123-132

Genomic, Prognostic, and Cell-Signaling Advances in Uveal Melanoma

Author(s): 
J. William Harbour, MD
Article Summary: 


American Society of Clinical Oncology Educational Book

2013 ASCO Annual Meeting

Melanoma

Molecular, Diagnostic, and Therapeutic Advances for Ocular Melanoma

Overview

Uveal melanoma (UM) is the second-most common form of melanoma and the most common primary intraocular malignancy. Up to one-half of patients are at risk for fatal metastatic disease. The metastatic potential of an individual tumor can be accurately determined by analysis of a fine-needle aspirate with gene expression profiling assay that is available for routine clinical use through a commercial Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory. The test renders one of two results—class 1 (low metastatic risk) or class 2 (high metastatic risk)—and has been extensively validated in multiple centers. Until recently, the genetic mutations and signaling aberrations in UM were largely unknown. With the advent of new genomic sequencing technologies, however, the molecular landscape of UM is rapidly emerging. Mutations in the Gq alpha subunits GNAQ and GNA11 are mutually exclusive and represent early or initiating events that constitutively activate the MAPK pathway. Mutations in BRCA1-associated protein-1 (BAP1) and splicing factor 3B subunit 1 (SF3B1) also appear to be largely mutually exclusive, and they occur later in tumor progression. BAP1 mutations are strongly associated with metastasis, whereas SF3B1 mutations are associated with a more favorable outcome. BAP1 mutations can arise in the germ line, leading to a newly described BAP1 familial cancer syndrome. These discoveries have led to new clinical trials to assess several classes of compounds, including MEK, protein kinase C, and histone deacetylase inhibitors, in the adjuvant setting for high-risk patients identified as class 2, as well as in the setting of advanced disseminated disease.

Uveal melanoma (UM) is the most common primary malignancy of the eye, with an incidence of about 1,200–1,500 new cases per year in the United States, and it accounts for approximately 5% of all melanomas.1,2 UMs can arise anywhere in the uveal tract, comprising the iris, ciliary body, and choroid, and they often involve more than one of these structures. Approximately 5% of UMs are confined to the iris and exhibit less aggressive behavior. UMs metastasize by hematogenous dissemination, and the most common sites are liver (93%), lung (24%), and bone (16%).3

MOLECULAR CLASSIFICATION OF UVEAL MELANOMA

Clinicopathologic staging systems like the American Joint Committee on Cancer (AJCC) tumor, node, metastasis staging system4 provide a uniform vocabulary for communication among health care professionals, and they allow patients to be organized into prognostically comparable groups based on retrospective analysis. In the case of UM, however, the complexity of such systems is not well suited for prospective, personalized clinical decision making in individual patients, such as whether a given patient should be offered adjuvant therapy.

It has been known for several decades that certain chromosomal copy number alterations can be used as prognostic markers in UM, the most accurate being loss of chromosome 3 (monosomy 3), which is associated with poor outcome.5 Because monosomy 3 is associated with high false-positive and -negative rates, the inclusion of other chromosomal gains and losses and clinicopathologic information has been advocated to improve prognostic accuracy.6 Unfortunately, this approach results in the same limitations as the tumor, node, metastasis staging system classification: namely, it generates multiple sub-groups that are not optimal for everyday clinical decision making. Further, chromosome-based tests suffer from a susceptibility to sampling error resulting from intratumoral genetic heterogeneity, limited clinical validation, lack of standardized testing platforms, and high technical failure rates.7

To overcome these limitations and provide clinicians with a practical, simple, straightforward and highly accurate prognostic tool, we developed a test based on gene expression profiling (GEP) using a highly sensitive microfluidics polymerase chain reaction (PCR) platform that can be used for analysis of minute tumor samples from fine-needle aspiration biopsies.8 The commercially available form of the test is known as DecisionDx-UM and is performed in a College of American Pathologists (CAP)/CLIA laboratory as a stand-alone test that requires no other data input for excellent prognostic accuracy. The test simultaneously measures the expression of 15 carefully selected genes from primary UM samples containing as few as a few dozen tumor cells. Low metastatic risk is reported as class 1, and high metastatic risk as class 2, which allows patients to be individualized into risk categories that allow appropriate intervention.9 For example, high-risk patients can be offered intensive metastatic surveillance and adjuvant therapy while low-risk patients can be spared these interventions. DecisionDx-UM is the only prognostic test in UM that has been prospectively validated in multiple centers9 and that meets the highest level “1” rating for cancer biomarkers according to the National Comprehensive Cancer Network (NCCN) task force and the Tumor Marker Utility Grading System.10,11 This test is now used in most North American ocular oncology centers as part of the standard of care. Biologically, the GEP of class 1 tumors closely resembles that of normal uveal melanocytes and low-grade, differentiated uveal melanocytic tumors, whereas the GEP of class 2 resembles that of primitive neural/ectodermal cells.12,13

