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

2019-11-22T18:27:20Z (GMT) 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.