Proteomics in uveal melanoma research: opportunities and challenges in biomarker discovery

Uveal melanoma (UM) is the most frequent primary intraocular tumor in adult humans. Despite the significant advances in diagnosis and treatment of UM in the last decades, the prognosis of UM sufferers is still poor. Metastatic liver disease is the leading cause of death in UM and can develop after a long disease-free interval, suggesting the presence of occult micrometastasis. Proteomics technology has opened new opportunities for elucidating the molecular mechanism of complex diseases, such as cancer. This article will review the recent developments in biomarker discovery for UM research by proteomics. In the last few years, the first UM proteomics-based analyses have been launched, yielding promising results. An update on recent developments on this field is presented.

[1]  F. Soylemezoğlu,et al.  Expression of Vascular Endothelial Growth Factor A, Matrix Metalloproteinase 9 and Extravascular Matrix Patterns in Iris and Ciliary Body Melanomas , 2006, Ophthalmic Research.

[2]  D. T. Wong,et al.  Human body fluid proteome analysis , 2006, Proteomics.

[3]  J. Harbour,et al.  Prognostic testing in uveal melanoma by transcriptomic profiling of fine needle biopsy specimens. , 2006, The Journal of molecular diagnostics : JMD.

[4]  G. Omenn.  Strategies for plasma proteomic profiling of cancers , 2006, Proteomics.

[5]  R. Dwek,et al.  The characterization of the invasion phenotype of uveal melanoma tumour cells shows the presence of MUC18 and HMG‐1 metastasis markers and leads to the identification of DJ‐1 as a potential serum biomarker , 2006, International journal of cancer.

[6]  Frank Vitzthum,et al.  Effects of preanalytical variables on peptide and protein measurements in human serum and plasma: implications for clinical proteomics , 2006, Expert review of proteomics.

[7]  N. Hayward,et al.  Increased p21-activated kinase-1 expression is associated with invasive potential in uveal melanoma , 2006, Melanoma research.

[8]  W. McDonald,et al.  Developments in mass spectrometry for the analysis of complex protein mixtures. , 2006, Briefings in functional genomics & proteomics.

[9]  J. Solassol,et al.  Clinical proteomics and mass spectrometry profiling for cancer detection , 2006, Expert review of proteomics.

[10]  K. Cottingham.  Meeting News: Speeding up biomarker discovery , 2006 .

[11]  L. Bonaldi,et al.  In vivo Detection of Monosomy 3 in Eyes with Medium-Sized Uveal Melanoma using Transscleral Fine Needle Aspiration Biopsy , 2006, European journal of ophthalmology.

[12]  N. Verrills.  Clinical proteomics: present and future prospects. , 2006, The Clinical biochemist. Reviews.

[13]  N. Gruis,et al.  Proteomic analysis of uveal melanoma reveals novel potential markers involved in tumor progression. , 2006, Investigative ophthalmology & visual science.

[14]  A. Jemal,et al.  Cancer Statistics, 2006 , 2006, CA: a cancer journal for clinicians.

[15]  R. Folberg,et al.  Osteopontin expression and serum levels in metastatic uveal melanoma: a pilot study. , 2006, Investigative ophthalmology & visual science.

[16]  C. Eng,et al.  High frequency of submicroscopic hemizygous deletion is a major mechanism of loss of expression of PTEN in uveal melanoma. , 2006, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[17]  T. Kivelä,et al.  KI-67 Immunopositivity in Choroidal and Ciliary Body Melanoma with Respect to Nucleolar Diameter and Other Prognostic Factors , 2006, Current eye research.

[18]  K. Mallikarjuna,et al.  Expression of Insulin-Like Growth Factor Receptor (IGF-1R), c-Fos, and c-Jun in Uveal Melanoma: An Immunohistochemical Study , 2006, Current Eye Research.

[19]  L. Germain,et al.  MMP-2 expression in uveal melanoma: differential activation status dictated by the cellular environment. , 2005, Molecular vision.

[20]  R. Dwek,et al.  Proteome analysis of a human uveal melanoma primary cell culture by 2‐DE and MS , 2005, Proteomics.

