CDKN1C (p57KIP2) Is a Direct Target of EZH2 and
Suppressed by Multiple Epigenetic Mechanisms in Breast
Xiaojing Yang1,2, R. K. Murthy Karuturi3, Feng Sun1,4, Meiyee Aau1, Kun Yu5, Rongguang Shao2, Lance D.
Miller1, Patrick Boon Ooi Tan5,6, Qiang Yu1*
1Cancer Biology and Pharmacology, Genome Institute of Singapore, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore, 2Institute of Medicinal
Biotechnology, Chinese Academy of Medical Sciences, Beijing, China, 3Information and Mathematical Science, Genome Institute of Singapore, A*STAR (Agency for
Science, Technology and Research), Biopolis, Singapore, 4Department of Pharmacy, National University of Singapore, Singapore, Singapore, 5Duke-NUS Graduate
Medical School, Singapore, Singapore, 6Cell and Medical Biology, Genome Institute of Singapore, A*STAR (Agency for Science, Technology and Research), Biopolis,
CDKN1C (encoding tumor suppressor p57KIP2) is a cyclin-dependent kinase (CDK) inhibitor whose family members are often
transcriptionally downregulated in human cancer via promoter DNA methylation. In this study, we show that CDKN1C is
repressed in breast cancer cells mainly through histone modifications. In particular, we show that CDKN1C is targeted by
histone methyltransferase EZH2-mediated histone H3 lysine 27 trimethylation (H3K27me3), and can be strongly activated by
inhibition of EZH2 in synergy with histone deacetylase inhibitor. Consistent with the overexpression of EZH2 in a variety of
human cancers including breast cancer, CDKN1C in these cancers is downregulated, and breast tumors expressing low levels
of CDKN1C are associated with a poor prognosis. We further show that assessing both EZH2 and CDKN1C expression levels
as a measurement of EZH2 pathway activity provides a more predictive power of disease outcome than that achieved with
EZH2 or CDKN1C alone. Taken together, our study reveals a novel epigenetic mechanism governing CDKN1C repression in
breast cancer. Importantly, as a newly identified EZH2 target with prognostic value, it has implications in patient
stratification for cancer therapeutic targeting EZH2-mediated gene repression.
Citation: Yang X, Karuturi RKM, Sun F, Aau M, Yu K, et al. (2009) CDKN1C (p57KIP2) Is a Direct Target of EZH2 and Suppressed by Multiple Epigenetic Mechanisms
in Breast Cancer Cells. PLoS ONE 4(4): e5011. doi:10.1371/journal.pone.0005011
Editor: Mikhail V. Blagosklonny, Ordway Research Institute, United States of America
Received December 17, 2008; Accepted March 4, 2009; Published April 2, 2009
Copyright: ? 2009 Yang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was supported by Agency for Science, Technology & Research (A* Star) of Singapore.(http://www.a-star.edu.sg). The funders had no role in
study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing Interests: The authors have declared that no competing interests exist.
* E-mail: email@example.com
Cyclin-dependent kinase inhibitors (CDKIs) are a large family
of proteins that regulate cell cycle progression, cell proliferation
and differentiation. CDKIs show widespread involvement in
tumor suppression and are deregulated in many types of human
cancers by genetic and epigenetic alterations. Loss of expression of
CDKIs, such as p16INK4A, due to promoter DNA hypermethyla-
tion, is frequent in human cancer and the CDKIs downregulation
is associated with aberrant cell proliferation and tumor growth. In
addition to promoter DNA methylation, histone modifications also
play a role in inactivation of the CDK inhibitors. It has been
shown that H3K9 methylation can occur at p16INK4Aindepen-
dently of DNA methylation . More recently, inactivation of the
INK4A locus by other mechanisms such as Polycomb-associated
histone H3K27 methylation have also been reported [2,3,4].
Pharmacological reagents have been used to understand the
regulatory components of gene silencing in cancer. DNA
methylation inhibitor 5-Aza-29-deoxycytidine (5-Aza-C) has been
used extensively to restore the expression of genes silenced by
DNA methylation , whereas histone deacetylase (HDAC)
inhibitors such as Trichostatin A (TSA) can induce gene
expression by reversing repressed chromatin . These two
classes of agents can also act in synergy for the reactivation of
epigenetically silenced genes . In addition to histone deacetyla-
tion, histone methylation also contributes to gene silencing. In
particular, Polycomb protein EZH2 (Enhancer of Zeste 2) is a
histone methyltransferase that is often overexpressed in human
cancers and is associated with cancer aggressiveness [8,9]. EZH2
specifically methylates lysine 27 of histone H3 (H3K27), a
repressive chromatin mark associated with gene silencing
[10,11,12] and often represses target genes associated with growth
control. It has been shown that EZH2-mediated gene repression
requires HDAC activity  and its functional relationship to
DNA methylation is also of current interest [14,15,16,17,18].
Furthermore, recent studies indicate that inhibiting DNA
methylation alone or even with the aid of HDAC inhibitors is
insufficient to induce an euchromatic chromatin state due to the
retention of repressive histone marks [19,20]. These findings
suggest that for a stable reversion of epigenetic silencing in cancer,
a complete reversal from the malignant heterochromatin to a
normal euchromatin is required.
