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Quantitative Proteomic Analysis and Gene Expression Profiling Microarray Re-analysis of Uveal Melanoma

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posted on 22.11.2019, 18:27 authored by Pathma Ramasamy

Uveal melanoma (UM) is the most common primary intraocular malignancy in adults and 40% develop fatal metastatic disease. Compared to tumours with chromosome 3 disomy, monosomy 3 tumours will nearly exclusively develop metastasis. To identify differentially expressed proteins, quantitative label-free LC-MS proteomic profiling of 8 primary UM tissues from patients with metastasis (M) and 8 from patients without metastasis (NM) was performed. Fifty proteins with ≥ 3 peptides matched and p < 0.05 between the two patient groups were differentially expressed. Thioredoxin-dependant peroxidase reductase (PRDX3) was upregulated and cytosolic non-specific dipeptidase (CNDP2) was downregulated in M compared to NM. To identify differentially expressed genes, bioinformatic reanalysis of publically available gene expression microarray datasets of 63 primary UM tumours was performed. Samples with confounding factors (chromosome 3 disomy with metastasis and chromosome 3 monosomy without metastasis) and outlying samples in principal component analysis were excluded. Eleven monosomy 3 tumours with metastasis (M3M) versus 9 disomy 3 tumours without metastasis (D3NM) were compared. A total of 449 differentially expressed genes with fold change of ≥ 1.3 and p < 0.05 were found between the two patient groups. Signal-induced proliferation-associated 1-like protein 2 (SIPA1L2) was upregulated and contactin 3 (CNTN3) was downregulated in M3M compared to D3NM. Pilot immunohistochemical (IHC) study of PRDX3, CNDP2, SIPA1L2 and CNTN3 expression in 13 full-face formalin-fixed paraffin-embedded tissues of patients that did (mUM) and 13 that did not develop metastasis (nmUM) showed a trend toward higher expression of PRDX3 in mUM compared to nmUM (p: 0.061). Expression of CNDP2, SIPA1L2 and CNTN3 were not significant (p: 0.752, p: 0.094 and p: 0.099 respectively). IHC of PRDX3 in tissue microarray samples of 55 mUM and 37 nmUM tumours showed statistically significant difference in expression between mUM and nmUM (p: 0.001). Significant difference in survival was found based on high and low expression of PRDX3 (67.61 vs. 130.64 months respectively, p: 0.013). In conclusion, differential proteomic analysis of primary UM tissues from patients with and without metastasis has identified PRDX3 to be associated with metastasis and poor survival.


Royal Victoria Eye and Ear Hospital Research Foundation


First Supervisor

Dr Paula Meleady

Second Supervisor

Professor Susan Kennedy

Third Supervisor

Professor Martin Clynes, Professor Conor Murphy


A thesis submitted for the degree of Doctor of Medicine from the Royal College of Surgeons in Ireland in 2015.

Published Citation

Ramasamy P. Proteomic Analysis and Gene Expression Profiling Microarray Re-analysis of Uveal Melanoma. [MD Thesis]. Dublin: Royal College of Surgeons in Ireland; 2015.

Degree Name

Doctor of Medicine (MD)

Date of award


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