Abstract
Purpose :
Determining metastatic risk in uveal melanoma (UM) patients requires genetic testing of tumor biopsies. The purpose of the study was to profile protein expression liquid vitreous biopsies from UM eyes to identify prognostic biomarkers, signaling pathways, and therapeutic targets.
Methods :
Vitreous biopsies were collected from two cohorts in a pilot study: comparative control eyes with epiretinal membranes (ERM; n = 3) and test eyes with UM (n = 8). Primary tumors underwent conventional genetic testing to establish prognostic class based on Gene Expression Profiling (GEP) and Preferentially Expressed Antigen in Melanoma (PRAME) status. Vitreous samples were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and a quantitative multiplex ELISA that measured the expression of 1,000 proteins. From this discovery dataset, twenty proteins were selected for prospective validation in separate cohort of patients.
Results :
A total of 69 significantly differentially expressed proteins were detected in the UM vitreous by multiplex ELISA. Analysis of differential protein expression by tumor molecular classification (GEP and PRAME) further identified proteins that correlated with these classifications. Patients with high-risk GEP tumors displayed elevated vitreous expression of HGF and SCFR while patients with PRAME positive tumors displayed elevated vitreous expression of DSG3, ENPP-2, and LEG9. Further analysis by LC-MS/MS allowed for unbiased characterization of the UM vitreous and identified 62 significantly upregulated proteins that were not detected by ELISA, including LYVE-1, NEO1, and LRP-1. Prospective verification in a separate cohort of UM patients established the elevated expression of HGF and SCFR in UM vitreous as well as the decreased expression of KLK7.
Conclusions :
Proteomic analysis of liquid biopsies may provide prognostic information supporting gene expression of tumor biopsies. The use of multiple protein detection platforms in the same patient samples increases the sensitivity of candidate biomarker detection and allows for precise characterization of the vitreous proteome. Moreover, unique patterns of proteins point to biologically plausible mechanisms for tumor proliferation and propagation, and suggest rational approaches for adjuvant therapy, drug repositioning, and metastatic risk surveillance.
This abstract was presented at the 2024 ARVO Annual Meeting, held in Seattle, WA, May 5-9, 2024.