Abstract
Uveal (ocular) melanoma is an aggressive cancer that metastasizes in up to half of patients. Uveal melanoma spreads preferentially to the liver, and the metastatic disease is almost always fatal. There are no effective therapies for advanced metastatic disease, so the most promising strategy for improving survival is to detect metastasis at an earlier stage or to treat high-risk patients in an adjuvant setting. An accurate test for identifying high-risk patients would allow for such personalized management as well as for stratification of high-risk patients into clinical trials of adjuvant therapy.
We developed a gene expression profile (GEP) that distinguishes between primary uveal melanomas that have a low metastatic risk (class 1 tumors) and those with a high metastatic risk (class 2 tumors). We migrated the GEP from a high-density microarray platform to a 15-gene, qPCR-based assay that is now performed in a College of American Pathologists (CAP)-accredited Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory on a routine clinical basis on very small samples obtained by fine needle aspiration and on archival formalin-fixed specimens. We collaborated with several centers to show that our specimen collection protocol was easily learned and performed and that it allowed samples to be safely and reliably transported from distant locations with a very low failure rate. Finally, we showed in a multicenter, prospective study that our GEP assay is highly accurate for predicting which patients will develop metastatic disease, and it was significantly superior to the previous gold standard, chromosome 3 testing for monosomy 3. This is the only prognostic test in uveal melanoma ever to undergo such extensive validation, and it is currently being used in a commercial format under the trade name DecisionDx-UM in over 100 centers in the USA and Canada.
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References
Harbour JW (2003) Clinical overview of uveal melanoma: introduction to tumors of the eye. In: Albert DM, Polans A (eds) Ocular oncology. Marcel Dekker, New York, pp 1–18
Onken MD, Worley LA, Ehlers JP, Harbour JW (2004) Gene expression profiling in uveal melanoma reveals two molecular classes and predicts metastatic death. Cancer Res 64:7205–7209
Egan KM, Seddon JM, Glynn RJ, Gragoudas ES, Albert DM (1988) Epidemiologic aspects of uveal melanoma. Surv Ophthalmol 32:239–251
Ramaiya KJ, Harbour JW (2007) Current management of uveal melanoma. Exp Rev Ophthalmol 2:939–946
Diener-West M, Reynolds SM, Agugliaro DJ, Caldwell R, Cumming K, Earle JD, Hawkins BS, Hayman JA, Jaiyesimi I, Jampol LM, Kirkwood JM, Koh WJ, Robertson DM, Shaw JM, Straatsma BR, Thoma J (2005) Development of metastatic disease after enrollment in the COMS trials for treatment of choroidal melanoma: Collaborative Ocular Melanoma Study Group Report No. 26. Arch Ophthalmol 123:1639–1643
Augsburger JJ, Gamel JW (1990) Clinical prognostic factors in patients with posterior uveal malignant melanoma. Cancer 66:1596–1600
Gamel JW, McLean IW, Foster WD, Zimmerman LE (1978) Uveal melanomas: correlation of cytologic features with prognosis. Cancer 41:1897–1901
de la Cruz PO Jr, Spech CS, McLean IW (1990) Lymphocytic infiltration in uveal malignant melanoma. Cancer 65:112–115
Folberg R, Pe’er J, Gruman LM, Woolson RF, Jeng G, Montague PR, Moninger TO, Yi H, Moore KC (1992) The morphologic characteristics of tumor blood vessels as a marker of tumor progression in primary human uveal melanoma: a matched case-control study. Hum Pathol 23:1298–1305
