Identification of potential key genes associated with osteosarcoma based on integrated bioinformatics analyses

Due to high rates of metastasis and poor clinical outcomes for patients, it is important to study the pathomechanisms of osteosarcoma. However, due to the fact that osteosarcoma shows significant interindividual variation and high heterogeneity, the identification of differentially expressed genes (DEGs) at the population level cannot answer many important questions related to osteosarcoma tumorigenesis. Therefore, a new strategy to identify dysregulated genes in osteosarcoma samples is required. The aim of this study was to improve our understanding of osteosarcoma pathogenesis by identifying genes with universal aberrant expression in osteosarcoma samples. Because the relative expression ordering of genes is stable in normal bone tissues but is disrupted in osteosarcoma tissues, we used the RankComp algorithm to identify DEGs in normal and osteosarcoma tissue samples. We then calculated the dysregulation frequency for each gene. Genes with deregulation frequencies above 80% were deemed to be universal DEGs. Next, coexpression, pathway enrichment, and protein-protein interaction network analyses were performed to characterize the functions of these genes. From 188 samples of osteosarcoma obtained from four datasets measured on different platforms, 51 universal DEGs were identified, including 4 universally upregulated genes and 47 universally downregulated genes. Genes that were differentially coexpressed with these universal DEGs were found to be enriched in 46 cancer-related pathways. In addition, functional and network analyses showed that genes with high dysregulation frequencies were involved in cancer-related functions. Thus, the commonly aberrant genes identified in osteosarcoma tissues may be important targets for osteosarcoma diagnosis and therapy.     

Integrative analysis of mRNA and microRNA expression profiles in laryngeal squamous cell carcinoma

Larynx cancer is a therapeutically challenging disease. Rapidly evolving experimentally validated data have significantly improved our understanding of the complex role of numerous RNA, DNA, and proteins that play a role in the development and progression of cancer. Based on the insights from approximately two decades of research, it seems clear that microRNAs (miRNAs) have revolutionized our concepts related to the main role of noncoding RNAs in different cancers’ progression, development, and metastasis. Mechanistically, miRNAs have been reported to regulate different RNAs and finally protein-coding genes. The expression profiling of miRNAs and messenger RNA (mRNAs) was conducted for a deeper analysis of the miRNAs and mRNAs which play an essential role in larynx cancer. Downregulation or upregulation over twofolds in the miRNAs was considered to be significant, and that of sixfolds or below was considered to be significant for the mRNAs. In accordance with this approach, the expression levels of 43 miRNAs were increased in this study, whereas the expression levels of 129 were decreased. Accordingly, all the genomic expression studies provided evidence of upregulation of 97 genes, whereas 128 genes were found to be downregulated. Among these miRNAs, hsa-miR-20a-3p and hsa-miR-1972 were noted to be important in the etiology of larynx cancer.     

Identification of differentially expressed genes in primary Sjögren's syndrome

Primary Sjögren's syndrome (pSS) is a chronic systemic autoimmune disease that affects exocrine glands. To study the molecular mechanism and identify crucial genes/pathways in pSS pathogenesis, the microarray-based whole-genome gene expression profiles from salivary glands of patients with pSS and non-sicca controls were retrieved. After normalization and subsequent batch effect adjustment, significance analysis of microarrays method was applied to five available datasets, and 379 differentially expressed genes (DEGs) were identified. The 300 upregulated DEGs were enriched in Gene Ontology terms of immune and inflammatory responses, including antigen processing and presentation, interferon-mediated signaling pathway, and chemotaxis. Previously reported pSS-associated genes, including HLA-DRA, TAP2, PRDM1, and IFI16, were found to be significantly upregulated. The downregulated DEGs were enriched in pathways of salivary secretion, carbohydrate digestion and absorption, and starch and sucrose metabolism, implying dysfunction of salivary glands during pathogenesis. Next, a protein-protein interaction network was constructed, and B2M, an upregulated DEG, was shown to be a hub, suggesting its potential involvement in pSS development. In summary, we found the activation of pSS-associated genes in pathogenesis, and provide clues for salivary glands dysfunction. Experimental investigation on the identified DEGs in this study will deepen our understanding on pSS.