EDC-Protein Network Formation in Uvea Melanoma; An Analysis of Melanoma Metastasis-Associated Genes
Journal of Ophthalmic and Optometric Sciences,
Vol. 4 No. 3 (2020),
23 June 2020
,
Page 1-16
https://doi.org/10.22037/joos.v4i3.36783
Abstract
Abstract:
Background: Melanoma is a kind of pigment cell cancer that affects the iris, ciliary body, or choroid of the eye (collectively referred to as the uvea). Tumors arise from pigment cells located inside the uvea that stain the eye. Metastasis of melanoma in the eye can damage a number of melanoma, such as the liver. Early diagnosis and treatment of melanoma can prevent possible problems, including decreased vision or complete loss of the eye. The most common manifestations of the disease are blurred vision, diplopia, photopsia and proptosis.
Material and Methods: First, the accession number GSE22138 was used to access the Gene Expression Omnibus at the National Center for Biotechnology Information (GEO). Then, 2000 metastatic and non-metastatic melanoma genes were extracted from the NCBI database together with their P-value. Then, by constructing the PPI network, we established ten modules for the genes with the highest expression levels. The comptox database was used to identify possible Endocrine Disrupting Chemicals (EDCs) for 17 high-expression genes. Cytoscape software was used to visualize the EDC-Protein network for these genes. Finally, we analyzed GO (Gene-Ontology) and molecular pathways using the DAVID database.
Result: In melanoma, 120 potential EDCs were identified to have regulatory effects on gene expression. We present oryzalin as a very effective EDC based on a comprehensive evaluation of various EDCs for metastatic Melanoma.
Conclusion: Oryzalin is the EDC with the highest degree in our network. However, these results need to be experimentally confirmed to suggest improved prevention.
- Uvea Melanoma
- PPIN
- EDC
- Systems Biology
How to Cite
References
Shields CL, Manalac J, Das C, Ferguson K, Shields JA. Choroidal melanoma: clinical features, classification, and top 10 pseudomelanomas. Current opinion in ophthalmology. 2014;25(3):177-85.
Kaliki S, Shields C. Uveal melanoma: relatively rare but deadly cancer. Eye. 2017;31(2):241-57.
Shain AH, Bagger MM, Yu R, Chang D, Liu S, Vemula S, et al. The genetic evolution of metastatic uveal melanoma. Nature genetics. 2019;51(7):1123-30.
Woodman SE. Metastatic uveal melanoma: biology and emerging treatments. Cancer journal (Sudbury, Mass). 2012;18(2):148.
Bakalian S, Marshall J-C, Logan P, Faingold D, Maloney S, Di Cesare S, et al. Molecular pathways mediating liver metastasis in patients with uveal melanoma. Clinical Cancer Research. 2008;14(4):951-6.
Terai M, Mastrangleo MJ, Sato T. Immunological aspect of the liver and metastatic uveal melanoma. Journal of Cancer Metastasis and Treatment. 2017;3:231-43.
Tavassoly I, Goldfarb J, Iyengar R. Systems biology primer: the basic methods and approaches. Essays in biochemistry. 2018;62(4):487-500.
Sonnenschein C, Soto AM. An updated review of environmental estrogen and androgen mimics and antagonists. The Journal of steroid biochemistry and molecular biology. 1998;65(1-6):143-50.
Kim SD, Cho J, Kim IS, Vanderford BJ, Snyder SA. Occurrence and removal of pharmaceuticals and endocrine disruptors in South Korean surface, drinking, and waste waters. Water research. 2007;41(5):1013-21.
Mendes JA. The endocrine disrupters: a major medical challenge. Food and Chemical Toxicology. 2002;40(6):781-8.
Auriol M, Filali-Meknassi Y, Tyagi RD, Adams CD, Surampalli RY. Endocrine disrupting compounds removal from wastewater, a new challenge. Process Biochemistry. 2006;41(3):525-39.
Shields CL, Furuta M, Thangappan A, Nagori S, Mashayekhi A, Lally DR, et al. Metastasis of uveal melanoma millimeter-by-millimeter in 8033 consecutive eyes. Archives of Ophthalmology. 2009;127(8):989-98.
Chen D, Lin Q, Box N, Roop D, Ishii S, Matsuzaki K, et al. SKI knockdown inhibits human melanoma tumor growth in vivo. Pigment cell & melanoma research. 2009;22(6):761-72.
