Identification of Co-Deregulated Genes in Urinary Bladder Cancer Using High-Throughput Methodologies

APPLIED SCIENCES-BASEL(2021)

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Abstract
Featured Application Urinary bladder cancer (UBC) is the second most common urogenital solid tumor and the eleventh in the rank among all types of solid tumors. Although several oncogenes and tumor suppressors are known to be implicated in the disease, the list of candidate prognostic markers has recently expanded, as a result of the power of new high-throughput methodologies. The prognosis and therapy of UBC have progressed greatly during the last years. However, a majority of the different tumor subtypes still relapses, manifesting poor prognosis. Here, we identified gene expression patterns being common across different histological phenotypes of UBC. Such an approach could be useful in the discovery of prognostic and therapeutic targets able to be applied in the majority of the tumor's subtypes. Although several genes are known to be deregulated in urinary bladder cancer (UBC), the list of candidate prognostic markers has expanded due to the advance of high-throughput methodologies, but they do not always accord from study to study. We aimed to detect global gene co-expressional profiles among a high number of UBC tumors. We mined gene expression data from 5 microarray datasets from GEO, containing 131 UBC and 15 normal samples. Data were analyzed using unsupervised classification algorithms. The application of clustering algorithms resulted in the isolation of 6 down-regulated genes (TMP2, ACTC1, TAGLN, MFAP4, SPARCL1, and GLP1R), which were mainly implicated in the proteasome, base excision repair, and DNA replication functions. We also detected 6 up-regulated genes (CDC20, KRT14, APOBEC3B, MCM5, STMN, and YWHAB) mainly involved in cancer pathways. We identified lists of drugs that could potentially associate with the Differentially Expressed Genes (DEGs), including Vardenafil, Pyridone 6, and Manganese (co-upregulated genes) or 1D-myo-inositol 1,4,5-triphosphate (co-down regulated genes). We propose 12 novel candidate markers for UBC, as well as potential drugs, shedding more light on the underlying cause of the development and progression of the disease.
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Key words
urinary bladder cancer,microarray,common gene expression,unsupervised machine learning algorithms
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