Maisha Tasneem , Shipan Das Gupta , Md Jubair Ahmed Jony , Maya Minkara , Rajib Kumar Dey , Jannatul Ferdoush
{"title":"肝细胞癌和肾透明细胞癌进展的关键生物标志物基因鉴定:一种具有靶向治疗干预潜力的共享高通量筛选和分子对接方法","authors":"Maisha Tasneem , Shipan Das Gupta , Md Jubair Ahmed Jony , Maya Minkara , Rajib Kumar Dey , Jannatul Ferdoush","doi":"10.1016/j.jgeb.2025.100497","DOIUrl":null,"url":null,"abstract":"<div><h3>Background and objectives</h3><div>Liver Hepatocellular Carcinoma (LIHC) and Kidney Renal Clear Cell Carcinoma (KIRC) are leading causes of cancer death worldwide, but their early detections remain hindered by a lack of genetic markers. Our study aims to find prospective biomarkers that could serve as prognostic indicators for efficient drug candidates for KIRC and LIHC treatment.</div></div><div><h3>Methods</h3><div>To detect differentially expressed genes (DEGs), four datasets were used: GSE66271 and GSE213324 for KIRC, and GSE135631 and GSE202853 for LIHC. Visualization of DEGs was done using heatmaps, volcano plots, and Venn diagrams. Hub genes were identified via PPI analysis and the cytoHubba plugin in Cytoscape. Their expression was evaluated using box plots, stage plots, and survival plots for prognostic assessment via GEPIA2. Molecular docking with PyRx’s AutoDock Vina identified optimal binding interactions between compounds and proteins. Pharmacokinetic and toxicity analyses reinforced the drug-likeness and safety of these compounds.</div></div><div><h3>Results</h3><div>In this study, 47 DEGs were identified, with the top 10 hub genes being <em>TOP2A</em>, <em>BUB1</em>, <em>PTTG1</em>, <em>CCNB2</em>, <em>NUSAP1</em>, <em>KIF20A</em>, <em>BIRC5</em>, <em>RRM2, NDC80</em> and <em>CDC45</em>, chosen for their high MCC scores. Data mining revealed a correlation between TOP2A expression and clinical survival outcomes in KIRC and LIHC patients. Docking studies of the TOP2A structure identified a promising compound from <em>Andrographis paniculata</em> with high binding energy and interactions with TOP2A. Pharmacokinetic and toxicity assessments support its potential as a drug candidate.</div></div><div><h3>Conclusion</h3><div>Our study emphasizes <em>TOP2A</em>’s prognostic significance in KIRC and LIHC and recognizes <em>Andrographis paniculata</em> compound as potential therapeutics, offering prospective for enhanced treatment and patient outcomes in these cancers.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100497"},"PeriodicalIF":3.5000,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Identification of key biomarker genes in liver hepatocellular carcinoma and kidney renal clear cell carcinoma progression: A shared high-throughput screening and molecular docking method with potentials for targeted therapeutic interventions\",\"authors\":\"Maisha Tasneem , Shipan Das Gupta , Md Jubair Ahmed Jony , Maya Minkara , Rajib Kumar Dey , Jannatul Ferdoush\",\"doi\":\"10.1016/j.jgeb.2025.100497\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Background and objectives</h3><div>Liver Hepatocellular Carcinoma (LIHC) and Kidney Renal Clear Cell Carcinoma (KIRC) are leading causes of cancer death worldwide, but their early detections remain hindered by a lack of genetic markers. Our study aims to find prospective biomarkers that could serve as prognostic indicators for efficient drug candidates for KIRC and LIHC treatment.</div></div><div><h3>Methods</h3><div>To detect differentially expressed genes (DEGs), four datasets were used: GSE66271 and GSE213324 for KIRC, and GSE135631 and GSE202853 for LIHC. Visualization of DEGs was done using heatmaps, volcano plots, and Venn diagrams. Hub genes were identified via PPI analysis and the cytoHubba plugin in Cytoscape. Their expression was evaluated using box plots, stage plots, and survival plots for prognostic assessment via GEPIA2. Molecular docking with PyRx’s AutoDock Vina identified optimal binding interactions between compounds and proteins. Pharmacokinetic and toxicity analyses reinforced the drug-likeness and safety of these compounds.