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Cited by 29Ocular Oncology and TreatmentsVeterinary Oncology ResearchOcular Disorders and Treatments

A Comparative Transcriptomic Analysis of Uveal Melanoma and Normal Uveal Melanocyte

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An, Jianhong, Wan, Haolei, Zhou, Xiangtian, Hu, Dan-Ning, Wang, Ledan, Hao, Lili, Yan, Dongsheng, Shi, Fanjun +5 more·2011·PLoS ONE
DOI 10.1371/journal.pone.0016516PMC PMC3030591
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Abstract

BACKGROUND: Uveal melanoma is the most common primary intraocular tumor in adults in western countries. It is associated with very severe visual morbidity and may lead to distant metastases even after successful treatment of the primary tumor. In order to gain better insight into molecular mechanisms related to tumorigenesis and metastasis of uveal melanoma, we used next-generation sequencing technology (SOLiD, Life Technologies) to acquire global transcriptome alteration between posterior uveal melanoma cells and normal uveal melanocyte. RESULTS: From mRNAs of the cultured uveal melanoma cells and normal uveal melanocytes, we annotated more than 3.7 × 10(7) and 2.7 × 10(7) sequencing tags based on human Ensembl databases, respectively. For detailed analysis, we chose 5155 well-annotated genes mainly involved in the MAPK signaling pathway, cell cycle, cell adhesion junction, apoptosis, and P53 signaling pathways as well as melanogenesis. In an effort to confirm the authenticity of our sequencing results, we validated twenty-one identically differentially expressed genes by using quantitative real time PCR from cultured cell lines of other posterior uveal melanoma cells and normal uveal melanocytes. CONCLUSION: We have identified a large number of potentially interesting genes for biological investigation of uveal melanoma. The expression profiling also provides useful resources for other functional genomic and transcriptome studies. These 21 potential genes could discriminate between uveal melanoma cells and normal uveal melanocyte, which may be indicative of tumorigenesis process. Our results further suggest that high-throughput sequencing technology provides a powerful tool to study mechanisms of tumogenesis in the molecular level.

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  • Melanocyte and RPE gene expression have been previously characterized.

    “Because melanocyte and RPE gene expression have been previously characterized, we do not discuss them in detail here, but present the data as the supplemental tables listed below [36]–[38], [68], [69].”

    From Gene Expression Analysis of Zebrafish Melanocytes, Iridophores, and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin (2013) · cites this paper as [69]

    The Results section (‘Gene profiling and the category of highly-expressed genes in two libraries’; page unavailable) reports gene-expression profiling of normal uveal melanocytes. The cited paper does not characterize RPE gene expression, so it supports only the melanocyte part of the claim. (LLM, conf=0.88)

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Cites

  • Stem cell transcriptome profiling via massive-scale mRNA sequencing

    Cloonan, N., Forrest, A. R. R., Kolle, G., Gardiner, B. B. A., Faulkner, G. J., Brown, M. K., Taylor, D. F., Steptoe, A. L., Wani, S., Bethel, G., et al. (2008) · Nature Methods · doi:10.1038/nmeth.1223 · Cited by 1,035 · cited 1× · see citing works

    “To further survey molecular mechanism of UM and to understand the oncogenesis of UM, we used the recentlydeveloped RNA-seq method to identify and quantify different gene expression between UM cells and normal uveal melanocyte (NUM) so that we could interrogate the dynamic variation of UM transcriptome [27].”
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Research works printed but not linked: 48