Tang L, Long J, Li K, Zhang X, Chen X, Peng C. A novel chalcone derivative suppresses melanoma cell growth through targeting Fyn/Stat3 pathway. Cancer cell international. 2020;20(1):1-16.
Lefevre G, Babchia N, Calipel A, Mouriaux F, Faussat A-M, Mrzyk S, et al. Activation of the FGF2/FGFR1 autocrine loop for cell proliferation and survival in uveal melanoma cells. Investigative ophthalmology & visual science. 2009;50(3):1047-57.
Swoboda A, Soukup R, Eckel O, Kinslechner K, Wingelhofer B, Schoerghofer D, et al. STAT3 promotes melanoma metastasis by CEBP-induced repression of the MITF pathway. Oncogene. 2021;40(6):1091-105.
Kubic JD, Little EC, Lui JW, Iizuka T, Lang D. PAX3 and ETS1 synergistically activate MET expression in melanoma cells. Oncogene. 2015;34(38):4964-74.
Yan F, Liao R, Farhan M, Wang T, Chen J, Wang Z, et al. Elucidating the role of the FoxO3a transcription factor in the IGF-1-induced migration and invasion of uveal melanoma cancer cells. Biomed Pharmacother. 2016;84:1538-50.
Dong Z, Yang J, Li L, Tan L, Shi P, Zhang J, et al. FOXO3aSIRT6 axis suppresses aerobic glycolysis in melanoma. Int J Oncol. 2020;56(3):728-42.
Freudlsperger C, Schumacher U, Reinert S, Hoffmann J. The critical role of PPARγ in human malignant melanoma. PPAR research. 2008;2008.
Guo W, Ma J, Yang Y, Guo S, Zhang W, Zhao T, et al. ATP-citrate lyase epigenetically potentiates oxidative phosphorylation to promote melanoma growth and adaptive resistance to MAPK inhibition. Clinical Cancer Research. 2020;26(11):2725-39.
Roskoski R, Jr. Cyclin-dependent protein serine/threonine kinase inhibitors as anticancer drugs. Pharmacol Res. 2019;139:471-88.
Du J, Widlund HR, Horstmann MA, Ramaswamy S, Ross K, Huber WE, et al. Critical role of CDK2 for melanoma growth linked to its melanocyte-specific transcriptional regulation by MITF. Cancer Cell. 2004;6(6):565-76.
Raza A, Su W, Gao A, Mehmood SS, Hussain MA, Nie W, et al. Catalase (CAT) Gene Family in Rapeseed (Brassica napus L.): Genome-Wide Analysis, Identification, and Expression Pattern in Response to Multiple Hormones and Abiotic Stress Conditions. Int J Mol Sci. 2021;22(8).
Silva IP, Salhi A, Giles KM, Vogelsang M, Han SW, Ismaili N, et al. Identification of a novel pathogenic germline KDR variant in melanoma. Clinical Cancer Research. 2016;22(10):2377-85.
Eyries M, Montani D, Girerd B, Favrolt N, Riou M, Faivre L, et al. Familial pulmonary arterial hypertension by KDR heterozygous loss of function. Eur Respir J. 2020;55(4).
Nelson AA, Tsao H. Melanoma and genetics. Clinics in dermatology. 2009;27(1):46-52.
Yun J, Li Y, Xu C-T, Pan B-R. Epidemiology and Rb1 gene of retinoblastoma. International Journal of Ophthalmology. 2011;4(1):103.
Friedl P, Wolf K. Plasticity of cell migration: a multiscale tuning model. Journal of Cell Biology. 2010;188(1):11-9.
Friedl P, Locker J, Sahai E, Segall JE. Classifying collective cancer cell invasion. Nature cell biology. 2012;14(8):777-83.
Benezra R, Rafii S, Lyden D. The Id proteins and angiogenesis. Oncogene. 2001;20(58):8334-41.
Fong S, Debs RJ, Desprez P-Y. Id genes and proteins as promising targets in cancer therapy. Trends in molecular medicine. 2004;10(8):387-92.
Ruzinova MB, Benezra R. Id proteins in development, cell cycle and cancer. Trends in cell biology. 2003;13(8):410-8.
Schlegel NC, Eichhoff OM, Hemmi S, Werner S, Dummer R, Hoek KS. Id2 suppression of p15 counters TGF‐β‐mediated growth inhibition of melanoma cells. Pigment cell & melanoma research. 2009;22(4):445-53.
