Integration of cap analysis of gene expression and chromatin immunoprecipitation analysis on array reveals genome-wide androgen receptor signaling in prostate cancer cells

Takayama, Ken‐ichi; Tsutsumi, Sadami; Katayama, Shintaro; Okayama, Toshitsugu; Horie‐Inoue, Kuniko; Ikeda, Kazuhiro; Urano, Tomohiko; Kawazu, Chika; Hasegawa, Akira; Ikeo, Kazuho; Gojyobori, T; Ouchi, Yasuyoshi; Hayashizaki, Yoshihide; Aburatani, Hiroyuki; Inoue, Satoshi

doi:10.1038/onc.2010.436

Cited by 100 publications

(115 citation statements)

References 44 publications

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“…In contrast to previous CAGE studies by the Genome sequencer FLX system (454) 48 , we observed 57% of the signals within 500 bp of the 5 0 -ends of messenger RNAs based on the genomic coordinates of the reference full-length transcripts of RefSeq. We aggregated neighbouring CAGE tags on the genome into TCs and obtained 19,644 TCs.…”

Section: Methodscontrasting

confidence: 99%

“…For ChIP using AR, FOXA1 and TET2 antibody, cells were crosslinked with 1% formaldehyde for 10 min and stopped by adding 0.2 M glycine. Cells were lysed by lysis buffer 48,49 and chromatin DNA was sheared by sonication. Sonicated lysates were incubated overnight at 4°C with specific antibodies.…”

Section: Methodsmentioning

confidence: 99%

“…The fold enrichment relative to the IgG-IP control or % of input was quantified by qPCR using SYBR Green PCR master mix and the ABI StepOne System (Life Technologies, Carlsbad, CA, USA). We used GAPDH locus as a negative control (NC) 48 . The primer sequences for the detection of ARBSs by qPCR are listed in Supplementary Table 6. qRT-PCR.…”

Section: Methodsmentioning

confidence: 99%

“…The primer sequences are listed in Supplementary Table 6. Expression levels were quantified by qPCR 48,49 using SYBR Green PCR master mix and the ABI StepOne system (Life technologies).…”

Section: Methodsmentioning

confidence: 99%

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TET2 repression by androgen hormone regulates global hydroxymethylation status and prostate cancer progression

et al. 2015

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Modulation of epigenetic patterns has promising efficacy for treating cancer. 5-Hydroxymethylated cytosine (5-hmC) is an epigenetic mark potentially important in cancer. Here we report that 5-hmC is an epigenetic hallmark of prostate cancer (PCa) progression. A member of the ten-eleven translocation (TET) proteins, which catalyse the oxidation of methylated cytosine (5-mC) to 5-hmC, TET2, is repressed by androgens in PCa. Androgen receptor (AR)-mediated induction of the miR-29 family, which targets TET2, are markedly enhanced in hormone refractory PCa (HRPC) and its high expression predicts poor outcome of PCa patients. Furthermore, decreased expression of miR-29b results in reduced tumour growth and increased TET2 expression in an animal model of HRPC. Interestingly, global 5-hmC modification regulated by miR-29b represses FOXA1 activity. A reduction in 5-hmC activates PCa-related key pathways such as mTOR and AR. Thus, DNA modification directly links the TET2-dependent epigenetic pathway regulated by AR to 5-hmC-mediated tumour progression.

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Section: Methodscontrasting

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…The primer sequences are listed in Supplementary Table 6. Expression levels were quantified by qPCR 48,49 using SYBR Green PCR master mix and the ABI StepOne system (Life technologies).…”

Section: Methodsmentioning

confidence: 99%

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TET2 repression by androgen hormone regulates global hydroxymethylation status and prostate cancer progression

et al. 2015

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“…A modest overexpression of AR enhances the chromatin binding of the receptor by sensitizing the cells to 100-fold lower ligand concentration. The majority of the previously reported ChIP-seq and ChIP-chip experiments (Jia et al, 2008;Wang et al, 2009;Takayama et al, 2010;Yu et al, 2010) have compared the binding of AR at the saturating concentration of androgens, and thus, missed the dynamics of AR binding. However, our data are in line with a recent work by Massie et al (2011), in which they found almost five times more ARBSs in the strongly AR-overexpressing cell line VCaP compared with LNCaP cells.…”