CDK inhibitor CDKN1C (p57KIP2) has been previously reported
to be inactivated via promoter DNA methylation in a variety of
PLoS ONE | www.plosone.org1April 2009 | Volume 4 | Issue 4 | e5011
human cancers [21,22]. In this study, we report that the CDKN1C
is repressed in breast cancer by multiple epigenetic mechanisms.
We demonstrate that the CDKN1C gene is the target of EZH2-
mediaed trimethylation of histone H3 at lysine 27 (H3K27me3)
that coordinates with histone deacetylation to suppress CDKN1C
expression. Combined treatment of DZNep, an inhibitor of
histone methylation , with HDAC inhibitor TSA causes a
robust reactivation of CDKN1C expression. We also demonstrate
the prognostic value of EZH2-mediated CDKN1C repression in
breast cancer and suggest its clinical significance for EZH2-
targeted cancer therapeutics.
CDKN1C repression in breast cancer cells is associated
with histone modifications independently of DNA
We have previously reported that S-adenosylhomocysteine
hydrolase inhibitor 3-Deazaneplanosin A (DZNep) is able to
inhibit histone methylation and depletes the EZH2 complex and
the associated H2K27 methylation  and combination of
DZNep with HDAC inhibitor TSA resulted in robust activation of
H3K27me3 target genes . In an effort to comprehensively
understand the epigenetic events in breast cancer, we performed
gene expression analysis in various breast cancer cell lines treated
with DZNep, TSA or Aza, alone or in various combinations. We
found that CDKN1C can be strongly induced by a combination of
DZNep and TSA treatment compared to a modest induction by
Aza (see below). This finding suggests that CDKN1C expression in
breast cancer is predominately regulated by histone modifications
instead of DNA hypermethylation.
To validate this finding, we first examined the relationship
between the DNA methylation status of the CDKN1C promoter
and the levels of CDKN1C expression in various breast cancer cell
lines as well as the non-cancerous breast epithelial cell line
(MCF10A). To this end, we have used methylation-specific PCR
(MSP) to examine three regions flanking the entire CpG island
surrounding the transcription start site (TSS) (Figure 1A). We
found that the immediate promoter regions (M2 and M3)
appeared to be unmethylated in all the breast cancer cell lines
tested (Figure 1B), though the similar regions have been previously
found to be methylated in lung cancer . In a more distal region
(M1) 500 bp upstream of the TSS, DNA was found to methylated
in certain breast cancer cell lines, including BT-474 and MDA-
MB-231, as well as in MCF10A cells, indicating this methylation is
not cancer specific (Figure 1B). Bisulfite genomic sequencing
results further confirmed the lack of methylation in M2 and M3
regions in SK-BR-3, BT-474 and MDA-MB-231 cells (Figure 1C).
Examination of CDKN1C expression from our breast cancer cell
lines gene expression database indicates that CDKN1C expression
displayed varied levels of expression but in general was reduced in
most of the breast cancer cell lines (except the MDA-MB-231 cells)
as compared to MCF10A cells (Figure 1D). RT-PCR analysis
further validated the array data (Figure 1D). Of important notice,
the expression pattern of CDKN1C does not seem to correlate with
the methylation status in these cell lines.
We next set out to determine whether histone modifications are
responsible for CDKN1C repression in breast cancer. We used
chromatin immunoprecipitation (ChIP) coupled with quantitative
PCR to assess the following histone marks: the repressive
chromatin marks H3K27me3, H3K9me3, H3K9me2, and
H4K20me3, as well as activating H3K4me3 and acetylated
histone (H3K9/14 ac) that are normally associated with gene
activation. A series of PCR primer sets were designed to probe the
4 kb chromatin region surrounding the CDKN1C TSS (Figure 2A).
We comprehensively characterized the chromatin state in SK-BR-
3, BT-474, MDA-MB-231 and MCF10A cell lines in which
CDKN1C is expressed at different levels. We detected an abundant
H3K27me3 in a region approximately 300 bp downstream of the
TSS in SK-BR-3 cells that express the lowest level of CDKN1C
(Figure 2B). This was also observed to a lesser extend in BT-474
cells that express a modest level of CDKN1C, and at low rates in
MDA-MB-231 and MCF10A cells that express abundant
CDKN1C. Consistent with the enrichment of H3K27me3, we also
detected a strong binding of H3K27 methyltransferase EZH2 to
the CDKN1C promoter in SK-BR-3, to a lesser extend in BT-474
cells but not in MDA-MB-231 and MCF10A cells. Thus, levels of
enrichment of EZH2 and H3K27me3 correlate very well
(inversely) with the levels of CDKN1C expression across these
diverse cell lines. This finding is consistent with the notion that
EZH2 and the associated H3K27me3 enrichment are correlated
with gene repression in cancer cells, and the majority of
H3K27me3 is detected in the region downstream of the TSS
In addition, abundant H3K4me3 near the TSS was detected in
all the four cell lines, irrespective of the levels of CDKN1C
expression (Figure 2B). This suggests that CDKN1C is marked by
both repressive and activating histone marks in SK-BR-3 and BT-
474 cells; a bivalent chromatin state that is generally associated
with gene repression [28,29]. Higher abundance of acetylated H3
(H3K9/14ac) was detected in CDKN1C-expressing MCF10A,
MDA-MB-231 and BT-474 cells but was less detectable in SK-
BR3 cells that express a lowest level of CDKN1C, indicating a
positive correlation of H3K9/14ac with CDKN1C expression in
these cells. We also detected the presence of another repressive
mark H3K9me2 in BT-474 cells but not in other three cell lines
(Figure 2B). Taken together, these results indicate that the
H3K27me3; activating H3K4me3 and H3K9/14ac, as well as
their combinatorial effects, correlate well with the levels of
CDKN1C expression in these cells. Other repressive histone
modifications such as H4K20me3 and H3K9me3 were not
detected at the CDKN1C locus (data not shown).
