Establishment of an Immune-Related Gene Signature for Risk Stratification for Patients with Glioma

Non-negative matrix factorization and differential expression analyses identify hub genes linked to progression and prognosis of glioblastoma multiforme

One of the most prevailing primary brain tumors in adult human male is glioblastoma multiforme (GBM), which is categorized by rapid cellular growth. Even though the combination therapy comprises surgery, chemotherapy, and adjuvant therapies, the survival rate, on average, is 14.6 months. Glioma stem cells (GSCs) have key roles in tumorigenesis, progression, and defiance against chemotherapy and radiotherapy. In our study, firstly, the gene expression dataset GSE124145 was retrieved; the non-negative matrix factorization (NMF) method was applied on GBM dataset, and differentially expressed genes analysis (DEGs) was performed. After which, overlapping genes between metagenes and DEGs were detected to examine the Gene Ontology (GO) categories in the biological process (BP) in the stemness of GBM. The common hub genes were used to construct protein-protein interaction (PPI) network and further GO, while Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway was utilized to pinpoint the real hub genes. The analysis of hub genes particular for the same GO categories demonstrated that specific hub genes triggered distinct features of the same biological processes. After utilizing GSE124145 and The Cancer Genome Atlas (TCGA) dataset for survival analysis, we screened five real hub genes: GUCA1A, RFC2, GNG11, MMP19, and NRG1, which are strongly associated with the progression and prognosis of GBM. The DEGs analysis revealed that all real hub genes were overexpressed in GBM and TCGA datasets, which further validates our results. The constructed study of PPI, GO, and KEGG pathway on common hub genes was performed. Finally, the KEGG pathways performed on the top 15 candidate hub genes (including six real hub genes) of the PPI network in the GBM gene expression dataset study found mitogen-activated protein kinase (Mapk) signaling pathway to be the most significant pathway. The rest of the hub genes reviewed throughout the analysis might be favorable targets for diagnosing and treating GBM and lower-grade gliomas.

Downregulation of MicroRNA-1 and Its Potential Molecular Mechanism in Nasopharyngeal Cancer: An Investigation Combined with In Silico and In-House Immunohistochemistry Validation

Background

This study was aimed at elucidating the molecular biological mechanisms of microRNA-1 (miR-1) in nasopharyngeal carcinoma (NPC).

Method

In this study, we performed a pooled analysis of miR-1 expression data derived from public databases, such as GEO, ArrayExpress, TCGA, and GTEx. The miRWalk 2.0 database, combined with the mRNA microarray datasets, was used to screen the target genes, and the genes were then subjected to Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis using the DAVID 6.8 database. We then used the STRING 11.0 database and Cytoscape 3.80 software to construct a protein-protein interaction (PPI) network for screening hub genes. Immunohistochemistry (IHC) was further used to validate the expression of hub genes. Finally, potential therapeutic agents for NPC were screened by the Connectivity Map (cMap) database.

Results

Pooled analysis showed that miR-1 expression was significantly decreased in NPC (SMD = −0.57; P < 0.05). The summary receiver operating characteristic curve suggested that miR-1 had a good ability to distinguish cancerous tissues from noncancerous tissues (AUC = 0.78). The results of GO analysis focused on mitotic nuclear division, DNA replication, cell division, cell adhesion, extracellular space, kinesin complex, and extracellular matrix (ECM) structural constituent. The KEGG analysis suggested that the target genes played a role in key signaling pathways, such as cell cycle, focal adhesion, cytokine-cytokine receptor interaction, ECM-receptor interaction, and PI3K/Akt signaling pathway. The PPI network suggested that cyclin-dependent kinase 1 (CDK1) was the hub gene, and the CDK1 protein was subsequently confirmed to be significantly upregulated in NPC tissues by IHC. Finally, potential therapeutic drugs, such as masitinib, were obtained by the cMap database.

Conclusion

miR-1 may play a vital part in NPC tumorigenesis and progression by regulating focal adhesion kinase to participate in cell mitosis, regulating ECM degradation, and affecting the PI3K/Akt signaling pathway. miR-1 has the potential to be a therapeutic target for NPC.