[21]  O. Larsson,et al.  Receptors for the liver synthesized growth factors IGF-1 and HGF/SF in uveal melanoma: intercorrelation and prognostic implications. , 2005, Investigative ophthalmology & visual science.

[22]  R. Dwek,et al.  Applying proteomics technology to platelet research. , 2005, Mass spectrometry reviews.

[23]  J. Marshall,et al.  The role of c-kit and imatinib mesylate in uveal melanoma , 2005, Journal of carcinogenesis.

[24]  R. Folberg,et al.  Association between microarray gene expression signature and extravascular matrix patterns in primary uveal melanomas. , 2005, American journal of ophthalmology.

[25]  Liliana Gheorghiu,et al.  Reduction of the concentration difference of proteins in biological liquids using a library of combinatorial ligands , 2005, Electrophoresis.

[26]  Graham B. I. Scott,et al.  HUPO Plasma Proteome Project specimen collection and handling: Towards the standardization of parameters for plasma proteome samples , 2005, Proteomics.

[27]  A. Bosserhoff,et al.  “Melanoma inhibitory activity” (MIA): a promising serological tumour marker in metastatic uveal melanoma , 2005, Graefe's Archive for Clinical and Experimental Ophthalmology.

[28]  M. Hussein.  Analysis of Bcl-2 protein expression in choroidal melanomas , 2005, Journal of Clinical Pathology.

[29]  V. Cicinnati,et al.  Unpulsed dendritic cells induce broadly applicable anti-tumor immunity in mice , 2005, Cancer biology & therapy.

[30]  M. Hussein.  The relationships between p53 protein expression and the clinicopathological features in the uveal melanomas , 2005, Cancer biology & therapy.

[31]  N. Bornfeld,et al.  Differential Expression of Tissue Inhibitor of Matrix Metalloproteinases 3 in Uveal Melanoma , 2003, Ophthalmic Research.

[32]  Hans E. Grossniklaus,et al.  Gene expression profiling in uveal melanoma reveals two molecular classes and predicts metastatic death. Onken MD, Worley LA, Ehlers JP, Harbour JW Canc Res 2004;64:7205–7209 , 2005 .

[33]  B. Damato.  Developments in the management of uveal melanoma , 2004, Clinical & experimental ophthalmology.

[34]  P. Ascierto,et al.  Prognostic value of serum VEGF in melanoma patients: a pilot study. , 2004, Anticancer research.

[35]  B. Davies,et al.  High‐mobility group protein 1(Y): Metastasis‐associated or metastasis‐inducing? , 2004, Journal of surgical oncology.

[36]  M. T. de la Fuente,et al.  Abnormal cell cycle regulation in primary human uveal melanoma cultures , 2004, Journal of cellular biochemistry.

[37]  Justis P. Ehlers,et al.  Gene Expression Profiling in Uveal Melanoma Reveals Two Molecular Classes and Predicts Metastatic Death , 2004, Cancer Research.

[38]  Y. Hod.  Differential control of apoptosis by DJ‐1 in prostate benign and cancer cells , 2004, Journal of cellular biochemistry.

[39]  E. Izbicka,et al.  Fine-needle aspiration in PreservCyt®: a novel and reproducible method for possible ancillary proteomic pattern expression of breast neoplasms by SELDI-TOF , 2004, Modern Pathology.

[40]  O. Larsson,et al.  c-Kit-dependent growth of uveal melanoma cells: a potential therapeutic target? , 2004, Investigative ophthalmology & visual science.

[41]  Daniel W Chan,et al.  Cancer Proteomics: Serum Diagnostics for Tumor Marker Discovery , 2004, Annals of the New York Academy of Sciences.

[42]  K. Jain.  Role of oncoproteomics in the personalized management of cancer , 2004, Expert review of proteomics.

[43]  J. Marshall,et al.  How in vitro techniques have increased our understanding of uveal melanoma cellular biology. , 2004, Canadian journal of ophthalmology. Journal canadien d'ophtalmologie.

[44]  M. Burnier,et al.  New prognostic factors in uveal melanomas: potential molecular targets for therapy. , 2004, Canadian journal of ophthalmology. Journal canadien d'ophtalmologie.