SIGNALING PATHWAY ABERRATIONS

The PI3K/AKT pathway is constitutively activated in a majority of UMs, and phosphorylated AKT correlates with poor prognosis.14 This may result, at least in part, from loss of PTEN activity. In one study, loss of heterozygosity at the PTEN locus was found in 76% of UMs, and mutations within the PTEN coding region were found in 11% of tumors.15 PTEN inactivation was also found to be associated with increased aneuploidy and decreased survival in UM.15,16

The mitogen-activated protein kinase (MAPK) pathway is also activated in most UMs, suggesting the presence of upstream activating mutations.17,18 However, mutations in known upstream activators such as KIT and the RAS and RAF family members are extremely rare in UM.18-22 A systemic interrogation of 21 other candidate oncogenes in the MAPK pathway identified no mutations in UM.23

More recently, mutually exclusive mutations in two closely related G-coupled protein receptor Gq alpha subunits Gαq and Gα11 were found to occur in almost 85% of UMs.24 These mutations lead to constitutive activation of the MAPK pathway.25GNAQ/11 mutations are found in benign uveal nevi and in the vast majority of UMs regardless of cytogenetic status or GEP class,23,26,27 suggesting that these mutations are early or perhaps initiating events and are not sufficient for full malignant transformation.25

BAP1

It has been known for many years that loss of one copy of chromosome 3 in UM is associated with metastasis and poor prognosis,5 which led to speculation that one or more tumor suppressor genes may reside on this chromosome that are mutated in UM.28 In 2010, we identified such a gene using exome sequencing.29 We found that BRCA1-associated protein 1 (BAP1), located at chromosome 3p21.1, was mutated in approximately 85% of class 2 UMs, but such mutations were rare in low-grade class 1 UMs, suggesting that BAP1 may function as a metastasis suppressor in this cancer. BAP1 encodes a deubiquitinating enzyme with several substrates, including BRCA1, histone H2A, host cell factor-1 (HCF-1) and O-linked N-acetylglucosamine transferase (OGT).30,31 The precise molecular explanation for why loss of BAP1 leads to metastasis in UM remains unclear.

BAP1 FAMILIAL CANCER SYNDROME

Familial UM is generally regarded as rare, so we were surprised to find that one patient with UM in our original study carried a germ-line BAP1 mutation that was reduced to homozygosity in tumor cells by loss of the other chromosome 3.29 Subsequently, there have been many groups reporting families with germ-line BAP1 mutations in association with UM and many other cancers, including mesothelioma, cutaneous melanoma, renal cell carcinoma, and others.32-36 Thus, although familial UM is uncommon, it is not as rare as once believed and may represent 2% to 3% of new patients with UM.

SF3B1 MUTATIONS

We searched for additional mutations in UM by exome sequencing and identified novel mutations in splicing factor 3B subunit 1 (SF3B1). Among 102 primary tumors, 19 (18.6%) contained mutations in SF3B1, similar to the frequency in myelodysplastic syndrome and chronic lymphocytic leukemia,37,38 and higher than that in breast cancer.39 Interestingly, the mutations always involved an amino acid substitution at arginine-625, and all were somatic in origin. The molecular effect of the mutations appeared to be dominant-negative, gain-of-function or haploinsufficiency, but this remains to be firmly established. SF3B1 mutations were largely mutually exclusive with BAP1 mutations and were associated with favorable prognosis. SF3B1 encodes a splicing factor subunit, but the cancer-promoting effect of these mutations remains unclear.

CONCLUSION

With the recent genetic discoveries in UM discussed herein, the genetic landscape of this cancer is rapidly coming into focus and is providing an unprecedented opportunity for individualized patient care and targeted therapy. Molecular GEP-based classification of UM allows patients to be stratified according to metastatic risk into class 1 (low risk) and class 2 (high risk) for purposes of individualized patient care and inclusion in clinical trials. GNAQ/11 mutations have stimulated interest in MEK and protein kinase C inhibitors in UM.40,41BAP1 mutations have suggested a utility for histone deacetylase (HDAC) inhibitors to reverse the biochemical effects of BAP1 loss by reversing histone H2A hyper-ubiquitination.42 With attention now focused on these mutations, not only in UM but in other cancers as well, it is anticipated that new classes of therapeutic compounds that target these pathways will soon emerge.

ACKNOWLEDGMENTS

Dr. Harbour is funded by grants from the National Cancer Institute (R01 CA125970 and R01 CA16187001), Melanoma Research Foundation, Melanoma Research Alliance, and a Research to Prevent Blindness Senior Investigator Award.

Dr. Harbour is the inventor of intellectual property described in this article, and he receives royalties from its commercialization. He is a paid consultant for Castle Biosciences, licensee of intellectual property presented in this article.