  1. [1]Singh AD Topham A 2003 Survival rates with uveal melanoma in the United States: 1973-1997. Ophthalmology 110 962 965 12750098
  2. [2]Peter H Clement T 2005 Genomic Investigations of Posterior Uveal Melanoma. Seminars in Ophthalmology 20 231 238 16352494
  3. [3]Singh AD Topham A 2003 Incidence of uveal melanoma in the United States: 1973-1997. Ophthalmology 110 956 961 12750097
  4. [4]Onken MD Worley LA Ehlers JP Harbour JW 2004 Gene expression profiling in uveal melanoma reveals two molecular classes and predicts metastatic death. Cancer Research 64 7205 7209 15492234 PMC5407684
  5. [5]Landreville S Agapova OA Harbour JW 2008 Emerging insights into the molecular pathogenesis of uveal melanoma. Future Oncology 4 629 636 18922120 PMC2577578
  6. [6]Cerbone L Van Ginderdeuren R Van den Oord J Fieuws S Spileers W 2009 Clinical presentation, pathological features and natural course of metastatic uveal melanoma (MUM) as an orphan and commonly fatal disease. Ejc Supplements 7 585 585 24776955
  7. [7]Coleman K Baak JPA Vandiest PJ Curran B Mullaney J 1995 DNA-Ploidy Status in 84 Ocular Melanomas - a Study of DNA Quantitation in Ocular Melanomas by Flow-Cytometry and Automatic and Interactive Static Image-Analysis. Human Pathology 26 99 105 7821923
  8. [8]Mooy C Vissers K Luyten G Mulder A Stijnen T 1995 DNA Flow-Cytometry in Uveal Melanoma - the Effect of Preenucleation Irradiation. British Journal of Ophthalmology 79 174 177 7696240 PMC505051
  9. [9]Karlsson M Boeryd B Carstensen J Kagedal B Wingren S 1995 DNA-Ploidy and S-Phase Fraction as Prognostic Factors in Patients with Uveal Melanomas. British Journal of Cancer 71 177 181 7819036 PMC2033436
  10. [10]Karlsson M Boeryd B Carstensen J Franlund B Gustafsson B 1996 Correlations of Ki-67 and PCNA to DNA ploidy, S-phase fraction and survival in uveal melanoma. European Journal of Cancer 32A 357 362 8664054
  11. [11]Mooy CM DeJong PTVM 1996 Prognostic parameters in uveal melanoma: A review. Survey of Ophthalmology 41 215 228 8970236
  12. [12]Ehlers JP Worley L Onken MD Harbour JW 2008 Integrative genomic analysis of aneuploidy in uveal melanoma. Clinical Cancer Research 14 115 122 18172260
  13. [13]Aalto Y Eriksson L Seregard S Larsson O Knuutila S 2001 Concomitant loss of chromosome 3 and whole arm losses and gains of chromosome 1, 6, or 8 in metastasizing primary uveal melanoma. Investigative Ophthalmology & Visual Science 42 313 317 11157859
  14. [14]White VA Chambers JD Courtright PD Chang WY Horsman DE 1998 Correlation of cytogenetic abnormalities with the outcome of patients with uveal melanoma. Cancer 83 354 359 9669819
  15. [15]Gray-Schopfer V Wellbrock C Marais R 2007 Melanoma biology and new targeted therapy. Nature 445 851 857 17314971
  16. [16]Loercher AE Harbour JW 2003 Molecular genetics of uveal melanoma. Current Eye Research 27 69 74 14632157
  17. [17]Onken MD Worley LA Long MD Duan SH Council ML 2008 Oncogenic Mutations in GNAQ Occur Early in Uveal Melanoma. Investigative Ophthalmology & Visual Science 49 5230 5234 18719078 PMC2634606
  18. [18]Honda S Hirai T Handa JT Okuno T Saito I 2004 Expression of cell cycle related proteins in a rapidly growing uveal malignant melanoma. Retina-the Journal of Retinal and Vitreous Diseases 24 646 649 15300098
  19. [20]Pardo M Pineiro A de la Fuente M Garcia A Prabhakar S 2004 Abnormal cell cycle regulation in primary human uveal melanoma cultures. Journal of Cellular Biochemistry 93 708 720 15660415
  20. [21]Lederman M Meir T Zeschnigk M Pe'er J Chowers I 2008 Inhibitor of Apoptosis Proteins Gene Expression and Its Correlation with Prognostic Factors in Primary and Metastatic Uveal Melanoma. Current Eye Research 33 876 884 18853322
  21. [22]Davies L Gray D Spiller D White MRH Damato B 2009 P53 apoptosis mediator PERP: localization, function and caspase activation in uveal melanoma. Journal of Cellular and Molecular Medicine 13 1995 2007 19040420 PMC6529966
  22. [24]Chowers I Folberg R Livni N Pe'er J 2002 P53 Immunoreactivity, Ki-67 expression, and microcirculation patterns in melanoma of the iris, ciliary body, and choroid. Current Eye Research 24 105 108 12187481
  23. [25]Stitt AW Simpson DAC Boocock C Gardiner TA Murphy GM 1998 Expression of vascular endothelial growth factor (VEGF) and its receptors is regulated in eyes with intra-ocular tumours. Journal of Pathology 186 306 312 10211121
  24. [26]Zuidervaart W van der Velden PA Hurks MH van Nieuwpoort FA Out-Luiting CJJ 2003 Gene expression profiling identifies tumour markers potentially playing a role in uveal melanoma development. British Journal of Cancer 89 1914 1919 14612903 PMC2394439
