kit+ cells in MSCs remain unclear. We investigated the differential potential of c-kit+VEGFR-2+ MSCs and evaluated their effects on repairing the infarcted myocardium after transplantation. Methods: c-kit+VEGFR-2+ MSCs were isolated from rat bone marrow. Gene expression profile of the cells was examined with RNA-sequencing. Differential potential of the cells was determined after induction with VEGF, TGF-β and BMP-2 for 2 weeks. Improvement of cardiac function and repair of the infarcted myocardium were assessed at 4 weeks after transplantation of the cells preconditioned with hypoxia and serum deprivation. Results: Gene expression profile revealed that the upregulated genes are enrichment of genes related to immune process and cell differentiation. The cells represented a potential of differentiation towards endothelial cell, smooth muscle cells and cardiamyocytes. In hypoxic condition, secretion of VEGF, SCF and SDF-1α from the cells was increased. VEGF and SCF promoted proliferation and migration of the cells. VEGF could induce the cells to incorporate to the microvessels. After transplantation of the preconditioned cells into the infarcted myocardium, cardiac function was improved, scar size of the infarcted myocardium was decreased, and angiogensis and myocardium repair were enhanced significantly. With preconditioning and delivery by fibrin gel, survival of the cells in the ischemic tissue was augmented. Conclusion: These results suggest that c-kit+VEGFR-2+ MSCs have a potential of differentiation towards cardiovascular cells. SCF/c-kit and VEGF/VEGFR-2 singnalling pathways regulate proliferation, migration and differentiation of the cells. Transplantation of c-kit+VEGFR-2+ MSCs may enhance repair of the infarcted myocardium effectively.

RNA Sequencing Reveals circRNA Expression Profiles in Chicken DF1 Cells Infected with H5N1 Influenza Virus

H5N1, a highly pathogenic avian influenza virus that is prevalent in Asia, seriously harms the poultry industry and global public health. However, its pathogenesis is still not well understood. Circular RNAs (circRNAs), a newly identified type of RNA, reportedly play crucial roles in various pathogenic processes. In this study, RNA sequencing was performed to analyze the expression profile of circRNAs in H5N1-infected chicken embryo fibroblast (DF1) cells. A total of 14,586 circRNAs were identified. The expression profiles of infected cells changed more significantly, relative to uninfected cells, as the infection period was extended; namely, 261, 626, and 1103 circRNAs exhibited differential expression in cells infected for 6 h, 12 h, and 20 h, respectively. GO and KEGG enrichment analysis revealed significant enrichment of the parental genes of the differentially expressed circRNAs for viral replication and immune response-related pathways, such as positive regulation of transcription from the RNA polymerase II promoter, positive regulation of I-kappaB kinase/NF-kappaB signaling, innate immune response, and ubiquitin protein ligase activity. In conclusion, we identified the expression profile of circRNAs in H5N1-infected chicken DF1 cells. Bioinformatic analyses of the dysregulated circRNAs suggest that circRNAs might play important roles in the pathogenesis of H5N1 infection, offering new insights into the mechanisms underlying H5N1–host interaction.

Comprehensive analysis of expression profile and prognostic significance of interferon regulatory factors in pancreatic cancer

Background Pancreatic cancer (PC) is a highly lethal disease and an increasing cause of cancer-associated mortality worldwide. Interferon regulatory factors (IRFs) play vital roles in immune response and tumor cellular biological processes. However, the specific functions of IRFs in PC and tumor immune response are far from systematically clarified. This study aimed to explorer the expression profile, prognostic significance, and biological function of IRFs in PC. Results We observed that the levels of IRF2, 6, 7, 8, and 9 were elevated in tumor compared to normal tissues in PC. IRF7 expression was significantly associated with patients’ pathology stage in PC. PC patients with high IRF2, low IRF3, and high IRF6 levels had significantly poorer overall survival. High mRNA expression, amplification and, deep deletion were the three most common types of genetic alterations of IRFs in PC. Low expression of IRF2, 4, 5, and 8 was resistant to most of the drugs or small molecules from Genomics of Drug Sensitivity in Cancer. Moreover, IRFs were positively correlated with the abundance of tumor infiltrating immune cells in PC, including B cells, CD8+ T cells, CD4+ T cells, macrophages, Neutrophil, and Dendritic cells. Functional analysis indicated that IRFs were involved in T cell receptor signaling pathway, immune response, and Toll-like receptor signaling pathway. Conclusions Our results indicated that certain IRFs could serve as potential therapeutic targets and prognostic biomarkers for PC patients. Further basic and clinical studies are needed to validate our findings and generalize the clinical application of IRFs in PC.

Post-Translational Tubulin Modifications in Differentiated Human Neural Stem Cells

The tubulin protein fulfills a variety of cellular functions that range from chromosomal separation to locomotion. The functional diversity of tubulin is achieved through the expression of specific tubulin isotypes in different cell types or developmental time periods. Post-translational modifications (PTMs) of tubulin also are vital for specific intracellular tasks, such as binding and recruiting motor proteins. In neurons, the isotypic expression profile for tubulin is well characterized, and the importance of PTMs for proper neuronal function has gained recent attention due to their implication in neurodegenerative disorders. In contrast, the role of tubulin specializations in the specification of neural cell fate has received minimal attention and studies of tubulin PTMs and isotypes in neuroglia such as astrocytes are relatively few. To bridge this knowledge gap, we undertook an analysis of PTMs in neurons and astrocytes derived from the federally approved H9 hESC-derived human neural stem cell (hNSC) line. In hNSCs, basal cells can be directed to assume neural fate as neurons or astrocytes by specifying different media growth conditions. Immunocytochemical methods, fluorescent antibody probes, and confocal microscopy facilitated image acquisition of fluorescent signals from class III β- tubulin (βIII-tubulin), acetylated tubulin, and polyglutamylated tubulin. Fluorescent probe intensities were assessed with the EBImage package for the statistical programming language R and compared using Student's t-tests. Qualitative analysis indicated that βIII-tubulin, acetylated tubulin, and polyglutamylated tubulin were expressed to some degree in basal hNSCs and their media-differentiated hNSC neuronal and astroglial progeny. In media-differentiated hNSC astrocyte progeny, quantification and statistical analysis of fluorescence probe intensity showed that acetylated tubulin/ βIII-tubulin ratios were greater than the ratio for polyglutamylated tubulin/ βIII-tubulin. These findings represent a snapshot of the dynamic and varied changes tubulin expression profile during the specification of neural cell fate. Results imply that investigations of tubulin PTMs have the potential to advance our understanding of the generation and regeneration of nervous tissue.