Identification of potential biomarkers for melanoma cancer (black tumor) using bioinformatics strategy: a study based on GEO and SRA datasets.

Autor: ALMatrafi TA; Anatomy Department, College of Medicine, King Saud University, Riyadh, Saudi Arabia., Mohammedsaleh ZM; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, 71491, Tabuk, Saudi Arabia., Moawadh MS; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, 71491, Tabuk, Saudi Arabia., Bassfar Z; Faculty of Computing and Information Technology, University of Tabuk, Tabuk, Saudi Arabia., Jalal MM; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, 71491, Tabuk, Saudi Arabia., Badahdah FA; Surgical Department, Prince Sultan Military Medical City, PSMMC, Riyadh, Saudi Arabia., Alghamdi YS; Department of Biology, Turabah University College, Taif University, 21995, Taif, Saudi Arabia., Almasoudi HH; Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia., Hakami MA; Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia., Binshaya AS; Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, 11942, AlKharj, Saudi Arabia., Almohaimeed HM; Department of Basic Science, College of Medicine, Princess Nourah bint Abdulrahman, University, P.O. Box 84428, 11671, Riyadh, Saudi Arabia., Soliman MH; Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, 12613, Egypt. hmona@sci.cu.edu.eg.; Biology Department, Faculty of Science, Taibah University, Al-Sharm, Yanbu El-Bahr, Yanbu, 46429, Saudi Arabia. hmona@sci.cu.edu.eg.
Jazyk: angličtina
Zdroj: Journal of applied genetics [J Appl Genet] 2024 Feb; Vol. 65 (1), pp. 83-93. Date of Electronic Publication: 2023 Oct 24.
DOI: 10.1007/s13353-023-00794-4
Abstrakt: Melanoma, a highly invasive type of skin cancer that penetrates the entire dermis layer, is associated with increased mortality rates. Excessive exposure of the skin to sunlight, specifically ultraviolet radiation, is the underlying cause of this malignant condition. The appearance of unique skin moles represents a visible clue, referred to as the "ugly duckling" sign, indicating the presence of melanoma and its association with cellular DNA damage. This research aims to explore potential biomarkers derived from microarray data, employing bioinformatics techniques and methodologies, for a thorough investigation of melanoma skin cancer. The microarray dataset for melanoma skin cancer was obtained from the GEO database, and thorough data analysis and quality control measures were performed to identify differentially expressed genes (DEGs). The top 14 highly expressed DEGs were identified, and their gene information and protein sequences were retrieved from the NCBI gene and protein database. These proteins were further analyzed for domain identification and network analysis. Gene expression analysis was conducted to visualize the upregulated and downregulated genes. Additionally, gene metabolite network analysis was carried out to understand the interactions between highly interconnected genes and regulatory transcripts. Molecular docking was employed to investigate the ligand-binding sites and visualize the three-dimensional structure of proteins. Our research unveiled a collection of genes with varying expression levels, some elevated and others reduced, which could function as promising biomarkers closely linked to the development and advancement of melanoma skin cancer. Through molecular docking analysis of the GINS2 protein, we identified two natural compounds (PubChem-156021169 and PubChem-60700) with potential as inhibitors against melanoma. This research has implications for early detection, treatment, and understanding the molecular basis of melanoma.
(© 2023. The Author(s), under exclusive licence to Institute of Plant Genetics Polish Academy of Sciences.)
Databáze: MEDLINE
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