Protein-Protein Interaction Network Analysis and Drug Repurposing for Uveal Melanoma Patients Drug Repurposing for Uveal Melanoma
Journal of Ophthalmic and Optometric Sciences,
Vol. 4 No. 4 (2020),
3 August 2022
,
Page 23-33
https://doi.org/10.22037/joos.v4i4.38462
Abstract
Background: Uveal melanoma is the most prevalent melanoma in adults. This malignancy arises from melanocytes. Patients with uveal melanoma were investigated according to their metastases and non-metastases status to propose candidate drugs.
Material and Methods: The studied data set included 63 patients (24 females and 39 males), among whom 35 patients were with metastases and 28 patients were without metastases. By comparing the metastases and non-metastases cases, 2000 genes were chosen as practical genes. A co-expression network was constructed, and protein complexes were extracted to find effective gene modules. Then drug-gene networks were constructed to find essential drugs.
Results: The STRING database was utilized to construct a co-expression network. Then, protein complexes were extracted using the MCODE clustering algorithm. Four meaningful modules were chosen for the next step. Afterward, drug-gene subnetworks were constructed and illustrated, and high degree drugs were chosen as effective drugs for this disease.
Conclusion: As a result, 12 important drugs were introduced as the proposed candidate drugs. By detailed investigation of the obtained results, drugs that were not previously reported were introduced as new drugs, which would be studied experimentally in future works. These were Bortezomib, Oprozomib, Clofarabine, ME-344 and NV-128.
- Protein-Protein interaction network
- Uveal Melanoma
- Drug repurposing
- Drug-gene
- Metastasis
How to Cite
References
Chang AE, Karnell LH, Menck HR. The National Cancer Data Base report on cutaneous and noncutaneous melanoma: a summary of 84,836 cases from the past decade. Cancer: Interdisciplinary International Journal of the American Cancer Society. 1998;83(8):1664-78.
Kivelä T. The epidemiological challenge of the most frequent eye cancer: retinoblastoma, an issue of birth and death. BMJ Publishing Group Ltd; 2009.
Singh AD, De Potter P, Fijal BA, Shields CL, Shields JA, Elston RC. Lifetime prevalence of uveal melanoma in white patients with oculo (dermal) melanocytosis. Ophthalmology. 1998;105(1):195-8.
Singh AD, Turell ME, Topham AK. Uveal melanoma: trends in incidence, treatment, and survival. Ophthalmology. 2011;118(9):1881-5.
Biswas J, Kabra S, Krishnakumar S, Shanmugam MP. Clinical and histopathological characteristics of uveal melanoma in Asian Indians. A study of 103 patients. Indian journal of ophthalmology. 2004;52(1):41-4.
Cerbone L, Van Ginderdeuren R, Van den Oord J, Fieuws S, Spileers W, Van Eenoo L, et al. Clinical presentation, pathological features and natural course of metastatic uveal melanoma, an orphan and commonly fatal disease. Oncology. 2014;86(3):185-9.
Canser.net. Available from: https://www.cancer.net/cancer-types/eye-cancer/stages-and-grades.
Kaliki S, Shields C. Uveal melanoma: relatively rare but deadly cancer. Eye. 2017;31(2):241-57.
Motieghader H, Kouhsar M, Najafi A, Sadeghi B, Masoudi-Nejad A. mRNA–miRNA bipartite network reconstruction to predict prognostic module biomarkers in colorectal cancer stage differentiation. Molecular BioSystems. 2017;13(10):2168-80.
MotieGhader H, Masoudi-Sobhanzadeh Y, Ashtiani SH, Masoudi-Nejad A. mRNA and microRNA selection for breast cancer molecular subtype stratification using meta-heuristic based algorithms. Genomics. 2020;112(5):3207-17.
Ghasemi M, Seidkhani H, Tamimi F, Rahgozar M, Masoudi-Nejad A. Centrality measures in biological networks. Current Bioinformatics. 2014;9(4):426-41.
Kouhsar M, Azimzadeh Jamalkandi S, Moeini A, Masoudi-Nejad A. Detection of novel biomarkers for early detection of Non-Muscle-Invasive Bladder Cancer using Competing Endogenous RNA network analysis. Scientific reports. 2019;9(1):1-15.
