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Harbour JW, Correa ZM, Schefler AC, Mruthyunjaya P, Materin MA, Aaberg TA, Skalet AH, Reichstein DA, Weis E, Kim IK, Fuller TS, Demirci H, Piggott KD, Williams BK, Shildkrot E, Capone A, Oliver SC, Walter SD, Mason J, Char DH, Altaweel M, Wells JR, Duker JS, Hovland PG, Gombos DS, Tsai T, Javid C, Marr BP, Gao A, Decatur CL, Dollar JJ, Kurtenbach S, Zhang S. 15-Gene Expression Profile and PRAME as Integrated Prognostic Test for Uveal Melanoma: First Report of Collaborative Ocular Oncology Group Study No. 2 (COOG2.1). J Clin Oncol 2024; 42:3319-3329. [PMID: 39052972 PMCID: PMC11421563 DOI: 10.1200/jco.24.00447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/01/2024] [Accepted: 05/13/2024] [Indexed: 07/27/2024] Open
Abstract
PURPOSEValidated and accurate prognostic testing is critical for precision medicine in uveal melanoma (UM). Our aims were to (1) prospectively validate an integrated prognostic classifier combining a 15-gene expression profile (15-GEP) and PRAME RNA expression and (2) identify clinical variables that enhance the prognostic accuracy of the 15-GEP/PRAME classifier.MATERIALS AND METHODSThis study included 1,577 patients with UM of the choroid and/or ciliary body who were enrolled in the Collaborative Ocular Oncology Group Study Number 2 (COOG2) and prospectively monitored across 26 North American centers. Test results for 15-GEP (class 1 or class 2) and PRAME expression status (negative or positive) were available for all patients. The primary end point was metastasis-free survival (MFS).RESULTS15-GEP was class 1 in 1,082 (68.6%) and class 2 in 495 (31.4%) patients. PRAME status was negative in 1,106 (70.1%) and positive in 471 (29.9%) patients. Five-year MFS was 95.6% (95% CI, 93.9 to 97.4) for class 1/PRAME(-), 80.6% (95% CI, 73.9 to 87.9) for class 1/PRAME(+), 58.3% (95% CI, 51.1 to 66.4) for class 2/PRAME(-), and 44.8% (95% CI, 37.9 to 52.8) for class 2/PRAME(+). By multivariable Cox proportional hazards analysis, 15-GEP was the most important independent predictor of MFS (hazard ratio [HR], 5.95 [95% CI, 4.43 to 7.99]; P < .001), followed by PRAME status (HR, 1.82 [95% CI, 1.42 to 2.33]; P < .001). The only clinical variable demonstrating additional prognostic value was tumor diameter.CONCLUSIONIn the largest prospective multicenter prognostic biomarker study performed to date in UM to our knowledge, the COOG2 study validated the superior prognostic accuracy of the integrated 15-GEP/PRAME classifier over 15-GEP alone and clinical prognostic variables. Tumor diameter was found to be the only clinical variable to provide additional prognostic information. This prognostic classifier provides an advanced resource for risk-adjusted metastatic surveillance and adjuvant trial stratification in patients with UM.
