Microarray gene-expression analysis in ocular oncology: uveal melanoma and retinoblastoma

References

• Singh AD, Bergman L, Seregard S. Uveal melanoma: epidemiologic aspects. Ophthalmol. Clin. North Am.18(1), 75–84, viii (2005).
   PubMedGoogle Scholar
• Shields CL, Furuta M, Berman EL et al. Choroidal nevus transformation into melanoma: analysis of 2514 consecutive cases. Arch. Ophthalmol.127(8), 981–987 (2009).
   PubMedGoogle Scholar
• The COMS randomized trial of iodine 125 brachytherapy for choroidal melanoma: V. Twelve-year mortality rates and prognostic factors: COMS report No. 28. Arch. Ophthalmol.124(12), 1684–1693 (2006).
   PubMed Web of Science ®Google Scholar
• Singh AD, Topham A. Survival rates with uveal melanoma in the United States: 1973–1997. Ophthalmology110(5), 962–965 (2003).
   PubMed Web of Science ®Google Scholar
• Kujala E, Makitie T, Kivela T. Very long-term prognosis of patients with malignant uveal melanoma. Invest. Ophthalmol. Vis. Sci.44(11), 4651–4659 (2003).
   PubMed Web of Science ®Google Scholar
• Eskelin S, Pyrhonen S, Hahka-Kemppinen M, Tuomaala S, Kivela T. A prognostic model and staging for metastatic uveal melanoma. Cancer97(2), 465–475 (2003).
   PubMed Web of Science ®Google Scholar
• Tamboli A, Podgor MJ, Horm JW. The incidence of retinoblastoma in the United States: 1974 through 1985. Arch. Ophthalmol.108(1), 128–132 (1990).
   PubMedGoogle Scholar
• Pendergrass TW, Davis S. Incidence of retinoblastoma in the United States. Arch. Ophthalmol.98(7), 1204–1210 (1980).
   PubMedGoogle Scholar
• Abramson DH. Retinoblastoma incidence in the United States. Arch. Ophthalmol.108(11), 1514 (1990).
   PubMedGoogle Scholar
• Devesa SS. The incidence of retinoblastoma. Am. J. Ophthalmol.80(2), 263–265 (1975).
   PubMed Web of Science ®Google Scholar
• Shields CL, Mashayekhi A, Au AK et al. The international classification of retinoblastoma predicts chemoreduction success. Ophthalmology113(12), 2276–2280 (2006).
   PubMed Web of Science ®Google Scholar
• Schefler AC, Cicciarelli N, Feuer W, Toledano S, Murray TG. Macular retinoblastoma: evaluation of tumor control, local complications, and visual outcomes for eyes treated with chemotherapy and repetitive foveal laser ablation. Ophthalmology114(1), 162–169 (2007).
   PubMed Web of Science ®Google Scholar
• Augsburger JJ, Gamel JW. Clinical prognostic factors in patients with posterior uveal malignant melanoma. Cancer66(7), 1596–1600 (1990).
   PubMed Web of Science ®Google Scholar
• Seddon JM, Polivogianis L, Hsieh CC, Albert DM, Gamel JW, Gragoudas ES. Death from uveal melanoma. Number of epithelioid cells and inverse SD of nucleolar area as prognostic factors. Arch. Ophthalmol.105(6), 801–806 (1987).
   PubMedGoogle Scholar
• Augsburger JJ, Schroeder RP, Territo C, Gamel JW, Shields JA. Clinical parameters predictive of enlargement of melanocytic choroidal lesions. Br. J. Ophthalmol.73(11), 911–917 (1989).
   PubMedGoogle Scholar
• Mooy CM, De Jong PT. Prognostic parameters in uveal melanoma: a review. Surv. Ophthalmol.41(3), 215–228 (1996).
   PubMed Web of Science ®Google Scholar
• Prescher G, Bornfeld N, Hirche H, Horsthemke B, Jockel KH, Becher R. Prognostic implications of monosomy 3 in uveal melanoma. Lancet347(9010), 1222–1225 (1996).