Key Points

  • Uveal melanomas can be divided into low and high risk for metastasis based on a validated test based on gene expression profile.
  • Mutually exclusive mutations in GNAQ and GNA11 represent early or initiating events in uveal melanoma.
  • Mutations in BAP1 and SF3B1 represent later events associated with poor and good outcome, respectively.
  • Targeted therapies to counteract the effects of these mutations are becoming increasingly available.

References

1. Egan KM, Seddon JM, Glynn RJ, et al. Epidemiologic aspects of uveal melanoma. Surv Ophthalmol. 1988;32:239-251.
PubMed | CrossRef
2. Ramaiya KJ, Harbour JW. Current management of uveal melanoma. Expert Rev Ophthalmol. 2007;2:939-946.
CrossRef
3. Collaborative Ocular Melanoma Study Group. Assessment of metastatic disease status at death in 435 patients with large choroidal melanoma in the Collaborative Ocular Melanoma Study (COMS): COMS report no. 15. Arch Ophthalmol. 2001;119:670-676.
CrossRef
4. Finger PT, 7th Edition, AJCC-UICC Ophthalmic Oncology Task Force. The 7th edition AJCC staging system for eye cancer: an international language for ophthalmic oncology. Arch Pathol Lab Med. 2009;133:1197-1198.
PubMed
5. Prescher G, Bornfeld N, Hirche H, et al. Prognostic implications of monosomy 3 in uveal melanoma. Lancet. 1996;347:1222-1225.
PubMed | CrossRef
6. Damato B, Dopierala J, Klaasen A, et al. Multiplex ligation-dependent probe amplification of uveal melanoma: correlation with metastatic death. Invest Ophthalmol Vis Sci. 2009;50:3048-3055.
PubMed | CrossRef
7. Dopierala J, Damato BE, Lake SL, et al. Genetic heterogeneity in uveal melanoma assessed by multiplex ligation-dependent probe amplification. Invest Ophthalmol Vis Sci. 2010;51:4898-4905.
PubMed | CrossRef
8. 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. 2010;12:461-468.
PubMed | CrossRef
9. Onken MD, Worley LA, Char DH, et al. Collaborative Ocular Oncology Group report number 1: prospective validation of a multi-gene prognostic assay in uveal melanoma. Ophthalmology. 2012;119:1596-1603.
PubMed | CrossRef
10. Febbo PG, Ladanyi M, Aldape KD, et al. NCCN Task Force report: Evaluating the clinical utility of tumor markers in oncology. J Natl Compr Canc Netw. 2011;9 Suppl 5:S1-32; quiz S33.
11. Simon RM, Paik S, Hayes DF. Use of archived specimens in evaluation of prognostic and predictive biomarkers. J Natl Cancer Inst. 2009;101:1446-1452.
PubMed | CrossRef
12. Onken MD, Ehlers JP, Worley LA, et al. Functional gene expression analysis uncovers phenotypic switch in aggressive uveal melanomas. Cancer Res. 2006;66:4602-4609.
PubMed | CrossRef
13. Chang SH, Worley LA, Onken MD, Harbour JW. Prognostic biomarkers in uveal melanoma: evidence for a stem cell-like phenotype associated with metastasis. Melanoma Res. 2008;18:191-200.
PubMed | CrossRef
14. Saraiva VS, Caissie AL, Segal L, et al. Immunohistochemical expression of phospho-Akt in uveal melanoma. Melanoma Res. 2005;15:245-250.
PubMed | CrossRef
15. Abdel-Rahman MH, Yang Y, Zhou XP, et al. High frequency of submicroscopic hemizygous deletion is a major mechanism of loss of expression of PTEN in uveal melanoma. J Clin Oncol. 2006;24:288-295.
PubMed | CrossRef
16. Ehlers JP, Worley L, Onken MD, Harbour JW. Integrative genomic analysis of aneuploidy in uveal melanoma. Clin Cancer Res. 2008;14:115-122.
PubMed | CrossRef
17. Weber A, Hengge UR, Urbanik D, et al. Absence of mutations of the BRAF gene and constitutive activation of extracellular-regulated kinase in malignant melanomas of the uvea. Lab Invest. 2003;83:1771-1776.
PubMed | CrossRef
18. Zuidervaart W, van Nieuwpoort F, Stark M, et al. Activation of the MAPK pathway is a common event in uveal melanomas although it rarely occurs through mutation of BRAF or RAS. Br J Cancer. 2005;92:2032-2038.
PubMed | CrossRef
19. Pache M, Glatz K, Bösch D, et al. Sequence analysis and high-throughput immunohistochemical profiling of KIT (CD 117) expression in uveal melanoma using tissue microarrays. Virchows Arch. 2003;443:741-744.