Shi K, Bing Z-T, Cao G-Q, Guo L, Cao Y-N, Jiang H-O, et al. Identify the signature genes for diagnose of uveal melanoma by weight gene co-expression network analysis. International journal of ophthalmology. 2015;8(2):269.
Ni Y, Zhang Z, Chen G, Long W, Tong L, Zeng J. Integrated analyses identify potential prognostic markers for uveal melanoma. Experimental Eye Research. 2019;187:107780.
Yang M, Wan Q, Hu X, Yin H, Hao D, Wu C, et al. Coexpression modules constructed by weighted gene co‑expression network analysis indicate ubiquitin‑mediated proteolysis as a potential biomarker of uveal melanoma. Experimental and Therapeutic Medicine. 2019;17(1):237-43.
Wan Q, Tang J, Han Y, Wang D. Co-expression modules construction by WGCNA and identify potential prognostic markers of uveal melanoma. Experimental eye research. 2018;166:13-20.
Abedi Z, MotieGhader H, Maghsoudloo M, Goharrizi MASB, Shojaei A. Novel potential drugs for therapy of age-related macular degeneration using Protein-Protein Interaction Network (PPIN) analysis. Journal of Ophthalmic and Optometric Sciences. 2019;3(4).
Norouzi M, Maghsoudloo M, Noroozizadeh MH. Collagen Cross-Linking Therapy on Important Functional Genes Involved in Keratoconus Patients. Journal of Ophthalmic and Optometric Sciences.3(3):1-15.
Maghsoudloo M, Noroozizadeh MH. A gene selection approach for Diabetic retinopathy microarray data classification using Ant Colony Optimization. Journal of Ophthalmic and Optometric Sciences Volume. 2019;3(4).
Ghorbani M, Pournoor E, Maghsoudloo M. Transcriptomic Analysis of Human Retina Reveals Molecular Mechanisms Underlying Diabetic Retinopathy in Sexually Divergent Manner. Journal of Ophthalmic and Optometric Sciences. 2020;4(2).
Hosseini SS, Abedi Z, Maghsoudloo M, Goharrizi MASB, Shojaei A. Investigation of genes associated with primary open-angle glaucoma (POAG) using expression profile analysis. Journal of Ophthalmic and Optometric Sciences. 2019;3(3).
Ahmadi H, Ahmadi A, Azimzadeh-Jamalkandi S, Shoorehdeli MA, Salehzadeh-Yazdi A, Bidkhori G, et al. HomoTarget: a new algorithm for prediction of microRNA targets in Homo sapiens. Genomics. 2013;101(2):94-100.
Alaei S, Sadeghi B, Najafi A, Masoudi-Nejad A. LncRNA and mRNA integration network reconstruction reveals novel key regulators in esophageal squamous-cell carcinoma. Genomics. 2019;111(1):76-89.
Mortezaei Z, Lanjanian H, Masoudi-Nejad A. Candidate novel long noncoding RNAs, MicroRNAs and putative drugs for Parkinson's disease using a robust and efficient genome-wide association study. Genomics. 2017;109(3-4):158-64.
Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, et al. NCBI GEO: archive for functional genomics data sets—update. Nucleic acids research. 2012;41(D1):D991-D5.
Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, et al. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic acids research. 2019;47(D1):D607-D13.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research. 2003;13(11):2498-504.
Wang J, Zhong J, Chen G, Li M, Wu F-x, Pan Y. ClusterViz: a cytoscape APP for cluster analysis of biological network. IEEE/ACM transactions on computational biology and bioinformatics. 2014;12(4):815-22.
Cotto KC, Wagner AH, Feng Y-Y, Kiwala S, Coffman AC, Spies G, et al. DGIdb 3.0: a redesign and expansion of the drug–gene interaction database. Nucleic acids research. 2018;46(D1):D1068-D73.
Velho T, Kapiteijn E, Jager M. New therapeutic agents in uveal melanoma. Anticancer research. 2012;32(7):2591-8.
Wang JZ, Lin V, Toumi E, Wang K, Zhu H, Conway RM, et al. Development of new therapeutic options for the treatment of uveal melanoma. The FEBS Journal. 2021.
Markovic SN, Geyer SM, Dawkins F, Sharfman W, Albertini M, Maples W, et al. A phase II study of bortezomib in the treatment of metastatic malignant melanoma. Cancer. 2005;103(12):2584-9.