   PubMed Web of Science ®Google Scholar
• Damato B, Eleuteri A, Fisher AC, Coupland SE, Taktak AF. Artificial neural networks estimating survival probability after treatment of choroidal melanoma. Ophthalmology115(9), 1598–1607 (2008).
   PubMed Web of Science ®Google Scholar
• Bissell MJ, Radisky DC, Rizki A, Weaver VM, Petersen OW. The organizing principle: microenvironmental influences in the normal and malignant breast. Differentiation70(9–10), 537–546 (2002).
   PubMed Web of Science ®Google Scholar
• Hanahan D, Weinberg RA. The hallmarks of cancer. Cell100(1), 57–70 (2000).
   PubMed Web of Science ®Google Scholar
• Coussens LM, Werb Z. Inflammation and cancer. Nature420(6917), 860–867 (2002).
   PubMed Web of Science ®Google Scholar
• Horsman DE, White VA. Cytogenetic analysis of uveal melanoma. Consistent occurrence of monosomy 3 and trisomy 8q. Cancer71(3), 811–819 (1993).
   PubMed Web of Science ®Google Scholar
• Trolet J, Hupe P, Huon I et al. Genomic profiling and identification of high-risk uveal melanoma by array CGH analysis of primary tumors and liver metastases. Invest. Ophthalmol. Vis. Sci.50(6), 2572–2580 (2009).
   PubMedGoogle Scholar
• Lake SL, Coupland SE, Taktak AF, Damato BE. Whole-genome microarray detects deletions and loss of heterozygosity of chromosome 3 occurring exclusively in metastasizing uveal melanoma. Invest. Ophthalmol. Vis. Sci.51(10), 4884–4891 (2010).
   PubMedGoogle Scholar
• Dopierala J, Damato BE, Lake SL, Taktak AF, Coupland SE. Genetic heterogeneity in uveal melanoma assessed by multiplex ligation-dependent probe amplification. Invest. Ophthalmol. Vis. Sci.51(10), 4898–4905 (2010).
   PubMed Web of Science ®Google Scholar
• Harbour JW. Molecular prognostic testing and individualized patient care in uveal melanoma. Am. J. Ophthalmol.148(6), 823–829 e821 (2009).
   PubMed Web of Science ®Google Scholar
• Corson TW, Gallie BL. One hit, two hits, three hits, more? Genomic changes in the development of retinoblastoma. Genes Chromosomes Cancer46(7), 617–634 (2007).
   PubMed Web of Science ®Google Scholar
• Damato B, Dopierala JA, Coupland SE. Genotypic profiling of 452 choroidal melanomas with multiplex ligation-dependent probe amplification. Clin. Cancer Res.16(24), 6083–6092 (2010).
   PubMed Web of Science ®Google Scholar
• Horsman DE, Sroka H, Rootman J, White VA. Monosomy 3 and isochromosome 8q in a uveal melanoma. Cancer Genet. Cytogenet.45(2), 249–253 (1990).
   PubMedGoogle Scholar
• Sisley K, Rennie IG, Cottam DW, Potter AM, Potter CW, Rees RC. Cytogenetic findings in six posterior uveal melanomas: involvement of chromosomes 3, 6, and 8. Genes Chromosomes Cancer2(3), 205–209 (1990).
   PubMed Web of Science ®Google Scholar
• Prescher G, Bornfeld N, Becher R. Nonrandom chromosomal abnormalities in primary uveal melanoma. J. Natl Cancer Inst.82(22), 1765–1769 (1990).
   PubMedGoogle Scholar
• Aalto Y, Eriksson L, Seregard S, Larsson O, Knuutila S. Concomitant loss of chromosome 3 and whole arm losses and gains of chromosome 1, 6, or 8 in metastasizing primary uveal melanoma. Invest. Ophthalmol. Vis. Sci.42(2), 313–317 (2001).
   PubMed Web of Science ®Google Scholar
• Horsthemke B, Prescher G, Bornfeld N, Becher R. Loss of chromosome 3 alleles and multiplication of chromosome 8 alleles in uveal melanoma. Genes Chromosomes Cancer4(3), 217–221 (1992).
