Aberrant promoter CpG methylation is a mechanism for impaired PHD3 expression in a diverse set of malignant cells

Trenton L Place; Matthew P Fitzgerald; Sujatha Venkataraman; Sabine U Vorrink; Adam J Case; Melissa L T Teoh; Frederick E Domann

doi:10.1371/journal.pone.0014617

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Aberrant promoter CpG methylation is a mechanism for impaired PHD3 expression in a diverse set of malignant cells

Journal article

Open access

Peer reviewed

Aberrant promoter CpG methylation is a mechanism for impaired PHD3 expression in a diverse set of malignant cells

Trenton L Place, Matthew P Fitzgerald, Sujatha Venkataraman, Sabine U Vorrink, Adam J Case, Melissa L T Teoh and Frederick E Domann

PloS one, Vol.6(1), e14617

01/28/2011

DOI: 10.1371/journal.pone.0014617

PMCID: PMC3030558

PMID: 21297970

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Abstract

Background The prolyl-hydroxylase domain family of enzymes (PHD1-3) plays an important role in the cellular response to hypoxia by negatively regulating HIF-α proteins. Disruption of this process can lead to up-regulation of factors that promote tumorigenesis. We observed decreased basal expression of PHD3 in prostate cancer tissue and tumor cell lines representing diverse tissues of origin. Furthermore, some cancer lines displayed a failure of PHD3 mRNA induction when introduced to a hypoxic environment. This study explores the mechanism by which malignancies neither basally express PHD3 nor induce PHD3 under hypoxic conditions. Methodology/Principal Findings Using bisulfite sequencing and methylated DNA enrichment procedures, we identified human PHD3 promoter hypermethylation in prostate, breast, melanoma and renal carcinoma cell lines. In contrast, non-transformed human prostate and breast epithelial cell lines contained PHD3 CpG islands that were unmethylated and responded normally to hypoxia by upregulating PHD3 mRNA. Only treatment of cells lines containing PHD3 promoter hypermethylation with the demethylating drug 5-aza-2′-deoxycytidine significantly increased the expression of PHD3. Conclusions/Significance We conclude that expression of PHD3 is silenced by aberrant CpG methylation of the PHD3 promoter in a subset of human carcinoma cell lines of diverse origin and that this aberrant cytosine methylation status is the mechanism by which these cancer cell lines fail to upregulate PHD3 mRNA. We further show that a loss of PHD3 expression does not correlate with an increase in HIF-1α protein levels or an increase in the transcriptional activity of HIF, suggesting that loss of PHD3 may convey a selective advantage in some cancers by affecting pathway(s) other than HIF.

Hypoxia

Hypoxia-Inducible Factor 1, alpha Subunit - analysis

Humans

Gene Expression Regulation, Neoplastic

Gene Silencing

RNA, Messenger - analysis

Dioxygenases - deficiency

Male

Hypoxia-Inducible Factor-Proline Dioxygenases

Promoter Regions, Genetic - genetics

DNA Methylation

Dioxygenases - genetics

Neoplasms - genetics

Cell Line, Tumor

CpG Islands - genetics

Female

Neoplasms - pathology

Details

Title: Subtitle: Aberrant promoter CpG methylation is a mechanism for impaired PHD3 expression in a diverse set of malignant cells
Creators: Trenton L Place - Molecular and Cellular Biology Program, The University of Iowa, Iowa City, Iowa, United States of America
Matthew P Fitzgerald
Sujatha Venkataraman
Sabine U Vorrink
Adam J Case
Melissa L T Teoh
Frederick E Domann
Resource Type: Journal article
Publication Details: PloS one, Vol.6(1), e14617
DOI: 10.1371/journal.pone.0014617
PMID: 21297970
PMCID: PMC3030558
NLM abbreviation: PLoS One
ISSN: 1932-6203
eISSN: 1932-6203
Publisher: Public Library of Science; United States
Grant note: T32 GM073610 / NIGMS NIH HHS P42 ES013661 / NIEHS NIH HHS R01CA115438 / NCI NIH HHS T32GM073610 / NIGMS NIH HHS 2P42ES013661 / NIEHS NIH HHS R01CA073612 / NCI NIH HHS R01 CA115438 / NCI NIH HHS P30CA086862 / NCI NIH HHS R01 CA073612 / NCI NIH HHS P30 CA086862 / NCI NIH HHS
Language: English
Date published: 01/28/2011
Academic Unit: Pathology; Surgery; Radiation Oncology; Obstetrics and Gynecology
Record Identifier: 9984047895702771

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