Abstract 2164: Revisiting the mechanisms of PTEN loss in melanoma

Introduction Inactivation of the PTEN tumor suppressor, a negative regulator of oncogenic PI3K/Akt signaling, occurs in a subset of melanomas and is correlated with disease progression, treatment resistance and reduced patient survival. PTEN loss of function in melanoma is thought to result largely from gene deletion, mutation and/or methylation. However, the low frequency of these genomic alterations cannot explain the higher rate of loss of PTEN protein expression that is observed in melanoma. In this study, we tested the hypothesis that loss of PTEN expression in melanoma might be the consequence of predominantly non-genomic mechanisms, including post-transcriptional and post-translational dysregulation. Specifically, we postulated that PTEN loss in some melanomas might result from aberrant expression of PTENP1, a PTEN pseudogene-derived long non-coding RNA, and from increased PTEN ubiquitination and hence protein degradation. Experimental Procedures We performed an integrated analysis of data obtained from The Cancer Genome Atlas (TCGA; n = 276) and metastatic melanoma human specimens from patients enrolled at NYU (n = 48). We examined the frequency of PTEN copy number loss using genomic qPCR, PTEN mutations using targeted sequencing and qPCR mutation arrays, and PTEN methylation status was determined in tumors lacking PTEN deletion or mutation with bisulfite treatment and pyrosequencing. Furthermore, we assessed PTEN and PTENP1 expression in tumor samples by RT-qPCR, western blotting and immunohistochemistry. Results Complete PTEN deletions were found in 8% of TCGA cases and in 10% of NYU cases, while partial PTEN deletions were detected in 27% of NYU cases. Somatic PTEN mutations were found in 8% of TCGA cases and 3% of NYU cases. The frequency of PTEN methylation at five CpG islands ranged between 0% and 28% and did not predict PTEN protein expression, thus identifying a subset of tumors that exhibit PTEN protein loss despite a lack of detectable PTEN deletions, mutations or methylation. Integration of PTEN and PTENP1 expression data from TCGA and the NYU cohort revealed a strong positive correlation between PTEN and PTENP1 levels in melanoma. Analysis of a role for aberrant PTEN ubiquitination in promoting PTEN loss in melanoma is ongoing. Conclusions Our data challenge the existing model in which PTEN loss in melanoma is thought to occur primarily as a result of gene deletion, mutation or methylation. Rather, we find that these are uncommon events in melanoma and that PTEN loss may instead be attributed to post-transcriptional or post-translational mechanisms, such as dysregulation by loss of the PTENP1 long non-coding RNA. A comprehensive understanding of these non-genomic processes could identify novel approaches (“PTEN-restoring therapy”) to block tumor progression and improve treatment responses and patient survival, suggesting that suppression of PTEN levels in melanoma might be reversible and thus could be exploited clinically. Citation Format: Keith Giles, Yang Li, Amel Salhi, Jinhua Wang, Eric Robinson, Iman Osman. Revisiting the mechanisms of PTEN loss in melanoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2164. doi:10.1158/1538-7445.AM2015-2164