   PubMedGoogle Scholar
• Scholes AG, Damato BE, Nunn J, Hiscott P, Grierson I, Field JK. Monosomy 3 in uveal melanoma: correlation with clinical and histologic predictors of survival. Invest. Ophthalmol. Vis. Sci.44(3), 1008–1011 (2003).
   PubMed Web of Science ®Google Scholar
• Ghazvini S, Char DH, Kroll S, Waldman FM, Pinkel D. Comparative genomic hybridization analysis of archival formalin-fixed paraffin-embedded uveal melanomas. Cancer Genet. Cytogenet.90(2), 95–101 (1996).
   PubMedGoogle Scholar
• Wiltshire RN, Elner VM, Dennis T, Vine AK, Trent JM. Cytogenetic analysis of posterior uveal melanoma. Cancer Genet. Cytogenet.66(1), 47–53 (1993).
   PubMedGoogle Scholar
• Prescher G, Bornfeld N, Friedrichs W, Seeber S, Becher R. Cytogenetics of twelve cases of uveal melanoma and patterns of nonrandom anomalies and isochromosome formation. Cancer Genet. Cytogenet.80(1), 40–46 (1995).
   PubMedGoogle Scholar
• Parrella P, Sidransky D, Merbs SL. Allelotype of posterior uveal melanoma: implications for a bifurcated tumor progression pathway. Cancer Res.59(13), 3032–3037 (1999).
   PubMed Web of Science ®Google Scholar
• Speicher MR, Prescher G, du Manoir S et al. Chromosomal gains and losses in uveal melanomas detected by comparative genomic hybridization. Cancer Res.54(14), 3817–3823 (1994).
   PubMed Web of Science ®Google Scholar
• Onken MD, Worley LA, Ehlers JP, Harbour JW. Gene expression profiling in uveal melanoma reveals two molecular classes and predicts metastatic death. Cancer Res.64(20), 7205–7209 (2004).
   PubMed Web of Science ®Google Scholar
• Sisley K, Rennie IG, Parsons MA et al. Abnormalities of chromosomes 3 and 8 in posterior uveal melanoma correlate with prognosis. Genes Chromosomes Cancer19(1), 22–28 (1997).
   PubMed Web of Science ®Google Scholar
• Tschentscher F, Husing J, Holter T et al. Tumor classification based on gene expression profiling shows that uveal melanomas with and without monosomy 3 represent two distinct entities. Cancer Res.63(10), 2578–2584 (2003).
   PubMed Web of Science ®Google Scholar
• Hoglund M, Gisselsson D, Hansen GB et al. Dissecting karyotypic patterns in malignant melanomas: temporal clustering of losses and gains in melanoma karyotypic evolution. Int. J. Cancer108(1), 57–65 (2004).
   PubMed Web of Science ®Google Scholar
• Lee EY, Lee WH. Molecular cloning of the human esterase D gene, a genetic marker of retinoblastoma. Proc. Natl Acad. Sci. USA83(17), 6337–6341 (1986).
   PubMedGoogle Scholar
• Lee WH, Bookstein R, Hong F, Young LJ, Shew JY, Lee EY. Human retinoblastoma susceptibility gene: cloning, identification, and sequence. Science235(4794), 1394–1399 (1987).
   PubMed Web of Science ®Google Scholar
• Friend SH, Bernards R, Rogelj S et al. A human DNA segment with properties of the gene that predisposes to retinoblastoma and osteosarcoma. Nature323(6089), 643–646 (1986).
   PubMed Web of Science ®Google Scholar
• Fung YK, Murphree AL, T’Ang A, Qian J, Hinrichs SH, Benedict WF. Structural evidence for the authenticity of the human retinoblastoma gene. Science236(4809), 1657–1661 (1987).
   PubMed Web of Science ®Google Scholar
• Squire J, Phillips RA, Boyce S, Godbout R, Rogers B, Gallie BL. Isochromosome 6p, a unique chromosomal abnormality in retinoblastoma: verification by standard staining techniques, new densitometric methods, and somatic cell hybridization. Hum. Genet.66(1), 46–53 (1984).
   PubMedGoogle Scholar
• Cano J, Oliveros O, Yunis E. Phenotype variants, malignancy, and additional copies of 6p in retinoblastoma. Cancer Genet. Cytogenet.76(2), 112–115 (1994).
