PAX3 is a biomarker and prognostic factor in melanoma: Database mining

Experimental and Clinical Biomarkers for Progressive Evaluation of Neuropathology and Therapeutic Interventions for Acute and Chronic Neurological Disorders

This article describes commonly used experimental and clinical biomarkers of neuronal injury and neurodegeneration for the evaluation of neuropathology and monitoring of therapeutic interventions. Biomarkers are vital for diagnostics of brain disease and therapeutic monitoring. A biomarker can be objectively measured and evaluated as a proxy indicator for the pathophysiological process or response to therapeutic interventions. There are complex hurdles in understanding the molecular pathophysiology of neurological disorders and the ability to diagnose them at initial stages. Novel biomarkers for neurological diseases may surpass these issues, especially for early identification of disease risk. Validated biomarkers can measure the severity and progression of both acute neuronal injury and chronic neurological diseases such as epilepsy, migraine, Alzheimer's disease, Parkinson's disease, Huntington's disease, traumatic brain injury, amyotrophic lateral sclerosis, multiple sclerosis, and other brain diseases. Biomarkers are deployed to study progression and response to treatment, including noninvasive imaging tools for both acute and chronic brain conditions. Neuronal biomarkers are classified into four core subtypes: blood-based, immunohistochemical-based, neuroimaging-based, and electrophysiological biomarkers. Neuronal conditions have progressive stages, such as acute injury, inflammation, neurodegeneration, and neurogenesis, which can serve as indices of pathological status. Biomarkers are critical for the targeted identification of specific molecules, cells, tissues, or proteins that dramatically alter throughout the progression of brain conditions. There has been tremendous progress with biomarkers in acute conditions and chronic diseases affecting the central nervous system.

Identifying FBLN1 (Gene ID: 2192) as a Potential Melanoma Biomarker for Melanoma based on an Analysis of microRNA Expression Profiles in the GEO and TCGA Databases

Aims: We analyzed and compared the gene expression profiles (GSE92763) from normal melanocytes with malignant melanoma cell lines to identify genes that were differentially expressed that could serve as potential biomarkers for melanoma diagnosis. Materials and Methods: Gene expression profiles from the GSE92763 dataset were downloaded from the Gene Expression Omnibus (GEO) database. By comparing normal human melanocytes with multiple melanoma cell lines we identified 127 differentially expressed genes whose expression was altered. These data were used to identify hub genes associated with protein-protein interaction networks using Cytoscape software. To explore the biological functions of the aforementioned hub genes, we utilized the clusterProfiler package in R studio to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. We then used the Gene Expression Profiling Interactive Analysis (GEPIA) website to determine the association of these hub genes with overall survival (OS). In addition, we utilized the Oncomine and Cancer Cell Line Encyclopedia (CCLE) databases to further analyze and compare the expression of these key genes associated with melanoma with other tumor types. Results: The hub genes included three upregulated and seven downregulated genes, which were linked with extracellular junctions, migration, paracrine and proliferation functions based on GO. In addition, we performed a confirmatory analysis of the hub genes using The Cancer Genome Atlas (TCGA) database. This analysis revealed that the expression of the Fibulin 1 (FBLN1; gene ID: 2192) gene was significantly downregulated in melanomas, and that its expression level in melanoma patients was significantly associated with OS with high expressors having better OS (log-rank p = 0.0034, hazard ratio = 1.5, p = 0.0036). We further analyzed the expression of FBLN1 in melanoma using the TCGA and Oncomine databases, and confirmed that FBLN1 is expressed at lower levels than in other cells (p = 2.03E^-15, t = -15.586). FBLN1 has extremely high DNA copy number and low messenger RNA expression in melanoma cell lines according to the CCLE analysis. Conclusion: These results suggest that FBLN1 expression may be utilized as a biomarker and essential prognostic factor for melanoma; as well as provide an important theoretical basis for the development of melanoma treatments.

Identification of potential key genes in gastric cancer using bioinformatics analysis

Gastric cancer (GC) is one of the most common types of cancer worldwide. Patients must be identified at an early stage of tumor progression for treatment to be effective. The aim of the present study was to identify potential biomarkers with diagnostic value in patients with GC. To examine potential therapeutic targets for GC, four Gene Expression Omnibus (GEO) datasets were downloaded and screened for differentially expressed genes (DEGs). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were subsequently performed to study the function and pathway enrichment of the identified DEGs. A protein-protein interaction (PPI) network was constructed. The CytoHubba plugin of Cytoscape was used to calculate the degree of connectivity of proteins in the PPI network, and the two genes with the highest degree of connectivity were selected for further analysis. Additionally, the two DEGs with the largest and smallest log Fold Change values were selected. These six key genes were further examined using Oncomine and the Kaplan-Meier plotter platform. A total of 99 upregulated and 172 downregulated genes common to all four GEO datasets were screened. The DEGs were primarily enriched in the Biological Process terms: ‘extracellular matrix organization’, ‘collagen catabolic process’ and ‘cell adhesion’. These three KEGG pathways were significantly enriched in the categories: ‘ECM-receptor interaction’, ‘protein digestion and absorption’, and ‘focal adhesion’. Based on Oncomine, expression of ATP4A and ATP4B were downregulated in GC, whereas expression of the other genes were all upregulated. The Kaplan-Meier plotter platform confirmed that upregulated expression of the identified key genes was significantly associated with worse overall survival of patients with GC. The results of the present study suggest that FN1, COL1A1, INHBA and CST1 may be potential biomarkers and therapeutic targets for GC. Additional studies are required to explore the potential value of ATP4A and ATP4B in the treatment of GC.

FNDC3B is associated with ER stress and poor prognosis in cervical cancer

Currently, the occurrence and mortality rate of cervical cancer is high, particularly in low-to-middle-income countries. Therefore, the development of novel diagnostic and treatment strategies for cervical cancer is urgently required. The aim of the present study was to assess the prognostic significance of fibronectin type III domain containing 3B (FNDC3B) expression in patients with cervical cancer and to determine the underlying mechanism of FNDC3 in tumor development. Analysis of the ONCOMINE database revealed that FNDC3B was significantly upregulated in cervical cancer tissue compared with normal tissue. Additionally, FNDC3B expression data and the clinical characteristics of patients with cervical cancer were obtained from the cBioPortal database. Correlations between FNDC3B expression and overall survival were subsequently investigated. The results revealed that increased FNDC3B expression was significantly correlated with a lower overall survival in patients with cervical cancer. A co-expression network was subsequently constructed to elucidate the function of FNDC3B in cervical cancer. Co-expression genes for FNDC3B were obtained from the cBioPortal database and were subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. The results demonstrated that the genes were enriched in pathways associated with migration, invasion, endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). Furthermore, immunofluorescence results obtained from the Human Protein Atlas revealed that the FNDC3B protein was localized to the ER. The results revealed that upregulated FNDC3B expression may be a biomarker for poor prognosis for patients with cervical cancer. Additionally, the results revealed that FNDC3B may serve an oncogenic role in cancer development via ER stress, UPR, cell migration and invasion. However, further studies are required to determine the exact molecular mechanism of FNDC3B in the development of cervical cancer and to assess its potential as a novel therapeutic target for the treatment of this disease.