Makitie T, Summanen P, Tarkkanen A, Kivela T (2001) Tumor-infiltrating macrophages (CD68(+) cells) and prognosis in malignant uveal melanoma. Invest Ophthalmol Vis Sci 42:1414–1421
Kujala E, Makitie T, Kivela T (2003) Very long-term prognosis of patients with malignant uveal melanoma. Invest Ophthalmol Vis Sci 44:4651–4659
Kath R, Hayungs J, Bornfeld N, Sauerwein W, Hoffken K, Seeber S (1993) Prognosis and treatment of disseminated uveal melanoma. Cancer 72:2219–2223
Griffin CA, Long PP, Schachat AP (1988) Trisomy 6p in an ocular melanoma. Cancer Genet Cytogenet 32:129–132
Horsman DE, Sroka H, Rootman J, White VA (1990) Monosomy 3 and isochromosome 8q in a uveal melanoma. Cancer Genet Cytogenet 45:249–253
Prescher G, Bornfeld N, Becher R (1990) Nonrandom chromosomal abnormalities in primary uveal melanoma. J Natl Cancer Inst 82:1765–1769
Sisley K, Rennie IG, Cottam DW, Potter AM, Potter CW, Rees RC (1990) Cytogenetic findings in six posterior uveal melanomas: involvement of chromosomes 3, 6, and 8. Genes Chromosomes Cancer 2:205–209
Wiltshire RN, Elner VM, Dennis T, Vine AK, Trent JM (1993) Cytogenetic analysis of posterior uveal melanoma. Cancer Genet Cytogenet 66:47–53
Singh AD, Boghosian-Sell L, Wary KK, Shields CL, De Potter P, Donoso LA, Shields JA, Cannizzaro LA (1994) Cytogenetic findings in primary uveal melanoma. Cancer Genet Cytogenet 72:109–115
Prescher G, Bornfeld N, Friedrichs W, Seeber S, Becher R (1995) Cytogenetics of twelve cases of uveal melanoma and patterns of nonrandom anomalies and isochromosome formation. Cancer Genet Cytogenet 80:40–46
McNamara M, Felix C, Davison EV, Fenton M, Kennedy SM (1997) Assessment of chromosome 3 copy number in ocular melanoma using fluorescence in situ hybridization. Cancer Genet Cytogenet 98:4–8
Patel KA, Edmondson ND, Talbot F, Parsons MA, Rennie IG, Sisley K (2001) Prediction of prognosis in patients with uveal melanoma using fluorescence in situ hybridisation. Br J Ophthalmol 85:1440–1444
Speicher MR, Prescher G, du Manoir S, Jauch A, Horsthemke B, Bornfeld N, Becher R, Cremer T (1994) Chromosomal gains and losses in uveal melanomas detected by comparative genomic hybridization. Cancer Res 54:3817–3823
Gordon KB, Thompson CT, Char DH, O’Brien JM, Kroll S, Ghazvini S, Gray JW (1994) Comparative genomic hybridization in the detection of DNA copy number abnormalities in uveal melanoma. Cancer Res 54:4764–4768
Ghazvini S, Char DH, Kroll S, Waldman FM, Pinkel D (1996) Comparative genomic hybridization analysis of archival formalin-fixed paraffin-embedded uveal melanomas. Cancer Genet Cytogenet 90:95–101
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. Invest Ophthalmol Vis Sci 42:313–317
Hughes S, Damato BE, Giddings I, Hiscott PS, Humphreys J, Houlston RS (2005) Microarray comparative genomic hybridisation analysis of intraocular uveal melanomas identifies distinctive imbalances associated with loss of chromosome 3. Br J Cancer 93:1191–1196
Kilic E, van Gils W, Lodder E, Beverloo HB, van Til ME, Mooy CM, Paridaens D, de Klein A, Luyten GP (2006) Clinical and cytogenetic analyses in uveal melanoma. Invest Ophthalmol Vis Sci 47:3703–3707
Ehlers JP, Worley L, Onken MD, Harbour JW (2008) Integrative genomic analysis of aneuploidy in uveal melanoma. Clin Cancer Res 14:115–122