   PubMedGoogle Scholar
• Potluri VR, Helson L, Ellsworth RM, Reid T, Gilbert F. Chromosomal abnormalities in human retinoblastoma. A review. Cancer58(3), 663–671 (1986).
   PubMedGoogle Scholar
• Gilbert F, Balaban G, Breg WR, Gallie B, Reid T, Nichols W. Homogeneously staining region in a retinoblastoma cell line: relevance to tumor initiation and progression. J. Natl Cancer Inst.67(2), 301–306 (1981).
   PubMedGoogle Scholar
• Chaum E, Ellsworth RM, Abramson DH, Haik BG, Kitchin FD, Chaganti RS. Cytogenetic analysis of retinoblastoma: evidence for multifocal origin and in vivo gene amplification. Cytogenet. Cell Genet.38(2), 82–91 (1984).
   PubMedGoogle Scholar
• Mairal A, Pinglier E, Gilbert E et al. Detection of chromosome imbalances in retinoblastoma by parallel karyotype and CGH analyses. Genes Chromosomes Cancer28(4), 370–379 (2000).
   PubMed Web of Science ®Google Scholar
• Chen D, Gallie BL, Squire JA. Minimal regions of chromosomal imbalance in retinoblastoma detected by comparative genomic hybridization. Cancer Genet. Cytogenet.129(1), 57–63 (2001).
   PubMedGoogle Scholar
• Lillington DM, Kingston JE, Coen PG et al. Comparative genomic hybridization of 49 primary retinoblastoma tumors identifies chromosomal regions associated with histopathology, progression, and patient outcome. Genes Chromosomes Cancer36(2), 121–128 (2003).
   PubMed Web of Science ®Google Scholar
• van der Wal JE, Hermsen MA, Gille HJ et al. Comparative genomic hybridisation divides retinoblastomas into a high and a low level chromosomal instability group. J. Clin. Pathol.56(1), 26–30 (2003).
   PubMedGoogle Scholar
• Herzog S, Lohmann DR, Buiting K et al. Marked differences in unilateral isolated retinoblastomas from young and older children studied by comparative genomic hybridization. Hum. Genet.108(2), 98–104 (2001).
   PubMedGoogle Scholar
• Bowles E, Corson TW, Bayani J et al. Profiling genomic copy number changes in retinoblastoma beyond loss of RB1. Genes Chromosomes Cancer46(2), 118–129 (2007).
   PubMedGoogle Scholar
• Tschentscher F, Prescher G, Horsman DE et al. Partial deletions of the long and short arm of chromosome 3 point to two tumor suppressor genes in uveal melanoma. Cancer Res.61(8), 3439–3442 (2001).
   PubMed Web of Science ®Google Scholar
• Onken MD, Ehlers JP, Worley LA, Makita J, Yokota Y, Harbour JW. Functional gene expression analysis uncovers phenotypic switch in aggressive uveal melanomas. Cancer Res.66(9), 4602–4609 (2006).
   PubMed Web of Science ®Google Scholar
• van Gils W, Kilic E, Bruggenwirth HT et al. Regional deletion and amplification on chromosome 6 in a uveal melanoma case without abnormalities on chromosomes 1p, 3 and 8. Melanoma. Res.18(1), 10–15 (2008).
   PubMedGoogle Scholar
• McCannel TA, Burgess BL, Rao NP, Nelson SF, Straatsma BR. Identification of candidate tumor oncogenes by integrative molecular analysis of choroidal melanoma fine-needle aspiration biopsy specimens. Arch. Ophthalmol.128(9), 1170–1177 (2010).
   PubMedGoogle Scholar
• Eskelin S, Pyrhonen S, Summanen P, Hahka-Kemppinen M, Kivela T. Tumor doubling times in metastatic malignant melanoma of the uvea: tumor progression before and after treatment. Ophthalmology107(8), 1443–1449 (2000).
   PubMed Web of Science ®Google Scholar
• Meir T, Dror R, Yu X et al. Molecular characteristics of liver metastases from uveal melanoma. Invest. Ophthalmol. Vis. Sci.48(11), 4890–4896 (2007).