</div></div><div><h3>Results</h3><div>In this study, 47 DEGs were identified, with the top 10 hub genes being <em>TOP2A</em>, <em>BUB1</em>, <em>PTTG1</em>, <em>CCNB2</em>, <em>NUSAP1</em>, <em>KIF20A</em>, <em>BIRC5</em>, <em>RRM2, NDC80</em> and <em>CDC45</em>, chosen for their high MCC scores. Data mining revealed a correlation between TOP2A expression and clinical survival outcomes in KIRC and LIHC patients. Docking studies of the TOP2A structure identified a promising compound from <em>Andrographis paniculata</em> with high binding energy and interactions with TOP2A. Pharmacokinetic and toxicity assessments support its potential as a drug candidate.</div></div><div><h3>Conclusion</h3><div>Our study emphasizes <em>TOP2A</em>’s prognostic significance in KIRC and LIHC and recognizes <em>Andrographis paniculata</em> compound as potential therapeutics, offering prospective for enhanced treatment and patient outcomes in these cancers.</div></div>\",\"PeriodicalId\":53463,\"journal\":{\"name\":\"Journal of Genetic Engineering and Biotechnology\",\"volume\":\"23 2\",\"pages\":\"Article 100497\"},\"PeriodicalIF\":3.5000,\"publicationDate\":\"2025-04-22\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Genetic Engineering and Biotechnology\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1687157X25000411\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"Biochemistry, Genetics and Molecular Biology\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Genetic Engineering and Biotechnology","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1687157X25000411","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"Biochemistry, Genetics and Molecular Biology","Score":null,"Total":0}
Identification of key biomarker genes in liver hepatocellular carcinoma and kidney renal clear cell carcinoma progression: A shared high-throughput screening and molecular docking method with potentials for targeted therapeutic interventions
Background and objectives
Liver Hepatocellular Carcinoma (LIHC) and Kidney Renal Clear Cell Carcinoma (KIRC) are leading causes of cancer death worldwide, but their early detections remain hindered by a lack of genetic markers. Our study aims to find prospective biomarkers that could serve as prognostic indicators for efficient drug candidates for KIRC and LIHC treatment.
Methods
To detect differentially expressed genes (DEGs), four datasets were used: GSE66271 and GSE213324 for KIRC, and GSE135631 and GSE202853 for LIHC. Visualization of DEGs was done using heatmaps, volcano plots, and Venn diagrams. Hub genes were identified via PPI analysis and the cytoHubba plugin in Cytoscape. Their expression was evaluated using box plots, stage plots, and survival plots for prognostic assessment via GEPIA2. Molecular docking with PyRx’s AutoDock Vina identified optimal binding interactions between compounds and proteins. Pharmacokinetic and toxicity analyses reinforced the drug-likeness and safety of these compounds.
Results
In this study, 47 DEGs were identified, with the top 10 hub genes being TOP2A, BUB1, PTTG1, CCNB2, NUSAP1, KIF20A, BIRC5, RRM2, NDC80 and CDC45, chosen for their high MCC scores. Data mining revealed a correlation between TOP2A expression and clinical survival outcomes in KIRC and LIHC patients. Docking studies of the TOP2A structure identified a promising compound from Andrographis paniculata with high binding energy and interactions with TOP2A. Pharmacokinetic and toxicity assessments support its potential as a drug candidate.
Conclusion
Our study emphasizes TOP2A’s prognostic significance in KIRC and LIHC and recognizes Andrographis paniculata compound as potential therapeutics, offering prospective for enhanced treatment and patient outcomes in these cancers.
期刊介绍:
Journal of genetic engineering and biotechnology is devoted to rapid publication of full-length research papers that leads to significant contribution in advancing knowledge in genetic engineering and biotechnology and provide novel perspectives in this research area. JGEB includes all major themes related to genetic engineering and recombinant DNA. The area of interest of JGEB includes but not restricted to: •Plant genetics •Animal genetics •Bacterial enzymes •Agricultural Biotechnology, •Biochemistry, •Biophysics, •Bioinformatics, •Environmental Biotechnology, •Industrial Biotechnology, •Microbial biotechnology, •Medical Biotechnology, •Bioenergy, Biosafety, •Biosecurity, •Bioethics, •GMOS, •Genomic, •Proteomic JGEB accepts