Development of a Prognostic Genetic Signature to Predict the Metastatic Risk Associated with Cutaneous Melanoma

Abstract

Purpose: The development of a genetic signature for the identification of high-risk cutaneous melanoma tumors would provide a valuable prognostic tool with value for stage I and II patients who represent a remarkably heterogeneous group with a 3% to 55% chance of disease progression and death 5 years from diagnosis.Experimental Design: A prognostic 28-gene signature was identified by analysis of microarray expression data. Primary cutaneous melanoma tumor tissue was evaluated by RT-PCR for expression of the signature, and radial basis machine (RBM) modeling was performed to predict risk of metastasis.Results: RBM analysis of cutaneous melanoma tumor gene expression reports low risk (class 1) or high risk (class 2) of metastasis. Metastatic risk was predicted with high accuracy in development (ROC ¼ 0.93) and validation (ROC ¼ 0.91) cohorts of primary cutaneous melanoma tumor tissue. Kaplan-Meier analysis indicated that the 5-year disease-free survival (DFS) rates in the development set were 100% and 38% for predicted classes 1 and 2 cases, respectively (P < 0.0001). DFS rates for the validation set were 97% and 31% for predicted classes 1 and 2 cases, respectively (P < 0.0001). Gene expression profile (GEP), American Joint Committee on Cancer stage, Breslow thickness, ulceration, and age were independent predictors of metastatic risk according to Cox regression analysis.Conclusions: The GEP signature accurately predicts metastasis risk in a multicenter cohort of primary cutaneous melanoma tumors. Preliminary Cox regression analysis indicates that the signature is an independent predictor of metastasis risk in the cohort presented.

Validation of a Gene Expression Test for Mesothelioma Prognosis in Formalin-Fixed Paraffin-Embedded Tissues

“…RNA isolation, complimentary DNA generation, and qPCR were performed using standard operating procedures at the DNA Diagnostics Laboratory at St. Joseph's Hospital and Medical Center (Phoenix, AZ) as previously described. 20 Briefly, RNA isolation was performed according to the Ambion RecoverAll Total Nucleic Acid Isolation Kit (Life Technologies, Carlsbad, CA). RNA quantity and quality were assessed using the NanoDrop 1000 system and the Agilent Bioanalyzer 2100, and RNA was converted to cDNA using the Applied Biosystems High Capacity cDNA Reverse Transcription Kit (Life Technologies).…”

Molecular techniques for predicting behaviour in melanocytic neoplasms

“…The 28-gene assay includes the following genes: BAP1, MGP, SPP1, CXCL14, CLCA2, S100A8, BTG1, SAP130, ARG1, KRT6B, GJA1, ID2, EIF1B, S100A9, CRABP2, KRT14, ROBO1, RBM23, TACSTD2, DSC1, SPRR1B, TRIM29, AQP3, TYRP1, PPL, LTA4H, and CST6, three of which are also included in the assay used for uveal melanoma. 40 Gene ontology data suggest that most of the genes involved are related to tissue development, cell differentiation, and cell junction. As noted previously, BRAF, NRAS, or CKIT, all recognised as important drivers of melanoma and regulators of the cell cycle, are not included in the assay.…”

Optimizing Follow-up Assessment of Patients with Cutaneous Melanoma

“…The future of optimizing this risk assessment clearly lies in genetic and molecular profiling. A validated polymerase chain reaction (PCR)-based multigene assay for cutaneous melanoma is available, 5,6 although how such a test should influence a follow-up plan-alone or in conjunction with clinicopathologic factor models-remains unclear and warrants further investigation.…”