Naus NC, van Drunen E, de Klein A, Luyten GP, Paridaens DA, Alers JC, Ksander BR, Beverloo HB, Slater RM (2001) Characterization of complex chromosomal abnormalities in uveal melanoma by fluorescence in situ hybridization, spectral karyotyping, and comparative genomic hybridization. Genes Chromosomes Cancer 30:267–273
Tschentscher F, Prescher G, Zeschnigk M, Horsthemke B, Lohmann DR (2000) Identification of chromosomes 3, 6, and 8 aberrations in uveal melanoma by microsatellite analysis in comparison to comparative genomic hybridization. Cancer Genet Cytogenet 122:13–17
Scholes AG, Damato BE, Nunn J, Hiscott P, Grierson I, Field JK (2003) Monosomy 3 in uveal melanoma: correlation with clinical and histologic predictors of survival. Invest Ophthalmol Vis Sci 44:1008–1011
Damato B, Dopierala JA, Coupland SE (2010) Genotypic profiling of 452 choroidal melanomas with multiplex ligation-dependent probe amplification. Clin Cancer Res 16:6083–6092
Onken MD, Worley LA, Person E, Char DH, Bowcock AM, Harbour JW (2007) Loss of heterozygosity of chromosome 3 detected with single nucleotide polymorphisms is superior to monosomy 3 for predicting metastasis in uveal melanoma. Clin Cancer Res 13:2923–2927
Prescher G, Bornfeld N, Hirche H, Horsthemke B, Jockel KH, Becher R (1996) Prognostic implications of monosomy 3 in uveal melanoma. Lancet 347:1222–1225
Maat W, Jordanova ES, van Zelderen-Bhola SL, Barthen ER, Wessels HW, Schalij-Delfos NE, Jager MJ (2007) The heterogeneous distribution of monosomy 3 in uveal melanomas: implications for prognostication based on fine-needle aspiration biopsies. Arch Pathol Lab Med 131:91–96
Tschentscher F, Husing J, Holter T, Kruse E, Dresen IG, Jockel KH, Anastassiou G, Schilling H, Bornfeld N, Horsthemke B, Lohmann DR, Zeschnigk M (2003) Tumor classification based on gene expression profiling shows that uveal melanomas with and without monosomy 3 represent two distinct entities. Cancer Res 63:2578–2584
Worley LA, Onken MD, Person E, Robirds D, Branson J, Char DH, Perry A, Harbour JW (2007) Transcriptomic versus chromosomal prognostic markers and clinical outcome in uveal melanoma. Clin Cancer Res 13:1466–1471
Petrausch U, Martus P, Tonnies H, Bechrakis NE, Lenze D, Wansel S, Hummel M, Bornfeld N, Thiel E, Foerster MH, Keilholz U (2007) Significance of gene expression analysis in uveal melanoma in comparison to standard risk factors for risk assessment of subsequent metastases. Eye 22:997–1007
van Gils W, Lodder EM, Mensink HW, Kilic E, Naus NC, Bruggenwirth HT, van Ijcken W, Paridaens D, Luyten GP, de Klein A (2008) Gene expression profiling in uveal melanoma: two regions on 3p related to prognosis. Invest Ophthalmol Vis Sci 49:4254–4262
Onken MD, Worley LA, Tuscan MD, Harbour JW (2010) An accurate, clinically feasible multi-gene expression assay for predicting metastasis in uveal melanoma. J Mol Diagn 12:461–468
Onken M, Worley L, Char D, Augsburger J, Correa Z, Nudleman E, Aaberg TM Jr, Altaweel M, Bardenstein D, Finger P, Gallie B, Harocopos G, Hovland P, McGowan H, Milman T, Mruthyunjaya P, Simpson E, Smith M, Wilson D, Wirostko W, Harbour J (2012) Collaborative Ocular Oncology Group Report No. 1: prospective validation of a multi-gene prognostic assay in uveal melanoma. Ophthalmology 119(8):1596–1603. doi:10.1016/j.ophtha.2012.02.017
Onken MD, Ehlers JP, Worley LA, Makita J, Yokota Y, Harbour JW (2006) Functional gene expression analysis uncovers phenotypic switch in aggressive uveal melanomas. Cancer Res 66:4602–4609