[45]  Z. Mariak,et al.  [Tumor angiogensis in uveal melanoma. Role of vascular endothelial growth factor (VEGF)]. , 2004, Klinika oczna.

[46]  P. Meltzer,et al.  Molecular determinants of human uveal melanoma invasion and metastasis , 2004, Clinical & Experimental Metastasis.

[47]  R. M. Sharrard,et al.  C-myc oncogene expression in ocular melanomas , 2004, Graefe's Archive for Clinical and Experimental Ophthalmology.

[48]  S. Pavey,et al.  Expression profiling reveals that methylation of TIMP3 is involved in uveal melanoma development. , 2004, International journal of cancer.

[49]  J. Keunen,et al.  Proteomics in uveal melanoma , 2003, Melanoma research.

[50]  R. Frants,et al.  Gene expression profiling identifies tumour markers potentially playing a role in uveal melanoma development , 2003, British Journal of Cancer.

[51]  E. Dalmasso,et al.  SELDI ProteinChip® Array Technology: Protein-Based Predictive Medicine and Drug Discovery Applications , 2003, Journal of biomedicine & biotechnology.

[52]  Y. Hod,et al.  Proteomic profiling drug-induced apoptosis in non-small cell lung carcinoma: identification of RS/DJ-1 and RhoGDIalpha. , 2003, Cancer research.

[53]  G. Sauter,et al.  Sequence analysis and high-throughput immunhistochemical profiling of KIT (CD 117) expression in uveal melanoma using tissue microarrays , 2003, Virchows Archiv.

[54]  P. V. Ginkel,et al.  Structural Alterations and Gene Expression in the Pathogenesis of Uveal Melanoma , 2003 .

[55]  H. D. de Bruijn,et al.  Sample preparation of human serum for the analysis of tumor markers. Comparison of different approaches for albumin and gamma-globulin depletion. , 2003, Journal of chromatography. A.

[56]  J. Keunen,et al.  Prognostic Value of S-100-β Serum Concentration in Patients With Uveal Melanoma , 2003 .

[57]  I. McLean,et al.  Cyclooxygenase-2 expression in uveal melanoma: novel classification of mixed-cell-type tumours. , 2003, Canadian journal of ophthalmology. Journal canadien d'ophtalmologie.

[58]  K. Jöckel,et al.  Tumor classification based on gene expression profiling shows that uveal melanomas with and without monosomy 3 represent two distinct entities. , 2003, Cancer research.

[59]  Arun D. Singh,et al.  Survival rates with uveal melanoma in the United States: 1973-1997. , 2003, Ophthalmology.

[60]  L. Parvinen,et al.  Bleomycin, vincristine, lomustine and dacarbazine (BOLD) in combination with recombinant interferon alpha-2b for metastatic uveal melanoma. , 2003, European journal of cancer.

[61]  G. de Rosa,et al.  Expression of cyclin-D1 in uveal malignant melanoma. , 2003, Anticancer research.

[62]  M. Tyers,et al.  From genomics to proteomics , 2003, Nature.

[63]  R. Aebersold,et al.  Mass spectrometry-based proteomics , 2003, Nature.

[64]  H. Radner,et al.  Expression of somatostatin receptors in uveal melanomas. , 2003, Investigative ophthalmology & visual science.

[65]  N. Anderson,et al.  The Human Plasma Proteome: History, Character, and Diagnostic Prospects , 2003, Molecular & Cellular Proteomics.

[66]  J. Harbour,et al.  Molecular genetics of uveal melanoma , 2003, Current eye research.

[67]  L. Fésüs,et al.  The Biology of the Post-Genomic ERA: The Proteomics , 2003, Acta biologica Hungarica.

[68]  A. Bosserhoff,et al.  Melanoma inhibitory activity: a novel serum marker for uveal melanoma , 2002, Melanoma research.

[69]  J. Heighway,et al.  Decreased endothelin receptor B expression in large primary uveal melanomas is associated with early clinical metastasis and short survival , 2002, British Journal of Cancer.

[70]  E. Petricoin,et al.  Clinical proteomics: translating benchside promise into bedside reality , 2002, Nature Reviews Drug Discovery.

