PTPRD is homozygously deleted and epigenetically downregulated in human hepatocellular carcinomas

Tolga Acun, Kubilay Demir, Emin Oztas, Diego Arango, M. Cengiz Yakicier

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    Abstract

    © Copyright 2015, Mary Ann Liebert, Inc. 2015. PTPRD (protein tyrosine phosphatase, receptor type, D) is a tumor suppressor gene, frequently inactivated through deletions or epigenetic mechanisms in several cancers with importance for global health. In this study, we provide new and functionally integrated evidence on genetic and epigenetic alterations of PTPRD gene in hepatocellular carcinomas (HCCs). Importantly, HCC is the sixth most common malignancy and the third most common cause of cancer-related mortality worldwide. We used a high throughput single nucleotide polymorphism (SNP) microarray assay (Affymetrix, 10K2.0 Assay) covering the whole genome to screen an extensive panel of HCC cell lines (N=14 in total) to detect DNA copy number changes. PTPRD expression was determined in human HCCs by Q-RT-PCR and immunohistochemistry. Promoter hypermethylation was assessed by combined bisulfite restriction analysis (COBRA). DNA methyl transferase inhibitor 5-azacytidine (5-AzaC) and/or histone deacetylase inhibitor Trichostain A (TSA) were used to restore the expression. We identified homozygous deletions in Mahlavu and SNU475 cells, in the 5′UTR and coding regions, respectively. PTPRD mRNA expression was downregulated in 78.5% of cell lines and 82.6% of primary HCCs. PTPRD protein expression was also found to be lost or reduced in HCC tumor tissues. We found promoter hypermethylation in 22.2% of the paired HCC samples and restored PTPRD expression by 5-AzaC and/or TSA treatments. In conclusion, PTPRD is homozygously deleted and epigenetically downregulated in HCCs. We hypothesize PTPRD as a tumor suppressor candidate and potential cancer biomarker in human HCCs. This hypothesis is consistent with compelling evidences in other organ systems, as discussed in this article. Further functional assays in larger samples may ascertain the contribution of PTPRD to hepatocarcinogenesis in greater detail, not to forget its broader importance for diagnostic medicine and the emerging field of personalized medicine in oncology.
    Original languageEnglish
    Pages (from-to)220-229
    JournalOMICS A Journal of Integrative Biology
    Volume19
    Issue number4
    DOIs
    Publication statusPublished - 1 Jan 2015

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    Acun, T., Demir, K., Oztas, E., Arango, D., & Yakicier, M. C. (2015). PTPRD is homozygously deleted and epigenetically downregulated in human hepatocellular carcinomas. OMICS A Journal of Integrative Biology, 19(4), 220-229. https://doi.org/10.1089/omi.2015.0010