J Cancer 2020; 11(10):2945-2956. doi:10.7150/jca.43010

Research Paper

A Functional Synonymous Variant in PDGFRA Is Associated with Better Survival in Acral Melanoma

Jie Dai1*, Lu Yang1,2*, Tianxiao Xu1, Lu Si1, Chuanliang Cui1, Xinan Sheng1, Zhihong Chi1, Lili Mao1, Bin Lian1, Bixia Tang1, Xue Bai1, Li Zhou1, Siming Li1, Xuan Wang1, Xieqiao Yan1, Yan Kong1✉, Jun Guo1✉

1. Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Renal Cancer and Melanoma, Peking University Cancer Hospital and Institute, Beijing 100142, China
2. Department of Radiology, Peking University Shougang Hospital, Beijing 100144, China
*J. Dai and L. Yang contributed equally to this work.

This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). See http://ivyspring.com/terms for full terms and conditions.
Dai J, Yang L, Xu T, Si L, Cui C, Sheng X, Chi Z, Mao L, Lian B, Tang B, Bai X, Zhou L, Li S, Wang X, Yan X, Kong Y, Guo J. A Functional Synonymous Variant in PDGFRA Is Associated with Better Survival in Acral Melanoma. J Cancer 2020; 11(10):2945-2956. doi:10.7150/jca.43010. Available from http://www.jcancer.org/v11p2945.htm

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Purpose: Polymorphisms of genes in the platelet-derived growth factor (PDGF) signaling pathway have been found to predict cutaneous melanoma (CM) survival, but their clinical effects in acral melanoma (AM) patients have not been explored. The aim of this study was to characterize the functional effect of the tag single-nucleotide polymorphism (SNP) rs2228230:C>T and assess its association with clinical outcomes in AM patients.

Methods: The effect of rs2228230:C>T on mRNA structures and codon usage values were evaluated using in silico analyses. PDGF receptor alpha (PDGFRA) expression vectors with the rs2228230:C or rs2228230:T allele were constructed to evaluate the expression and signaling activity of PDGFRA. The expression of PDGFRA in AM samples was measured using in situ RNAscope hybridization and immunohistochemical staining. The association of the rs2228230 genotype with survival was analyzed in two independent AM cohorts.

Results: In silico analyses indicated that the rs2228230:T allele increases the minimum free energy and reduces synonymous codon usage. The rs2228230:T allele decreased the expression of PDGFRA by reducing the stability of its mRNA and protein as well as the signaling activity of the MAPK and PI3K/AKT pathways. PDGFRA mRNA and protein expression was significantly reduced in AM tissues with the rs2228230:T allele. The progression-free survival and overall survival of AM patients with the rs2228230:T allele were significantly longer than those of patients with the CC genotype.

Conclusion: Our study indicated that rs2228230:T can reduce the expression of PDGFRA and downstream signaling activity and is associated with better survival in AM patients.

Keywords: acral melanoma, PDGFRA, genetic variation, gene expression regulation, survival