   PubMed Web of Science ®Google Scholar
• Petrausch U, Martus P, Tonnies H et al. Significance of gene expression analysis in uveal melanoma in comparison to standard risk factors for risk assessment of subsequent metastases. Eye (Lond.)22(8), 997–1007 (2008).
   PubMedGoogle Scholar
• Worley LA, Onken MD, Person E et al. Transcriptomic versus chromosomal prognostic markers and clinical outcome in uveal melanoma. Clin. Cancer Res.13(5), 1466–1471 (2007).
   PubMed Web of Science ®Google Scholar
• Onken MD, Worley LA, Tuscan MD, Harbour JW. An accurate, clinically feasible multi-gene expression assay for predicting metastasis in uveal melanoma. J. Mol. Diagn.12(4), 461–468 (2010).
   PubMed Web of Science ®Google Scholar
• Di Cesare S, Nantel A, Marshall JC et al. Expression profiling of formalin-fixed paraffin embedded primary human uveal melanomas using DASL matrices. J. Cancer Res. Clin. Oncol.136(4), 577–586 (2010).
   PubMedGoogle Scholar
• Knudson AG Jr. Mutation and cancer: statistical study of retinoblastoma. Proc. Natl Acad. Sci. USA68(4), 820–823 (1971).
   PubMed Web of Science ®Google Scholar
• Gratias S, Schuler A, Hitpass LK et al. Genomic gains on chromosome 1q in retinoblastoma: consequences on gene expression and association with clinical manifestation. Int. J. Cancer116(4), 555–563 (2005).
   PubMedGoogle Scholar
• Chakraborty S, Khare S, Dorairaj SK, Prabhakaran VC, Prakash DR, Kumar A. Identification of genes associated with tumorigenesis of retinoblastoma by microarray analysis. Genomics90(3), 344–353 (2007).
   PubMed Web of Science ®Google Scholar
• Meric-Bernstam F, Gonzalez-Angulo AM. Targeting the mTOR signaling network for cancer therapy. J. Clin. Oncol.27(13), 2278–2287 (2009).
   PubMed Web of Science ®Google Scholar
• Rademakers SE, Span PN, Kaanders JH, Sweep FC, van der Kogel AJ, Bussink J. Molecular aspects of tumour hypoxia. Mol. Oncol.2(1), 41–53 (2008).
   PubMed Web of Science ®Google Scholar
• Martin TA, Jiang WG. Tight junctions and their role in cancer metastasis. Histol. Histopathol.16(4), 1183–1195 (2001).
   PubMed Web of Science ®Google Scholar
• Vermeulen SJ, Nollet F, Teugels E et al. The αE-catenin gene (CTNNA1) acts as an invasion-suppressor gene in human colon cancer cells. Oncogene18(4), 905–915 (1999).
   PubMedGoogle Scholar
• Ganguly A, Shields CL. Differential gene expression profile of retinoblastoma compared to normal retina. Mol. Vis.16, 1292–1303 (2010).
   PubMed Web of Science ®Google Scholar
• Gramatzki D, Pantazis G, Schittenhelm J et al. Aryl hydrocarbon receptor inhibition downregulates the TGF-β/Smad pathway in human glioblastoma cells. Oncogene28(28), 2593–2605 (2009).
   PubMed Web of Science ®Google Scholar
• Boutrid H, Jockovich ME, Murray TG et al. Targeting hypoxia, a novel treatment for advanced retinoblastoma. Invest. Ophthalmol. Vis. Sci.49(7), 2799–2805 (2008).
   PubMedGoogle Scholar
• Pina Y, Boutrid H, Schefler A et al. Blood vessel maturation in retinoblastoma tumors: spatial distribution of neovessels and mature vessels and its impact on ocular treatment. Invest. Ophthalmol. Vis. Sci.50(3), 1020–1024 (2009).
   PubMed Web of Science ®Google Scholar
• Houston SK, Pina Y, Clarke J et al. Regional and temporal differences in gene expression of LHBETATAG retinoblastoma tumors. Invest. Ophthalmol. Vis. Sci.52(8), 5359–5368 (2011).
   PubMed Web of Science ®Google Scholar