  25. [29]Hu DN Mccormick SA Ritch R Peltonhenrion K 1993 Studies of Human Uveal Melanocytes Invitro - Isolation, Purification and Cultivation of Human Uveal Melanocytes. Investigative Ophthalmology & Visual Science 34 2210 2219 8505203
  26. [30]Mortazavi A Williams BA Mccue K Schaeffer L Wold B 2008 Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 5 621 628 18516045 PMC13303166
  27. [31]Wang LK Feng ZX Wang X Wang XW Zhang XG 2010 DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26 136 138 19855105
  28. [33]Kanehisa M Goto S 2000 KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research 28 27 30 10592173 PMC102409
  29. [34]Salomonis N Hanspers K Zambon AC Vranizan K Lawlor SC 2007 GenMAPP 2: new features and resources for pathway analysis. Bmc Bioinformatics 8 PMC1924866 17588266
  30. [35]van Iersel MP Kelder T Pico AR Hanspers K Coort S 2008 Presenting and exploring biological pathways with PathVisio. Bmc Bioinformatics 9 PMC2569944 18817533
  31. [36]Soulieres D Rousseau A Deschenes J Tremblay M Tardif M 1991 Characterization of Gangliosides in Human Uveal Melanoma-Cells. International Journal of Cancer 49 498 503 1917148
  32. [37]Yan DS Zhou XT Chen XY Hu DN Da Dong X 2009 MicroRNA-34a Inhibits Uveal Melanoma Cell Proliferation and Migration through Downregulation of c-Met. Investigative Ophthalmology & Visual Science 50 1559 1565 19029026
  33. [38]Xiao Y Yang FQ Li SP Gao JL Hu G 2007 Furanodiene induces G(2)/M cell cycle arrest and apoptosis through MAPK signaling and mitochondria-caspase pathway in human hepatocellular carcinoma cells. Cancer Biology & Therapy 6 1044 1050 17611410
  34. [39]Bauer J Kilic E Vaarwater J Bastian BC Garbe C 2009 Oncogenic GNAQ mutations are not correlated with disease-free survival in uveal melanoma. British Journal of Cancer 101 813 815 19654573 PMC2736834
  35. [40]Olga Dratviman-Storobinsky YC Frenkel Shahar Peter Jacob Goldenberg-Cohen Nitza 2010 Lack of oncogenic GNAQ mutations in melanocytic lesions of the conjunctiva as compared to uveal melanoma. Investigative Ophthalmology and Visual Science In Press 20631239
  36. [42]Elledge SJ 1996 Cell cycle checkpoints: Preventing an identity crisis. Science 274 1664 1672 8939848
  37. [43]Bartek J Bartkova J Lukas J 1997 The retinoblastoma protein pathway in cell cycle control and cancer. Experimental Cell Research 237 1 6 9417859
  38. [44]Sherr CJ 1996 Cancer cell cycles. Science 274 1672 1677 8939849
  39. [45]Kerr JFR Wyllie AH Currie AR 1972 Apoptosis - Basic Biological Phenomenon with Wide-Ranging Implications in Tissue Kinetics. British Journal of Cancer 26 239-& 4561027 PMC2008650
  40. [46]Popov SG Villasmil R Bernardi J Grene E Cardwell J 2002 Lethal toxin of Bacillus anthracis causes apoptosis of macrophages. Biochemical and Biophysical Research Communications 293 349 355 12054607
  41. [47]Wajant H 2002 The Fas signaling pathway: More than a paradigm. Science 296 1635 1636 12040174
  42. [48]Chen GQ Goeddel DV 2002 TNF-R1 signaling: A beautiful pathway. Science 296 1634 1635 12040173
  43. [49]Jung IL Kang HJ Kim KC Kim IG 2010 PTEN/pAkt/p53 signaling pathway correlates with the radioresponse of non-small cell lung cancer. International Journal of Molecular Medicine 25 517 523 20198299
  44. [50]Seo JH Moon HS Kim IY Guo DD Lee HG 2008 PEGylated conjugated linoleic acid stimulation of apoptosis via a p53-mediated signaling pathway in MCF-7 breast cancer cells. European Journal of Pharmaceutics and Biopharmaceutics 70 621 626 18573337
  45. [52]Zhou MX Gu LB Li FZ Zhu YR Woods WG 2002 DNA damage induces a novel p53-survivin signaling pathway regulating cell cycle and apoptosis in acute lymphoblastic leukemia cells. Journal of Pharmacology and Experimental Therapeutics 303 124 131 12235242
  46. [53]Cantorias MV Figueroa SD Quinn TP Lever JR Hoffman TJ 2009 Development of high-specific-activity Ga-68-labeled DOTA-rhenium-cyclized alpha-MSH peptide analog to target MC1 receptors overexpressed by melanoma tumors. Nuclear Medicine and Biology 36 505 513 19520291
  47. [54]Lopez MN Pereda C Ramirez M Mendoza-Naranjo A Serrano A 2007 Melanocortin 1 receptor is expressed by uveal malignant melanoma and can be considered a new target for diagnosis and immunotherapy. Investigative Ophthalmology & Visual Science 48 1219 1227 17325166
  48. [55]Herraiz C Jimenez-Cervantes C Zanna P Garcia-Borron JC 2009 Melanocortin 1 receptor mutations impact differentially on signalling to the cAMP and the ERK mitogen-activated protein kinase pathways. Febs Letters 583 3269 3274 19755124