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Affiliation(s)
- J. William Harbour
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, TX
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX
| | - Zelia M. Correa
- Bascom Palmer Eye Institute and Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL
| | | | - Prithvi Mruthyunjaya
- Byers Eye Institute, Department of Ophthalmology, Stanford University, Stanford, CA
| | | | - Thomas A. Aaberg
- Retina Specialists of Michigan, Foundation for Vision Research, and Michigan State University College of Human Medicine, Grand Rapids, MI
| | - Alison H. Skalet
- Casey Eye Institute, Oregon Health and Science University, Portland, OR
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | | | - Ezekiel Weis
- Department of Ophthalmology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
- Division of Ophthalmology, Department of Surgery, Faculty of Medicine, University of Calgary, Calgary, Canada
| | - Ivana K. Kim
- Massachusetts Eye and Ear Infirmary and Department of Ophthalmology, Harvard Medical School, Boston, MA
| | | | - Hakan Demirci
- Kellogg Eye Center and Department of Ophthalmology, University of Michigan, Ann Arbor, MI
| | - Kisha D. Piggott
- Department of Ophthalmology and Visual Sciences, Washington University, St Louis, MO
| | - Basil K. Williams
- Department of Ophthalmology, University of Cincinnati, Cincinnati, OH
| | - Eugene Shildkrot
- Department of Ophthalmology, University of Virginia, Charlottesville, VA
| | | | - Scott C. Oliver
- Sue Anschutz-Rodgers Eye Center and Department of Ophthalmology, University of Colorado, Aurora, CO
| | - Scott D. Walter
- Retina Consultants, Hartford, CT
- Helen and Harry Gray Cancer Center, Hartford, CT
| | - John Mason
- Department of Ophthalmology, University of Alabama, Birmingham, AL
| | | | - Michael Altaweel
- Department of Ophthalmology, University of Wisconsin, Madison, WI
| | - Jill R. Wells
- Department of Ophthalmology, Emory University, Atlanta, GA
| | - Jay S. Duker
- New England Eye Center and Department of Ophthalmology, Tufts University, Boston, MA
| | | | - Dan S. Gombos
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Tony Tsai
- Retinal Consultants Medical Group, Sacramento, CA
| | | | - Brian P. Marr
- Department of Ophthalmology, Columbia University, New York, NY
| | - Ang Gao
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX
- O'Donnell School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX
| | - Christina L. Decatur
- Bascom Palmer Eye Institute and Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL
| | - James J. Dollar
- Bascom Palmer Eye Institute and Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL
| | - Stefan Kurtenbach
- Bascom Palmer Eye Institute and Department of Ophthalmology, University of Miami Miller School of Medicine, Miami, FL
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL
| | - Song Zhang
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX
- O'Donnell School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX
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Alsoudi AF, Skrehot HC, Chévez-Barrios P, Divatia M, De La Garza M, Bretana ME, Schefler AC. COMPREHENSIVE MOLECULAR PROFILING OF UVEAL MELANOMA EVALUATED WITH GENE EXPRESSION PROFILING, PREFERENTIALLY EXPRESSED ANTIGEN IN MELANOMA EXPRESSION, AND NEXT-GENERATION SEQUENCING. Retina 2024; 44:1580-1589. [PMID: 39167579 DOI: 10.1097/iae.0000000000004153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
PURPOSE To determine the association between gene-expression profiling (GEP), next-generation sequencing (NGS), preferentially expressed antigen in melanoma (PRAME) features, and metastatic risk in patients with uveal melanoma (UM). METHODS A retrospective analysis of patients with UM treated by brachytherapy or enucleation by a single ocular oncologist was conducted from November 2020 and July 2022. Clinicopathologic features, patient outcomes, GEP classification, NGS, and PRAME results were recorded. RESULTS Comprehensive GEP, PRAME, and NGS testing was performed on 135 UMs. The presence of eukaryotic translation initiation factor 1A, X-chromosomal and splicing factor 3B subunit 1 mutations was significantly associated with GEP class 1A and GEP class 1B, respectively. The presence of BRCA- associated protein-1 mutation was significantly associated with GEP class 2. The average largest basal diameter for tumors with eukaryotic translation initiation factor 1A, X-chromosomal mutations was significantly smaller than those with splicing factor 3B subunit 1 mutations and BRCA1-associated protein-1 mutations. Class 2 tumors metastasized sooner than GEP class 1 tumors. Tumors with splicing factor 3B subunit 1 and/or BRCA1-associated protein-1 mutations metastasized sooner compared with tumors that had either no driver mutation or no mutations at all. Tumors with splicing factor 3B subunit 1 did not have a significantly different time to metastasis compared with tumors with BRCA1-associated protein-1 (P value = 0.97). Forty tumors (30%) were PRAME positive, and the remaining 95 tumors (70%) were PRAME negative. Tumors with PRAME-positive status did not have a significantly different time to metastasis compared with tumors without PRAME-positive status (P value = 0.11). CONCLUSION GEP, NGS, and PRAME expression analysis help determine different levels of metastatic risk in UM. Although other prognostic tests exist, the following study reports on the use of NGS for metastatic prognostication in UM. However, limitations of NGS exist, especially with small lesions that are technically difficult to biopsy.