Chang SH, Worley LA, Onken MD, Harbour JW (2008) Prognostic biomarkers in uveal melanoma: evidence for a stem cell-like phenotype associated with metastasis. Melanoma Res 18:191–200
Harbour JW, Onken MD, Roberson ED, Duan S, Cao L, Worley LA, Council ML, Matatall KA, Helms C, Bowcock AM (2010) Frequent mutation of BAP1 in metastasizing uveal melanomas. Science 330:1410–1413
Scheuermann JC, de Ayala Alonso AG, Oktaba K, Ly-Hartig N, McGinty RK, Fraterman S, Wilm M, Muir TW, Muller J (2010) Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB. Nature 465:243–247
Abdel-Rahman MH, Pilarski R, Cebulla CM, Massengill JB, Christopher BN, Boru G, Hovland P, Davidorf FH (2011) Germline BAP1 mutation predisposes to uveal melanoma, lung adenocarcinoma, meningioma, and other cancers. J Med Genet 48:856–859
Bott M, Brevet M, Taylor BS, Shimizu S, Ito T, Wang L, Creaney J, Lake RA, Zakowski MF, Reva B, Sander C, Delsite R, Powell S, Zhou Q, Shen R, Olshen A, Rusch V, Ladanyi M (2011) The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma. Nat Genet 43:668–672
Testa JR, Cheung M, Pei J, Below JE, Tan Y, Sementino E, Cox NJ, Dogan AU, Pass HI, Trusa S, Hesdorffer M, Nasu M, Powers A, Rivera Z, Comertpay S, Tanji M, Gaudino G, Yang H, Carbone M (2011) Germline BAP1 mutations predispose to malignant mesothelioma. Nat Genet 43:1022–1025
Wiesner T, Obenauf AC, Murali R, Fried I, Griewank KG, Ulz P, Windpassinger C, Wackernagel W, Loy S, Wolf I, Viale A, Lash AE, Pirun M, Socci ND, Rutten A, Palmedo G, Abramson D, Offit K, Ott A, Becker JC, Cerroni L, Kutzner H, Bastian BC, Speicher MR (2011) Germline mutations in BAP1 predispose to melanocytic tumors. Nat Genet 43:1018–1021
Njauw CN, Kim I, Piris A, Gabree M, Taylor M, Lane AM, Deangelis MM, Gragoudas E, Duncan LM, Tsao H (2012) Germline BAP1 inactivation is preferentially associated with metastatic ocular melanoma and cutaneous-ocular melanoma families. PLoS One 7(4):e35295. doi:10.1371/journal.pone.0035295
Pena-Llopis S, Vega-Rubin-de-Celis S, Liao A, Leng N, Pavia-Jimenez A, Wang S, Yamasaki T, Zhrebker L, Sivanand S, Spence P, Kinch L, Hambuch T, Jain S, Lotan Y, Margulis V, Sagalowsky AI, Summerour PB, Kabbani W, Wong SW, Grishin N, Laurent M, Xie XJ, Haudenschild CD, Ross MT, Bentley DR, Kapur P, Brugarolas J (2012) BAP1 loss defines a new class of renal cell carcinoma. Nat Genet 44(7):751–759. doi:10.1038/ng.2323
Wiesner T, Murali R, Fried I, Cerroni L, Busam K, Kutzner H, Bastian BC (2012) A distinct subset of atypical spitz tumors is characterized by BRAF mutation and loss of BAP1 expression. Am J Surg Pathol 36(6):818–830
Yoshikawa Y, Sato A, Tsujimura T, Emi M, Morinaga T, Fukuoka K, Yamada S, Murakami A, Kondo N, Matsumoto S, Okumura Y, Tanaka F, Hasegawa S, Nakano T, Hashimoto-Tamaoki T (2012) Frequent inactivation of the BAP1 gene in epithelioid-type malignant mesothelioma. Cancer Sci 103:868–874
Brown MP, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, Ares M Jr, Haussler D (2000) Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci U S A 97:262–267
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Harbour, J.W. (2014). A Prognostic Test to Predict the Risk of Metastasis in Uveal Melanoma Based on a 15-Gene Expression Profile. In: Thurin, M., Marincola, F. (eds) Molecular Diagnostics for Melanoma. Methods in Molecular Biology, vol 1102. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-727-3_22
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DOI: https://doi.org/10.1007/978-1-62703-727-3_22
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