Lasorella A, Noseda M, Beyna M, Iavarone A. Id2 is a retinoblastoma protein target and mediates signalling by Myc oncoproteins. Nature. 2000;407(6804):592-8.
Iavarone A, Garg P, Lasorella A, Hsu J, Israel MA. The helix-loop-helix protein Id-2 enhances cell proliferation and binds to the retinoblastoma protein. Genes & development. 1994;8(11):1270-84.
Fong LWR, Yang DC, Chen C-H. Myristoylated alanine-rich C kinase substrate (MARCKS): a multirole signaling protein in cancers. Cancer and Metastasis Reviews. 2017;36(4):737-47.
Li H, Chen G, Zhou B, Duan S. Actin Filament Assembly by Myristoylated, Alanine-rich C Kinase Substrate–Phosphatidylinositol-4, 5-diphosphate Signaling Is Critical for Dendrite Branching. Molecular biology of the cell. 2008;19(11):4804-13.
Mohapatra P, Yadav V, Toftdahl M, Andersson T. WNT5A-induced activation of the protein kinase C substrate MARCKS is required for melanoma cell invasion. Cancers. 2020;12(2):346.
Short B, Preisinger C, Körner R, Kopajtich R, Byron O, Barr FA. A GRASP55-rab2 effector complex linking Golgi structure to membrane traffic. The Journal of cell biology. 2001;155(6):877-84.
Edwards SL, Charlie NK, Richmond JE, Hegermann J, Eimer S, Miller KG. Impaired dense core vesicle maturation in Caenorhabditis elegans mutants lacking Rab2. Journal of Cell Biology. 2009;186(6):881-95.
Destaing O, Block MR, Planus E, Albiges-Rizo C. Invadosome regulation by adhesion signaling. Current opinion in cell biology. 2011;23(5):597-606.
Appenzeller-Herzog C, Hauri H-P. The ER-Golgi intermediate compartment (ERGIC): in search of its identity and function. Journal of cell science. 2006;119(11):2173-83.
Sugawara T, Kano F, Murata M. Rab2A is a pivotal switch protein that promotes either secretion or ER-associated degradation of (pro) insulin in insulin-secreting cells. Scientific reports. 2014;4(1):1-14.
De Bolle X, Letesson J-J, Gorvel J-P. Small GTPases and Brucella entry into the endoplasmic reticulum. Portland Press Ltd.; 2012; 40:1348 –52.
Fugier E, Salcedo SP, De Chastellier C, Pophillat M, Muller A, Arce-Gorvel V, et al. The glyceraldehyde-3-phosphate dehydrogenase and the small GTPase Rab 2 are crucial for Brucella replication. PLoS pathogens. 2009;5(6):e1000487.
Huang G, Li H, Zhang H. Abnormal expression of mitochondrial ribosomal proteins and their encoding genes with cell apoptosis and diseases. International journal of molecular sciences. 2020;21(22):8879.
Cahill LS, Cameron JM, Winterburn J, Macos P, Hoggarth J, Dzamba M, et al. Structural Variant in Mitochondrial-Associated Gene (MRPL3) induces adult-onset neurodegeneration with memory impairment in the mouse. Journal of Neuroscience. 2020;40(23):4576-85.
Andrawus M, Sharvit L, Shekhidem HA, Roichman A, Cohen HY, Atzmon G. The effects of environmental stressors on candidate aging associated genes. Experimental Gerontology. 2020;137:110952.
Haglund K, Dikic I. Ubiquitylation and cell signaling. The EMBO journal. 2005;24(19):3353-9.
Ma J, Guo W, Li C. Ubiquitination in melanoma pathogenesis and treatment. Cancer medicine. 2017;6(6):1362-77.
Shao R, Wang X, Xu T, Xia Y, Cui D. The balance between AIM2-associated inflammation and autophagy: the role of CHMP2A in brain injury after cardiac arrest. Journal of neuroinflammation. 2021;18(1):1-20.
Demirci H, Reed D, Elner VM. Tissue-based microarray expression of genes predictive of metastasis in uveal melanoma and differentially expressed in metastatic uveal melanoma. Journal of Ophthalmic & Vision Research. 2013;8(4):303.
- Abstract Viewed: 156 times
- pdf Downloaded: 151 times
