Identification of hub genes, non-coding RNAs and pathways in Renal cell carcinoma (RCC): A comprehensive in silico study
Backgrounds: Renal cell carcinoma (RCC) is the most common type of kidney cancer in adults. RCC begins in the renal tubule epithelial cells, essential for blood filtration and urine production. Methods: In this study, we aim to uncover the molecular mechanisms underlying kidney renal clear cell carc...
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Elsevier
2025-03-01
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| Series: | Biochemistry and Biophysics Reports |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405580825000299 |
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| author | Ahmad Golestanifar Hengameh Khedri Parisa Noorabadi Mohammadreza Saberiyan |
| author_facet | Ahmad Golestanifar Hengameh Khedri Parisa Noorabadi Mohammadreza Saberiyan |
| author_sort | Ahmad Golestanifar |
| collection | DOAJ |
| description | Backgrounds: Renal cell carcinoma (RCC) is the most common type of kidney cancer in adults. RCC begins in the renal tubule epithelial cells, essential for blood filtration and urine production. Methods: In this study, we aim to uncover the molecular mechanisms underlying kidney renal clear cell carcinoma (KIRC) by analyzing various non-coding RNAs (ncRNAs) and protein-coding genes involved in the disease. Using high-throughput sequencing datasets from the Gene Expression Omnibus (GEO), we identified differentially expressed mRNAs (DEMs), miRNAs (DEMIs), and circRNAs (DECs) in KIRC samples compared to normal kidney tissues. Our approach combined differential expression analysis, functional enrichment through Gene Ontology (GO) and KEGG pathway mapping, and a Protein-Protein Interaction (PPI) network to identify crucial hub genes in KIRC progression. Results: Key findings include the identification of hub genes such as EGFR, FN1, IL6, and ITGAM, which were closely associated with immune responses, cell signaling, and metabolic dysregulation in KIRC. Further analysis indicated that these genes could be potential biomarkers for prognosis and therapeutic targets. We constructed a competitive endogenous RNA (ceRNA) network involving lncRNAs, circRNAs, and miRNAs, suggesting complex regulatory interactions that drive KIRC pathogenesis.Additionally, the study examined drug sensitivity associated with the expression of hub genes, revealing the potential for personalized treatments. Immune cell infiltration patterns showed significant correlations with hub gene expression, highlighting the importance of immune modulation in KIRC. Conclusion: This research provides a foundation for developing targeted therapies and diagnostic biomarkers for KIRC while underscoring the need for experimental validation to confirm these bioinformatics insights. |
| format | Article |
| id | doaj-art-17fc12a7aa734a38b130444e85da658d |
| institution | Kabale University |
| issn | 2405-5808 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Biochemistry and Biophysics Reports |
| spelling | doaj-art-17fc12a7aa734a38b130444e85da658d2025-02-03T04:16:47ZengElsevierBiochemistry and Biophysics Reports2405-58082025-03-0141101942Identification of hub genes, non-coding RNAs and pathways in Renal cell carcinoma (RCC): A comprehensive in silico studyAhmad Golestanifar0Hengameh Khedri1Parisa Noorabadi2Mohammadreza Saberiyan3Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, IranDepartment of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, IranDepartment of Internal Medicine, School of Medicine, Urmia University of Medical sciences, Urmia, Iran; Corresponding author.Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran; Corresponding author. Department of Medical Genetics, School of Medical Sciences, Hormozgan University of Medical Sciences. P.O.Box: 7919693116, Bandar Abbas, Iran.Backgrounds: Renal cell carcinoma (RCC) is the most common type of kidney cancer in adults. RCC begins in the renal tubule epithelial cells, essential for blood filtration and urine production. Methods: In this study, we aim to uncover the molecular mechanisms underlying kidney renal clear cell carcinoma (KIRC) by analyzing various non-coding RNAs (ncRNAs) and protein-coding genes involved in the disease. Using high-throughput sequencing datasets from the Gene Expression Omnibus (GEO), we identified differentially expressed mRNAs (DEMs), miRNAs (DEMIs), and circRNAs (DECs) in KIRC samples compared to normal kidney tissues. Our approach combined differential expression analysis, functional enrichment through Gene Ontology (GO) and KEGG pathway mapping, and a Protein-Protein Interaction (PPI) network to identify crucial hub genes in KIRC progression. Results: Key findings include the identification of hub genes such as EGFR, FN1, IL6, and ITGAM, which were closely associated with immune responses, cell signaling, and metabolic dysregulation in KIRC. Further analysis indicated that these genes could be potential biomarkers for prognosis and therapeutic targets. We constructed a competitive endogenous RNA (ceRNA) network involving lncRNAs, circRNAs, and miRNAs, suggesting complex regulatory interactions that drive KIRC pathogenesis.Additionally, the study examined drug sensitivity associated with the expression of hub genes, revealing the potential for personalized treatments. Immune cell infiltration patterns showed significant correlations with hub gene expression, highlighting the importance of immune modulation in KIRC. Conclusion: This research provides a foundation for developing targeted therapies and diagnostic biomarkers for KIRC while underscoring the need for experimental validation to confirm these bioinformatics insights.http://www.sciencedirect.com/science/article/pii/S2405580825000299Non-coding RNAsRenal cell carcinomaDiagnostic biomarkersProtein-protein interaction (PPI) network |
| spellingShingle | Ahmad Golestanifar Hengameh Khedri Parisa Noorabadi Mohammadreza Saberiyan Identification of hub genes, non-coding RNAs and pathways in Renal cell carcinoma (RCC): A comprehensive in silico study Biochemistry and Biophysics Reports Non-coding RNAs Renal cell carcinoma Diagnostic biomarkers Protein-protein interaction (PPI) network |
| title | Identification of hub genes, non-coding RNAs and pathways in Renal cell carcinoma (RCC): A comprehensive in silico study |
| title_full | Identification of hub genes, non-coding RNAs and pathways in Renal cell carcinoma (RCC): A comprehensive in silico study |
| title_fullStr | Identification of hub genes, non-coding RNAs and pathways in Renal cell carcinoma (RCC): A comprehensive in silico study |
| title_full_unstemmed | Identification of hub genes, non-coding RNAs and pathways in Renal cell carcinoma (RCC): A comprehensive in silico study |
| title_short | Identification of hub genes, non-coding RNAs and pathways in Renal cell carcinoma (RCC): A comprehensive in silico study |
| title_sort | identification of hub genes non coding rnas and pathways in renal cell carcinoma rcc a comprehensive in silico study |
| topic | Non-coding RNAs Renal cell carcinoma Diagnostic biomarkers Protein-protein interaction (PPI) network |
| url | http://www.sciencedirect.com/science/article/pii/S2405580825000299 |
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