Section: Discussionmentioning

confidence: 99%

Overexpression of androgen receptor enhances the binding of the receptor to the chromatin in prostate cancer

et al. 2011

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Androgen receptor (AR) is overexpressed in the majority of castration-resistant prostate cancers (CRPCs). Our goal was to study the effect of AR overexpression on the chromatin binding of the receptor and to identify AR target genes that may be important in the emergence of CRPC. We have established two sublines of LNCaP prostate cancer (PC) cell line, one overexpressing AR 2-3-fold and the other 4-5-fold compared with the control cells. We used chromatin immunoprecipitation (ChIP) and deep-sequencing (seq) to identify AR-binding sites (ARBSs). We found that the number of ARBSs and the AR-binding strength were positively associated with the level of AR when cells were stimulated with low concentrations of androgens. In cells overexpressing AR, the chromatin binding of the receptor took place in 100-fold lower concentration of the ligand than in control cells. We confirmed the association of AR level and chromatin binding in two PC xenografts, one containing AR gene amplification with high AR expression, and the other with low expression. By combining the ChIP-seq and expression profiling, we identified AR target genes that are upregulated in PC. Of them, the expression of ZWINT, SKP2 (S-phase kinase-associated protein 2 (p45)) and FEN1 (flap structure-specific endonuclease 1) was demonstrated to be increased in CRPC, while the expression of SNAI2 was decreased in both PC and CRPC. FEN1 protein expression was also associated with poor prognosis in prostatectomytreated patients. Finally, the knock-down of FEN1 with small interfering RNA inhibited the growth of LNCaP cells. Our data demonstrate that the overexpression of AR sensitizes the receptor binding to chromatin, thus, explaining how AR signaling pathway is reactivated in CRPC cells.

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Androgen pathway stimulates MicroRNA-216a transcription to suppress the tumor suppressor in lung cancer-1 gene in early hepatocarcinogenesis

Chen¹,

Yeh²,

Liu³

et al. 2012

Hepatology

103

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Deregulation of microRNAs (miRNAs) is common in advanced human hepatocellular carcinoma (HCC); however, the ones involved in early carcinogenesis have not yet been investigated. By examining the expression of 22 HCC-related miRNAs between precancerous and cancerous liver tissues, we found miR-216a and miR-224 were significantly up-regulated, starting from the precancerous stage. Furthermore, the elevation of miR-216a was mainly identified in male patients. To study this gender difference, we demonstrated that pri-miR-216a is activated transcriptionally by the androgen pathway in a ligand-dependent manner and is further enhanced by the hepatitis B virus X protein. The transcription initiation site for pri-miR-216a was delineated, and one putative androgen-responsive element site was identified within its promoter region. Mutation of this site abolished the elevation of pri-miR-216a by the androgen pathway. One target of miR-216a was shown to be the tumor suppressor in lung cancer-1 gene (TSLC1) messenger RNA (mRNA) through the three target sites at its 3 0 untranslated region. Finally, the androgen receptor level increased in male liver tissues during hepatocarcinogenesis, starting from the precancerous stage, with a concomitant elevation of miR-216a but a decrease of TSLC1. Conclusion: The current study discovered the up-regulation of miRNA-216a by the androgen pathway and a subsequent suppression of TSLC1 as a new mechanism for the androgen pathway in early hepatocarcinogenesis. (HEPATOLOGY 2012;56:632-643) T he incidence of hepatocellular carcinoma (HCC) ranks fifth for cancers worldwide and causes about half a million deaths every year. 1 HCC is usually the ultimate outcome of chronic hepatitis caused by persistent viral infection (hepatitis B or C virus [HBV/HCV]) or by alcoholic/metabolic etiologies. After decades of chronic hepatitis, which might induce persistent necrosis and regeneration and accumulate the carcinogenic events in the hepatocytes, about 30%-40% of patients will progress into liver cirrhosis, and those will subsequently develop HCC with an annual incidence around 1%-5%. 2 Due to the multistep characteristic of cancer development, on average six to seven successive mutations are generally believed to be required to convert a normal hepatocyte into an invasive HCC. 3 As every mutation contributes to the formation of an expanded clone and thus presents a larger target population of cells for the next mutation, the cells surrounding the HCC could be considered precancerous cells, retaining the potential to become the subsequent HCC. 4 This

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Integration of cap analysis of gene expression and chromatin immunoprecipitation analysis on array reveals genome-wide androgen receptor signaling in prostate cancer cells

Cited by 100 publications

References 44 publications

TET2 repression by androgen hormone regulates global hydroxymethylation status and prostate cancer progression

TET2 repression by androgen hormone regulates global hydroxymethylation status and prostate cancer progression

Overexpression of androgen receptor enhances the binding of the receptor to the chromatin in prostate cancer

Androgen pathway stimulates MicroRNA-216a transcription to suppress the tumor suppressor in lung cancer-1 gene in early hepatocarcinogenesis

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