PTPRD is homozygously deleted and epigenetically downregulated in human hepatocellular carcinomas

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. © Copyright 2015, Mary Ann Liebert, Inc. 2015.

Yazar Acun T.
Demir K.
Oztas E.
Arango D.
Yakicier M.C.
Yayın Türü Article
Tek Biçim Adres https://hdl.handle.net/20.500.12628/7257
Tek Biçim Adres 10.1089/omi.2015.0010
Koleksiyonlar Araştırma Çıktıları | WoS | Scopus | TR-Dizin | PubMed | SOBİAD
Scopus İndeksli Yayınlar Koleksiyonu
WoS İndeksli Yayınlar Koleksiyonu
Dergi Adı OMICS A Journal of Integrative Biology
Dergi Cilt Bilgisi 19
Dergi Sayısı 4
Sayfalar 220 - 229
Yayın Yılı 2015
Eser Adı
[dc.title]
PTPRD is homozygously deleted and epigenetically downregulated in human hepatocellular carcinomas
Yazar
[dc.contributor.author]
Acun T.
Yazar
[dc.contributor.author]
Demir K.
Yazar
[dc.contributor.author]
Oztas E.
Yazar
[dc.contributor.author]
Arango D.
Yazar
[dc.contributor.author]
Yakicier M.C.
Yayın Yılı
[dc.date.issued]
2015
Yayıncı
[dc.publisher]
Mary Ann Liebert Inc.
Yayın Türü
[dc.type]
article
Özet
[dc.description.abstract]
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. © Copyright 2015, Mary Ann Liebert, Inc. 2015.
Kayıt Giriş Tarihi
[dc.date.accessioned]
2019-12-23
Açık Erişim Tarihi
[dc.date.available]
2019-12-23
Yayın Dili
[dc.language.iso]
eng
Haklar
[dc.rights]
info:eu-repo/semantics/closedAccess
ISSN
[dc.identifier.issn]
1536-2310
İlk Sayfa Sayısı
[dc.identifier.startpage]
220
Son Sayfa Sayısı
[dc.identifier.endpage]
229
Dergi Adı
[dc.relation.journal]
OMICS A Journal of Integrative Biology
Dergi Sayısı
[dc.identifier.issue]
4
Dergi Cilt Bilgisi
[dc.identifier.volume]
19
Tek Biçim Adres
[dc.identifier.uri]
https://dx.doi.org/10.1089/omi.2015.0010
Tek Biçim Adres
[dc.identifier.uri]
https://hdl.handle.net/20.500.12628/7257
Görüntülenme Sayısı ( Şehir )
Görüntülenme Sayısı ( Ülke )
Görüntülenme Sayısı ( Zaman Dağılımı )
Görüntülenme
13
09.12.2022 tarihinden bu yana
İndirme
1
09.12.2022 tarihinden bu yana
Son Erişim Tarihi
17 Şubat 2024 07:28
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expression and/or common hypermethylation inhibitor samples downregulated epigenetic suppressor importance deletions medicine Copyright broader oncology reduced tissues promoter protein regions Mahlavu SNU475 coding Liebert respectively personalized primary paired restored larger systems discussed article diagnostic Further
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