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Affiliation(s)
- Amer F Alsoudi
- Department of Ophthalmology, Baylor College of Medicine, Houston, Texas
| | - Henry C Skrehot
- School of Medicine, Baylor College of Medicine, Houston, Texas
| | - Patricia Chévez-Barrios
- Department of Ophthalmology, Baylor College of Medicine, Houston, Texas
- Department of Pathology and Genomic Medicine, Weill Cornell Medicine, Houston Methodist Hospital, Houston, Texas
- Blanton Eye Institute, Weill Cornell Medicine, Houston Methodist Hospital, Houston, Texas; and
| | - Mukul Divatia
- Department of Pathology and Genomic Medicine, Weill Cornell Medicine, Houston Methodist Hospital, Houston, Texas
| | - Maria De La Garza
- Department of Pathology and Genomic Medicine, Weill Cornell Medicine, Houston Methodist Hospital, Houston, Texas
| | | | - Amy C Schefler
- Blanton Eye Institute, Weill Cornell Medicine, Houston Methodist Hospital, Houston, Texas; and
- Retina Consultants of Texas, Houston, Texas
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Suwajanakorn D, Lane AM, Go AK, Hartley CD, Oxenreiter M, Wu F, Gragoudas ES, Sullivan RJ, Montazeri K, Kim IK. Impact of gene expression profiling on diagnosis and survival after metastasis in patients with uveal melanoma. Melanoma Res 2024; 34:319-325. [PMID: 38578293 DOI: 10.1097/cmr.0000000000000971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Surveillance frequency for metastasis is guided by gene expression profiling (GEP). This study evaluated the effect of GEP on time to diagnosis of metastasis, subsequent treatment and survival. A retrospective study was conducted of 110 uveal melanoma patients with GEP (DecisionDx-UM, Castle Biosciences, Friendswood, Texas, USA) and 110 American Joint Committee on Cancer-matched controls. Surveillance testing and treatment for metastasis were compared between the two groups and by GEP class. Rates of metastasis, overall survival and melanoma-related mortality were calculated using Kaplan-Meier estimates. Baseline characteristics and follow-up time were balanced in the two groups. Patients' GEP classification was 1A in 41%, 1B in 25.5% and 2 in 33.6%. Metastasis was diagnosed in 26.4% ( n = 29) in the GEP group and 23.6% ( n = 26) in the no GEP group ( P = 0.75). Median time to metastasis was 30.5 and 22.3 months in the GEP and no GEP groups, respectively ( P = 0.44). Median months to metastasis were 34.7, 75.8 and 26.1 in class 1A, 1B and 2 patients, respectively ( P = 0.28). Disease-specific 5-year survival rates were 89.4% [95% confidence interval (CI): 81.0-94.2%] and 84.1% (95% CI: 74.9-90.1%) in the GEP and no GEP groups respectively ( P = 0.49). Median time to death from metastasis was 10.1 months in the GEP group and 8.5 months in the no GEP group ( P = 0.40). There were no significant differences in time to metastasis diagnosis and survival outcomes in patients with and without GEP. To realize the full benefit of GEP, more sensitive techniques for detection of metastasis and adjuvant therapies are required.