[71]  D. Kelsell,et al.  Mutational analysis of selected genes in the TGFbeta, Wnt, pRb, and p53 pathways in primary uveal melanoma. , 2002, Investigative ophthalmology & visual science.

[72]  D. Lev,et al.  Cellular Adhesion Pathways and Metastatic Potential of Human Melanoma , 2002, Cancer biology & therapy.

[73]  T. Yip,et al.  SELDI ProteinChip® Array in Oncoproteomic Research , 2002, Technology in cancer research & treatment.

[74]  R. E. Kalina,et al.  Immunophenotypic differences between uveal and cutaneous melanomas. , 2002, Archives of ophthalmology.

[75]  C. Bunce,et al.  Vascular endothelial growth factor is elevated in ocular fluids of eyes harbouring uveal melanoma: identification of a potential therapeutic window , 2002, The British journal of ophthalmology.

[76]  I. Chowers,et al.  p53 Immunoreactivity, Ki-67 expression, and microcirculation patterns in melanoma of the iris, ciliary body, and choroid , 2002, Current eye research.

[77]  Martine J Jager,et al.  Insulin-like growth factor-1 receptor in uveal melanoma: a predictor for metastatic disease and a potential therapeutic target. , 2002, Investigative ophthalmology & visual science.

[78]  M. Amin,et al.  Isolation and characterization of the major form of human MUC18 cDNA gene and correlation of MUC18 over-expression in prostate cancer cell lines and tissues with malignant progression. , 2001, Gene.

[79]  David E. Misek,et al.  Proteomics-based identification of RS/DJ-1 as a novel circulating tumor antigen in breast cancer. , 2001, Clinical cancer research : an official journal of the American Association for Cancer Research.

[80]  R. Simpson,et al.  Cancer proteomics: from signaling networks to tumor markers. , 2001, Trends in biotechnology.

[81]  L. Liotta,et al.  Proteomic profiling of the cancer microenvironment by antibody arrays , 2001, Proteomics.

[82]  S Hanash,et al.  Proteomics in early detection of cancer. , 2001, Clinical chemistry.

[83]  K. Wakamatsu,et al.  5-S-cysteinyldopa as diagnostic tumor marker for uveal malignant melanoma. , 2001, Japanese journal of ophthalmology.

[84]  A. Stang,et al.  Expression of Fas and Fas ligand in uveal melanoma: biological implication and prognostic value , 2001, The Journal of pathology.

[85]  C. Maurage,et al.  Implication of stem cell factor in the proliferation of choroidal melanocytes. , 2001, Experimental eye research.

[86]  D. Sidransky,et al.  Detection of c-myc amplification in uveal melanoma by fluorescent in situ hybridization. , 2001, Investigative ophthalmology & visual science.

[87]  M. Parsons,et al.  Expression of integrins, degradative enzymes and their inhibitors in uveal melanoma: differences between in vitro and in vivo expression , 2001, Melanoma research.

[88]  H. Radner,et al.  MMP‐9 is predominantly expressed in epithelioid and not spindle cell uveal melanoma , 2001, The Journal of pathology.

[89]  J. Yates,et al.  Large-scale analysis of the yeast proteome by multidimensional protein identification technology , 2001, Nature Biotechnology.

[90]  R. Aebersold,et al.  Mass spectrometry in proteomics. , 2001, Chemical reviews.

[91]  L. Chyczewskî,et al.  Bcl-2 Expression in Primary Uveal Melanoma , 2001, Tumori.

[92]  R. Reeves,et al.  Architectural Transcription Factor HMGI(Y) Promotes Tumor Progression and Mesenchymal Transition of Human Epithelial Cells , 2001, Molecular and Cellular Biology.

[93]  L. Chyczewskî,et al.  Expression of P53 protein in primary uveal melanoma. , 2001, Folia histochemica et cytobiologica.

[94]  M. Mann,et al.  Analysis of proteins and proteomes by mass spectrometry. , 2001, Annual review of biochemistry.

[95]  J. Harbour,et al.  Deregulation of the Rb and p53 pathways in uveal melanoma. , 2000, American Journal of Pathology.

[96]  J. Darbon,et al.  Cyclin-dependent kinase inhibitory protein expression in human choroidal melanoma tumors. , 2000, Investigative ophthalmology & visual science.

