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Active natural compounds perturb the melanoma risk-gene network

Shao, L, Zhao, Y, Heinrich, M, Prieto-Garcia, JM and Manzoni, C (2023) Active natural compounds perturb the melanoma risk-gene network. G3 Genes|Genomes|Genetics, 14 (2). pp. 1-13. ISSN 2160-1836

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Cutaneous melanoma is an aggressive type of skin cancer with a complex genetic landscape caused by the malignant transformation of melanocytes. This study aimed at providing an in silico network model based on the systematic profiling of the melanoma-associated genes considering germline mutations, somatic mutations, and genome-wide association study signals accounting for a total of 232 unique melanoma risk genes. A protein–protein interaction network was constructed using the melanoma risk genes as seeds and evaluated to describe the functional landscape in which the melanoma genes operate within the cellular milieu. Not only were the majority of the melanoma risk genes able to interact with each other at the protein level within the core of the network, but this showed significant enrichment for genes whose expression is altered in human melanoma specimens. Functional annotation showed the melanoma risk network to be significantly associated with processes related to DNA metabolism and telomeres, DNA damage and repair, cellular ageing, and response to radiation. We further explored whether the melanoma risk network could be used as an in silico tool to predict the efficacy of anti-melanoma phytochemicals, that are considered active molecules with potentially less systemic toxicity than classical cytotoxic drugs. A significant portion of the melanoma risk network showed differential expression when SK-MEL-28 human melanoma cells were exposed to the phytochemicals harmine and berberine chloride. This reinforced our hypothesis that the network modeling approach not only provides an alternative way to identify molecular pathways relevant to disease but it may also represent an alternative screening approach to prioritize potentially active compounds.

Item Type: Article
Uncontrolled Keywords: Melanocytes; Humans; Melanoma; Skin Neoplasms; Gene Regulatory Networks; Genome-Wide Association Study; berberine chloride; differential gene expression; harmine; melanoma; network analysis; Humans; Melanoma; Skin Neoplasms; Gene Regulatory Networks; Genome-Wide Association Study; Melanocytes; 0604 Genetics
Subjects: Q Science > QH Natural history > QH426 Genetics
R Medicine > RC Internal medicine > RC0254 Neoplasms. Tumors. Oncology (including Cancer)
R Medicine > RS Pharmacy and materia medica
Divisions: Pharmacy & Biomolecular Sciences
Publisher: Oxford University Press (OUP)
SWORD Depositor: A Symplectic
Date Deposited: 05 Apr 2024 11:55
Last Modified: 05 Apr 2024 12:00
DOI or ID number: 10.1093/g3journal/jkad274
Editors: Pearce, S
URI: https://researchonline.ljmu.ac.uk/id/eprint/22960
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