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Authors
An, J., Wan, H., Zhou, X., Hu, D.-N., Wang, L., Hao, L., Yan, D., Shi, F., Zhou, Z., Wang, J., Hu, S., Yu, J., & Qu, J.
Affiliations
  • Wenzhou Medical University (CN)
  • Chinese Academy of Sciences (CN)
  • New York Medical College (US)
Corresponding author
  • Yu, Jun
  • Qu, Jia
ORCID
Venue
PLoS ONE
Publisher
Public Library of Science (PLoS)
Published
2011-01-28
Volume
6
Issue
1
Pages
e16516
ISSN
1932-6203 (ISSN-L)
DOI
10.1371/journal.pone.0016516
PMC
PMC3030591
OpenAlex
W2010732784
Cited by
29
References
1
Citations by year
2025: 2 · 2024: 1 · 2023: 1 · 2021: 4 · 2019: 5 · 2018: 1 · 2017: 2 · 2016: 1 · 2014: 4 · 2013: 5 · 2012: 3
FWCI
3.41
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS ONE (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • Figshare (submittedVersion, cc-by)
Funders
  • National Natural Science Foundation of China
  • Natural Science Foundation of Zhejiang Province
Topics
  • Health Sciences › Medicine › Ophthalmology › Ocular Oncology and Treatments
  • Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Veterinary Oncology Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Ocular Disorders and Treatments
Keywords
uveal melanoma, uveal melanocytes, gene expression profiling, differentially expressed genes, MAPK signaling, cell cycle, cell adhesion junctions, apoptosis, p53 pathway, melanogenesis, carcinogenesis, metastasis
MeSH terms
Uveal Melanoma, Cell Line, Humans, Melanocytes, Melanoma, Tumor Cells, Cultured, Uvea, Uveal Neoplasms, Expressed Sequence Tags, Gene Expression Profiling, Molecular Sequence Annotation, High-Throughput Nucleotide Sequencing

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