[97]  T. Kivelä,et al.  Tumor doubling times in metastatic malignant melanoma of the uvea: tumor progression before and after treatment. , 2000, Ophthalmology.

[98]  E. Mayhew,et al.  Human Uveal Melanoma Cells Produce Macrophage Migration-Inhibitory Factor to Prevent Lysis by NK Cells1 , 2000, The Journal of Immunology.

[99]  S. Hoving,et al.  Towards high performance two‐dimensional gel electrophoresis using ultrazoom gels , 2000, Electrophoresis.

[100]  C. Crukley,et al.  Expression of vascular endothelial growth factor in uveal melanoma and its correlation with metastasis , 2000, The British journal of ophthalmology.

[101]  A. Zwinderman,et al.  Expression of epidermal growth factor receptor: risk factor in uveal melanoma. , 2000, Investigative ophthalmology & visual science.

[102]  H. Stein,et al.  The prognostic value of cyclin D1, p53, and MDM2 protein expression in uveal melanoma , 2000, The Journal of pathology.

[103]  D. Schadendorf,et al.  Comparison of S100 protein and MIA protein as serum marker for malignant melanoma. , 2000, Anticancer research.

[104]  A. Görg,et al.  The current state of two‐dimensional electrophoresis with immobilized pH gradients , 2000, Electrophoresis.

[105]  Mary F. Lopez,et al.  Better approaches to finding the needle in a haystack: Optimizing proteome analysis through automation , 2000, Electrophoresis.

[106]  H. Stein,et al.  Telomerase expression in uveal melanoma , 2000, The British journal of ophthalmology.

[107]  A. Heiligenhaus,et al.  Expression of the Cell Adhesion Molecules ICAM-1, VCAM-1 and NCAM in Uveal Melanoma: A Clinicopathological Study , 2000, Oncology.

[108]  J. Rohrbach,et al.  [Telomerase activity in uveal melanomas]. , 2000, Der Ophthalmologe : Zeitschrift der Deutschen Ophthalmologischen Gesellschaft.

[109]  J. Harbour,et al.  Inactivation of retinoblastoma protein in uveal melanoma by phosphorylation of sites in the COOH-terminal region. , 2000, Cancer research.

[110]  Petricoin Ef rd,et al.  The promise of proteomics , 2003, Nature.

[111]  I. Shih.  The role of CD146 (Mel‐CAM) in biology and pathology , 1999, The Journal of pathology.

[112]  J. Yates,et al.  Direct analysis of protein complexes using mass spectrometry , 1999, Nature Biotechnology.

[113]  M. Kallioinen,et al.  Matrix metalloproteinase‐2 (MMP‐2) immunoreactive protein—a new prognostic marker in uveal melanoma? , 1999, The Journal of pathology.

[114]  S. Gygi,et al.  Correlation between Protein and mRNA Abundance in Yeast , 1999, Molecular and Cellular Biology.

[115]  A. Tarkkanen,et al.  Microvascular loops and networks as prognostic indicators in choroidal and ciliary body melanomas. , 1999, Journal of the National Cancer Institute.

[116]  A. Foss,et al.  c-myc, p53, and Bcl-2 expression and clinical outcome in uveal melanoma , 1999, The British journal of ophthalmology.

[117]  D. Pappin,et al.  The potential use of laser capture microdissection to selectively obtain distinct populations of cells for proteomic analysis — Preliminary findings , 1999, Electrophoresis.

[118]  B Herbert,et al.  Advances in protein solubilisation for two‐dimensional electrophoresis , 1999, Electrophoresis.

[119]  E. Wang,et al.  Development and characterization of melanoma cell lines established by fine-needle aspiration biopsy: advances in the monitoring of patients with metastatic melanoma. , 1999, Cancer detection and prevention.

[120]  H. Stein,et al.  Expression patterns of cyclin D1 and related proteins regulating G1-S phase transition in uveal melanoma and retinoblastoma , 1998, The British journal of ophthalmology.

[121]  J. Niederkorn,et al.  Antibody-Mediated Cytolysis of Epidermal Growth Factor Receptor — Positive Human Uveal Melanoma Cells , 2005 .