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Affiliation(s)
- D Suwajanakorn
- Ocular Melanoma Center, Retina Service, Massachusetts Eye and Ear, Boston, Massachusetts, USA
- Department of Ophthalmology, Center of Excellence in Retina, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - A M Lane
- Ocular Melanoma Center, Retina Service, Massachusetts Eye and Ear, Boston, Massachusetts, USA
| | - A K Go
- Ocular Melanoma Center, Retina Service, Massachusetts Eye and Ear, Boston, Massachusetts, USA
| | - C D Hartley
- Ocular Melanoma Center, Retina Service, Massachusetts Eye and Ear, Boston, Massachusetts, USA
- Current address: Department of Ophthalmology and Visual Sciences, University of Nebraska Medical Center, Omaha, Nebraska
| | - M Oxenreiter
- Ocular Melanoma Center, Retina Service, Massachusetts Eye and Ear, Boston, Massachusetts, USA
- Close Concerns, San Francisco, California, USA
| | - F Wu
- Ocular Melanoma Center, Retina Service, Massachusetts Eye and Ear, Boston, Massachusetts, USA
| | - E S Gragoudas
- Ocular Melanoma Center, Retina Service, Massachusetts Eye and Ear, Boston, Massachusetts, USA
| | - R J Sullivan
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts, USA
| | - K Montazeri
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts, USA
| | - I K Kim
- Ocular Melanoma Center, Retina Service, Massachusetts Eye and Ear, Boston, Massachusetts, USA
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Maher NG, Vergara IA, Long GV, Scolyer RA. Prognostic and predictive biomarkers in melanoma. Pathology 2024; 56:259-273. [PMID: 38245478 DOI: 10.1016/j.pathol.2023.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/20/2023] [Indexed: 01/22/2024]
Abstract
Biomarkers help to inform the clinical management of patients with melanoma. For patients with clinically localised primary melanoma, biomarkers can help to predict post-surgical outcome (including via the use of risk prediction tools), better select patients for sentinel lymph node biopsy, and tailor catch-all follow-up protocols to the individual. Systemic drug treatments, including immune checkpoint inhibitor (ICI) therapies and BRAF-targeted therapies, have radically improved the prognosis of metastatic (stage III and IV) cutaneous melanoma patients, and also shown benefit in the earlier setting of stage IIB/C primary melanoma. Unfortunately, a response is far from guaranteed. Here, we review clinically relevant, established, and emerging, prognostic, and predictive pathological biomarkers that refine clinical decision-making in primary and metastatic melanoma patients. Gene expression profile assays and nomograms are emerging tools for prognostication and sentinel lymph node risk prediction in primary melanoma patients. Biomarkers incorporated into clinical practice guidelines include BRAF V600 mutations for the use of targeted therapies in metastatic cutaneous melanoma, and the HLA-A∗02:01 allele for the use of a bispecific fusion protein in metastatic uveal melanoma. Several predictive biomarkers have been proposed for ICI therapies but have not been incorporated into Australian clinical practice guidelines. Further research, validation, and assessment of clinical utility is required before more prognostic and predictive biomarkers are fluidly integrated into routine care.
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Affiliation(s)
- Nigel G Maher
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Ismael A Vergara
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Royal North Shore and Mater Hospitals, Sydney, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.
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Aye J, Gold A, Rodriguez B, Murray T. Gene Expression Profile Class Change in a Case of Aggressive, Recurrent Melanoma. JOURNAL OF VITREORETINAL DISEASES 2024; 8:93-96. [PMID: 38223774 PMCID: PMC10786084 DOI: 10.1177/24741264231215536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Purpose: To report a novel case of a recurrent melanoma that had a change in its genetic expression profile (GEP) class over a 2-year period. Methods: This retrospective case study evaluated a patient with a recurrent uveal melanoma that changed classes from 1A to 1B. Results: A large melanoma was first treated with brachytherapy, and during that time genetic testing revealed a class 1A tumor. Two years later the tumor was noted to be enlarging, and the patient elected for enucleation. Subsequent GEP showed a class 1B tumor. Conclusions: An aggressive and large recurrent uveal melanoma that had changed from a class 1A to a class 1B tumor on subsequent GEP testing has never been reported before to our knowledge. It may imply that a recurrent or aggressive tumor has more mutations over time that could lead to a higher risk for metastasis. The natural course of a tumor's GEP class should be explored further.
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Affiliation(s)
- Jennifer Aye
- Murray Ocular Oncology and Retina, Miami, FL, USA
| | - Aaron Gold
- Murray Ocular Oncology and Retina, Miami, FL, USA
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Augsburger JJ, Skinner CC, Correa ZM. Response to Cook and Alsina's Letter to Editor (Reply to Augsburger et al.). Ocul Oncol Pathol 2023; 9:68-70. [PMID: 37600850 PMCID: PMC10433092 DOI: 10.1159/000529562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 01/21/2023] [Indexed: 08/22/2023] Open
Affiliation(s)
- James J. Augsburger
- Department of Ophthalmology, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | | | - Zelia M. Correa
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, USA
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Cook RW, Alsina KM. Reply to Augsburger et al: Selection Bias May Impact Reported Metastasis Risk for 15-Gene Expression Profile Class 1A/B Patients. Ocul Oncol Pathol 2023; 9:66-67. [PMID: 37600849 PMCID: PMC10433088 DOI: 10.1159/000529561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/23/2023] [Indexed: 08/22/2023] Open
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