An Accurate, Clinically Feasible Multi-Gene Expression Assay for Predicting Metastasis in Uveal Melanoma

Abstract

Uveal (ocular) melanoma is an aggressive cancer that often forms undetectable micrometastases before diagnosis of the primary tumor. These micrometastases later multiply to generate metastatic tumors that are resistant to therapy and are uniformly fatal. We have previously identified a gene expression profile derived from the primary tumor that is extremely accurate for identifying patients at high risk of metastatic disease. Development of a practical clinically feasible platform for analyzing this expression profile would benefit high-risk patients through intensified metastatic surveillance , earlier intervention for metastasis , and stratification for entry into clinical trials of adjuvant therapy. Here , we migrate the expression profile from a hybridization-based microarray platform to a robust , clinically practical , PCR-based 15-gene assay comprising 12 discriminating genes and three endogenous control genes. We analyze the technical performance of the assay in a prospective study of 609 tumor samples , including 421 samples sent from distant locations. We show that the assay can be performed accurately on fine needle aspirate biopsy samples , even when the quantity of RNA is below detectable limits. Preliminary outcome data from the prospective study affirm the prognostic accuracy of the assay. This prognostic assay provides an important addition to the armamentarium for managing patients with uveal melanoma , and it provides a proof of principle for the development of similar assays for other cancers.

Prognostication in eye cancer: the latest tumor, node, metastasis classification and beyond

“…[21][22][23] Genetic prognostication Genetic analysis provides the single best estimate for the risk of metastasis from uveal melanoma. 12,24,25 Such an analysis can be performed by charting chromosomal alternations 26,27 or by gene expression profiling. 24,25,28 The latest TNM edition encourages recording of genetic features.…”

“…12,24,25 Such an analysis can be performed by charting chromosomal alternations 26,27 or by gene expression profiling. 24,25,28 The latest TNM edition encourages recording of genetic features. 9 A major breakthrough was the observation that many uveal melanomas lack one copy of chromosome 3, and that these monosomic tumours are usually those that metastatise.…”

“…24,25 The profiling is based on the analysis of tumour RNA, and unlike chromosomal alterations, which can vary within a tumour, the expression profile is claimed to be uniform throughout the tumour. Gene expression profiling is available as a commercial, internally validated service from Castle Biosciences Inc. (Friendswood, TX, USA).…”

Management of Uveal Melanoma: A Consensus-Based Provincial Clinical Practice Guideline

“…Two genetic tests more precisely identify patients with worse prognosis: testing for monosomy 3 and gene-expression profiling (gep). Monosomy 3, with a gain in chromosome 8q, and gep class 2 are associated with 3-year metastasis-free survival rates of 53% and 50% respectively 8,13,14 ; these genetic variations occur in about 50% of patients 13,[15][16][17][18] . A prospective validation study of gep class 2 showed that, on multivariate analysis, gep class was the only significant factor 14 .…”

The pathology of ocular cancer

“…21 A proprietary GEP assay using a microarray of only 13 genes has been reported to be the most accurate prognostic marker for melanoma mortality and metastasis, although this remains controversial. 22,23 Although greatly inferior to chromosomal analysis and GEP, clinical examination and routine histopathological examination of uveal melanoma can reveal a number of important prognostic factors. Tumor size (largest tumor diameter and thickness) and the presence or absence of ciliary body involvement and extraocular extension are the most important factors that can be determined on clinical examination.…”