[122]  K. Wakamatsu,et al.  [5-S-cysteinyldopa as a tumor marker for primary uveal malignant melanoma]. , 1998, Nippon Ganka Gakkai zasshi.

[123]  A. Foss,et al.  The prognostic significance of c‐myc oncogene expression in uveal melanoma , 1998, Melanoma research.

[124]  M. Hendrix,et al.  Regulation of uveal melanoma interconverted phenotype by hepatocyte growth factor/scatter factor (HGF/SF). , 1998, The American journal of pathology.

[125]  M. Hendrix,et al.  Biologic determinants of uveal melanoma metastatic phenotype: role of intermediate filaments as predictive markers. , 1998, Laboratory investigation; a journal of technical methods and pathology.

[126]  P. D. de Jong,et al.  Expression of MAGE, gp100 and tyrosinase genes in uveal melanoma cell lines , 1998, Melanoma research.

[127]  T. Taira,et al.  DJ-1, a novel oncogene which transforms mouse NIH3T3 cells in cooperation with ras. , 1997, Biochemical and biophysical research communications.

[128]  P. D. de Jong,et al.  Prognostic parameters in uveal melanoma: a review. , 1996, Survey of ophthalmology.

[129]  K. Daniels,et al.  Expression of type VI collagen in uveal melanoma: its role in pattern formation and tumor progression. , 1996, Laboratory investigation; a journal of technical methods and pathology.

[130]  K. Kishore,et al.  p53 gene and cell cycling in uveal melanoma. , 1996, American journal of ophthalmology.

[131]  V. Jay,et al.  Expression of bcl-2 in uveal malignant melanoma. , 1996, Archives of pathology & laboratory medicine.

[132]  S. Wingren,et al.  Correlations of Ki-67 and PCNA to DNA ploidy, S-phase fraction and survival in uveal melanoma. , 1996, European journal of cancer.

[133]  V. Jay,et al.  P53 Expression In Uveal Malignant Melanomas , 1996, Pathology.

[134]  P T de Jong,et al.  Immunohistochemical and prognostic analysis of apoptosis and proliferation in uveal melanoma. , 1995, The American journal of pathology.

[135]  A. Alaiya,et al.  Sample preparation of human tumors prior to two‐dimensional electrophoresis of proteins , 1995, Electrophoresis.

[136]  R. Folberg,et al.  The prognostic value of tumor blood vessel morphology in primary uveal melanoma. , 1993, Ophthalmology.

[137]  N. Bornfeld,et al.  Loss of chromosome 3 alleles and multiplication of chromosome 8 alleles in uveal melanoma , 1992, Genes, chromosomes & cancer.

[138]  S. Wallace,et al.  The prevalence and location of metastases from ocular melanoma: imaging study in 110 patients. , 1991, AJR. American journal of roentgenology.

[139]  P T de Jong,et al.  Ki-67 immunostaining in uveal melanoma. The effect of pre-enucleation radiotherapy. , 1990, Ophthalmology.

[140]  I. McLean,et al.  Lymphocytic infiltration in uveal malignant melanoma , 1990, Cancer.

[141]  M. Mann,et al.  Electrospray ionization for mass spectrometry of large biomolecules. , 1989, Science.

[142]  A. Balmain,et al.  Analysis of the HMGI nuclear proteins in mouse neoplastic cells induced by different procedures. , 1989, Experimental cell research.

[143]  M. Karas,et al.  Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. , 1988, Analytical chemistry.

[144]  J. Gamel,et al.  Modifications of Callender's classification of uveal melanoma at the Armed Forces Institute of Pathology. , 1983, American journal of ophthalmology.

[145]  H. V. van Peperzeel,et al.  Uveal melanoma: location, size, cell type, and enucleation as risk factors in metastasis. , 1982, Human pathology.

[146]  J. Shields,et al.  Evaluation of metastatic cancer to the eye. Carcinoembryonic antigen and gamma glutamyl transpeptidase. , 1977, Archives of ophthalmology.

[147]  P. O’Farrell.  High resolution two-dimensional electrophoresis of proteins. , 1975, The Journal of biological chemistry.