PubMed | CrossRef
20. Mooy CM, Van der Helm MJ, Van der Kwast TH, et al. No N-ras mutations in human uveal melanoma: the role of ultraviolet light revisited. Br J Cancer. 1991;64:411-413.
PubMed | CrossRef
21. Soparker CN, O'Brien JM, Albert DM. Investigation of the role of the ras protooncogene point mutation in human uveal melanomas. Invest Ophthalmol Vis Sci. 1993;34:2203-2209.
PubMed
22. Cruz F, Rubin BP, Wilson D, et al. Absence of BRAF and NRAS mutations in uveal melanoma. Cancer Res. 2003;63:5761-5766.
PubMed
23. Onken MD, Worley LA, Long MD, et al. Oncogenic mutations in GNAQ occur early in uveal melanoma. Invest Ophthalmol Vis Sci. 2008;49:5230-5234.
PubMed | CrossRef
24. Van Raamsdonk CD, Griewank KG, Crosby MB, et al. Mutations in GNA11 in uveal melanoma. N Engl J Med. 2010;363:2191-2199.
PubMed | CrossRef
25. Van Raamsdonk CD, Bezrookove V, Green G, et al. Frequent somatic mutations of GNAQ in uveal melanoma and blue naevi. Nature. 2009;457:599-602.
PubMed | CrossRef
26. Bauer J, Kilic E, Vaarwater J, et al. Oncogenic GNAQ mutations are not correlated with disease-free survival in uveal melanoma. Br J Cancer. 2009;101:813-815.
PubMed | CrossRef
27. Jensen DE, Rauscher FJ. BAP1, a candidate tumor suppressor protein that interacts with BRCA1. Ann N Y Acad Sci. 1999;886:191-194.
PubMed | CrossRef
28. Horsthemke B, Prescher G, Bornfeld N, et al. Loss of chromosome 3 alleles and multiplication of chromosome 8 alleles in uveal melanoma. Genes Chromosomes Cancer. 1992;4:217-221.
PubMed | CrossRef
29. Harbour JW, Onken MD, Roberson ED, et al. Frequent mutation of BAP1 in metastasizing uveal melanomas. Science. 2010;330:1410-1413.
PubMed | CrossRef
30. Jensen DE, Proctor M, Marquis ST, et al. BAP1: a novel ubiquitin hydrolase which binds to the BRCA1 RING finger and enhances BRCA1-mediated cell growth suppression. Oncogene. 1998;16:1097-1112.
PubMed | CrossRef
31. Dey A, Seshasayee D, Noubade R, et al. Loss of the tumor suppressor BAP1 causes myeloid transformation. Science. 2012;337:1541-1546.
PubMed | CrossRef
32. Murali R, Wiesner T, Scolyer RA. Tumours associated with BAP1 mutations. Pathology. 2013;45:116-126.
PubMed | CrossRef
33. Carbone M, Ferris LK, Baumann F, et al. BAP1 cancer syndrome: malignant mesothelioma, uveal and cutaneous melanoma, and MBAITs. J Transl Med. 2012;10:179.
PubMed | CrossRef
34. Wiesner T, Obenauf AC, Murali R, et al. Germline mutations in BAP1 predispose to melanocytic tumors. Nat Genet. 2011;43:1018-1021.
PubMed | CrossRef
35. Testa JR, Cheung M, Pei J, et al. Germline BAP1 mutations predispose to malignant mesothelioma. Nat Genet. 2011;43:1022-1025.
PubMed | CrossRef
36. Abdel-Rahman MH, Pilarski R, Cebulla CM, et al. Germline BAP1 mutation predisposes to uveal melanoma, lung adenocarcinoma, meningioma, and other cancers. J Med Genet. 2011;48:856-859.
PubMed | CrossRef
37. Papaemmanuil E, Cazzola M, Boultwood J, et al. Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts. N Engl J Med. 2011;365:1384-1395.
PubMed | CrossRef
38. Wang L, Lawrence MS, Wan Y, et al. SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med. 2011;365:2497-2506.
PubMed | CrossRef
39. Ellis MJ, Ding L, Shen D, et al. Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature. 2012;486:353-360.
PubMed
40. Falchook GS, Lewis KD, Infante JR, et al. Activity of the oral MEK inhibitor trametinib in patients with advanced melanoma: a phase 1 dose-escalation trial. Lancet Oncol. 2012;13:782-789.
PubMed | CrossRef
41. Wu X, Zhu M, Fletcher JA, et al. The protein kinase C inhibitor enzastaurin exhibits antitumor activity against uveal melanoma. PLoS ONE. 2012;7:e29622.
PubMed | CrossRef
42. Landreville S, Agapova OA, Matatall KA, et al. Histone deacetylase inhibitors induce growth arrest and differentiation in uveal melanoma. Clin Cancer Res. 2012;18:408-416.
PubMed | CrossRef