Su Y, Amiri KI, Horton LW, Yu Y, Ayers GD, Koehler E, et al. A phase I trial of bortezomib with temozolomide in patients with advanced melanoma: toxicities, antitumor effects, and modulation of therapeutic targets. Clinical Cancer Research. 2010;16(1):348-57.
Zhou X, Flüchter P, Nickel K, Meckel K, Messerschmidt J, Böckle D, et al. Carfilzomib based treatment strategies in the management of relapsed/refractory multiple myeloma with extramedullary disease. Cancers. 2020;12(4):1035.
Conticello C, Martino EA, Del Fabro V, Sapienza G, Calafiore V, Garibaldi B, et al. Impact of Cumulative Dose of Carfilzomib in Combination with Lenalidomide and Desamethasone in Relapsed Refractory Myeloma Patients: A Retrospective Real Life Survey of the Sicilian Myeloma Network. American Society of Hematology Washington, DC; 2018.
Dolland R. Chemotherapy in eye cancer. Continuing Medical Education. 2013;31(4):138-42.
Neale M, Myatt N, Cree I, Kurbacher C, Foss A, Hungerford J, et al. Combination chemotherapy for choroidal melanoma: ex vivo sensitivity to treosulfan with gemcitabine or cytosine arabinoside. British journal of cancer. 1999;79(9):1487-93.
Orloff M. Clinical Trials in Metastatic Uveal Melanoma: Immunotherapy. Ocular Oncology and Pathology. 2021:1-9.
Chandran SS, Somerville RP, Yang JC, Sherry RM, Klebanoff CA, Goff SL, et al. Treatment of metastatic uveal melanoma with adoptive transfer of tumour-infiltrating lymphocytes: a single-centre, two-stage, single-arm, phase 2 study. The Lancet Oncology. 2017;18(6):792-802.
Corrie P, Shaw J, Spanswick V, Sehmbi R, Jonson A, Mayer A, et al. Phase I trial combining gemcitabine and treosulfan in advanced cutaneous and uveal melanoma patients. British journal of cancer. 2005;92(11):1997-2003.
Schmittel A, Scheulen ME, Bechrakis NE, Strumberg D, Baumgart J, Bornfeld N, et al. Phase II trial of cisplatin, gemcitabine and treosulfan in patients with metastatic uveal melanoma. Melanoma research. 2005;15(3):205-7.
Jaune E, Rocchi S. Metformin: Focus on melanoma. Frontiers in endocrinology. 2018;9:472.
de Andrade BDM, Lasiste J, Miyamoto D, Rezende CP, Mastromonaco C, Burnier MN. Metformin inhibits survival, migration, and vascular endothelial growth factor production in uveal melanoma cells. Investigative Ophthalmology & Visual Science. 2017;58(8):3964-.
Zhang X, Linder S, Bazzaro M. Drug development targeting the ubiquitin–proteasome system (UPS) for the treatment of human cancers. Cancers. 2020;12(4):902.
Millward M, Price T, Townsend A, Sweeney C, Spencer A, Sukumaran S, et al. Phase 1 clinical trial of the novel proteasome inhibitor marizomib with the histone deacetylase inhibitor vorinostat in patients with melanoma, pancreatic and lung cancer based on in vitro assessments of the combination. Investigational new drugs. 2012;30(6):2303-17.
Choi S, Ha M, Lee JS, Heo HJ, Kim GH, Oh S-O, et al. Novel prognostic factor for uveal melanoma: bioinformatics analysis of three independent cohorts. Anticancer Research. 2020;40(7):3839-46.
Masoudi-Sobhanzadeh Y, Omidi Y, Amanlou M, Masoudi-Nejad A. DrugR+: a comprehensive relational database for drug repurposing, combination therapy, and replacement therapy. Computers in biology and medicine. 2019;109:254-62.
Haack TB, Madignier F, Herzer M, Lamantea E, Danhauser K, Invernizzi F, et al. Mutation screening of 75 candidate genes in 152 complex I deficiency cases identifies pathogenic variants in 16 genes including NDUFB9. Journal of medical genetics. 2012;49(2):83-9.
GeneCards Organization. 1996-2022.
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