Bioinformatics analysis and verification of gene targets for renal clear cell carcinoma |
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| Affiliation: | 1. Department of Urology, The Fourth Hospital of Hebei Medical University, No.12 Jiankang Road Shijiazhuang, 050011, Hebei Province, China;2. Department of Oncology, Affiliated Xing Tai People Hospital of Hebei Medical University, Xingtai, 054001, Hebei Province, China;3. Department of Oncology, The Heibei General Hospital, No.348 Heping Road Shijiazhuang, 050051, Hebei Province, China;4. School of Basic Medical Sciences, Hebei Medical University, 361 Zhongshan East Road, Shijiazhuang, Hebei, 050017, China;5. Department of Orthopedics, The Fourth Hospital of Hebei Medical University, No.12 Jiankang Road Shijiazhuang, 050011, Hebei Province, China;6. Department of Immuno-oncology, The Fourth Hospital of Hebei Medical University, No.12 Jiankang Road Shijiazhuang, 050011, Hebei Province, China;1. Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Via F.Cervi 93, 20090, Segrate, Milan, Italy;2. Department of Pharmacological & Biomolecular Sciences (DiSFeB), University of Milan, Via Pascal 36, 20133, Milan, Italy;1. Victor Chang Cardiac Research Institute, Sydney, Australia;2. University of New South Wales, Sydney, Australia;3. School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China;1. Department für Geo- und Umweltwissenschaften, Ludwig-Maximilians-Universität München, 80333 Munich, Germany;2. Departamento de Estratigrafía y Paleontología, Universidad de Granada, Granada, Spain, and Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, Armilla, Spain;3. Nuclear Research & Consultancy Group (NRG), 1755 LE Petten, the Netherlands;4. Centro de Instrumentación Científica, Universidad de Granada, 18071 Granada, Spain;5. Zentrale Einrichtung Elektronenmikroskopie, Universität Ulm, 89081 Ulm, Germany |
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| Abstract: | BackgroundIt is estimated that there are 338,000 new renal-cell carcinoma releases every year in the world. Renal cell carcinoma (RCC) is a heterogeneous tumor, of which more than 70% is clear cell renal cell carcinoma (ccRCC). It is estimated that about 30% of new renal-cell carcinoma patients have metastases at the time of diagnosis. However, the pathogenesis of renal clear cell carcinoma has not been elucidated. Therefore, it is necessary to further study the pathogenesis of ccRCC.MethodsTwo expression profiling datasets (GSE68417, GSE71963) were downloaded from the GEO database. Differentially expressed genes (DEGs) between ccRCC and normal tissue samples were identified by GEO2R. Functional enrichment analysis was made by the DAVID tool. Protein-protein interaction (PPI) network was constructed. The hub genes were excavated. The clustering analysis of expression level of hub genes was performed by UCSC (University of California Santa Cruz) Xena database. The hub gene on overall survival rate (OS) in patients with ccRCC was performed by Kaplan-Meier Plotter. Finally, we used the ccRCC renal tissue samples to verify the hub genes.Results1182 common DEGs between the two datasets were identified. The results of GO and KEGG analysis revealed that variations in were predominantly enriched in intracellular signaling cascade, oxidation reduction, intrinsic to membrane, integral to membrane, nucleoside binding, purine nucleoside binding, pathways in cancer, focal adhesion, cell adhesion molecules. 10 hub genes ITGAX, CD86, LY86, TLR2, TYROBP, FCGR2A, FCGR2B, PTPRC, ITGB2, ITGAM were identified. FCGR2B and TYROBP were negatively correlated with the overall survival rate in patients with ccRCC (P < 0.05). RT-qPCR analysis showed that the relative expression levels of CD86, FCGR2A, FCGR2B, TYROBP, LY86, and TLR2 were significantly higher in ccRCC samples, compared with the adjacent renal tissue groups.ConclusionsIn summary, bioinformatics technology could be a useful tool to predict the progression of ccRCC. In addition, there are DEGs between ccRCC tumor tissue and normal renal tissue, and these DEGs might be considered as biomarkers for ccRCC. |
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| Keywords: | Renal clear cell carcinoma Bioinformatic Differentially expressed genes Hub gene |
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