To further determine the association of H3K27me3 with the
level of CDKN1C expression in human breast tumors, we took the
advantage of an independent microarray dataset of human breast
tumors stained with H3K27me3 in Oncomine microarray
database (www.oncomine.org). Figure 2C shows that breast
tumors stained positive for H3K27me3 display a consistent
downregulation of CDKN1C compared with those negative for
H3K27me3. Of important note, genes exhibiting the similar
expression patterns to CDKN1C include KRT17, KRT5 and
LAMB3 that have been validated to be EZH2 target in our
previous study . Thus, the data from both clinical breast tumor
samples and cancer cell lines all support that CDKN1C downreg-
ulation in breast cancer is associated with a higher level of
Robust activation of CDKN1C expression by a
combination treatment with DZNep and TSA
The different chromatin configurations at CDKN1C in SK-BR-
3, BT-474 and MDA-MB-231 cells may predict differential
response of CDKN1C expression to various epigenetic drug
treatments. We next treated these breast cancer cell lines with
DZNep, TSA, or Aza alone or in various combinations and
performed quantitative RT-PCR to assess the changes of CDKN1C
expression upon these treatments. To determine the specificity of
the gene response, other CDKI family members were also
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included for the expression analysis. The results indicate that the
combination of DZNep with TSA resulted in a robust induction of
CDKN1C expression in SK-BR-3 cells, whereas the single drug
treatment or other drug combinations, such as DZNep/Aza or
TSA/Aza, did not give rise to such a strong induction (Figure 3A).
As a marked contrast to CDKN1C, other CDKI family members
did not respond to a similar extent, revealing the sensitivity of
CDKN1C to this combination treatment (Figure 3A). Moreover, in
Figure 1. DNA methylation status of CDKN1C promoter in breast cancer cells. (A) Schematic representation of CDKN1C locus. Vertical bars
indicate the CpG sites. TSS, transcription start site. M1, M2 and M3 represent genomic regions for methylation specific PCR (MSP) analysis. (B) MSP
analysis of genomic regions surrounding the TSS of CDKN1C. SFRP1 was used as a positive control of effective bisulfite conversation. (C) Bisulfite
genomic DNA sequencing results of indicated regions in SK-BR-3, BT-474 and MDA-MB-231 cells. (D) Upper panel, expression values of CDKN1C in
Illumina expression data of breast cancer cell lines. Lower panel, expression of CDKN1C in indicated cell lines are determined by RT-PCR.
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BT-474 cells that display a lower abundance of H3K27me3,
DZNep/TSA treatment only induced a 12-fold induction of
CDKN1C, as opposed to a 70-fold induction in SKBR-3 cells. This
response was much weaker in MDA-MB-231 cells and MCF10A
cells that exhibit low levels of H3K27me3 in CDKN1C (Figure 3A).
Taken together with the previous results, the data further support
the conclusion that H3K27me3 level in CDKN1C is closely
associated with its expression inversely. It also suggests that
inhibition of H3K27me3 by DZNep alone is insufficient but
requires TSA treatment for a full reactivation of CDKN1C. Lack of
response of other CDKN family members to DZNep/TSA
indicates the lack of similar chromatin state in these genes.
Indeed, we found that other CDKIs, such as CDKN1D, were not
marked by H3K27me3 in SK-BR-3 cells (data not shown). Finally,
we confirmed the induction of CDKN1C protein expression in a
similar manner by western blot (Figure 3B).
CDKN1C is an imprinting gene, whose expression is also
negatively regulated by an imprinted control region that contains a
non-coding transcript DMR-LIT1. To test the possibility that
the induction of CDKN1C might arise from the downregulation of
DMR-LIT1, we looked at the expression of LIT1 upon above drug
treatment. The result shows that LIT1 expression is not changed
upon DZNep/TSA treatment (Figure 3C), excluding the possibil-
ity that CDKN1C induction by DZNep/TSA is the result of LIT1
Combination treatment with DZNep and TSA
synergistically reverses histone modifications
We next examined the bulk histone modifications in cells
treated with DZNep, TSA or both. Cellular histone was isolated
from cell extracts and subjected to Western blot analysis using
antibodies against relevant histone modifications. As shown in
Figure 3A, DZNep treatment alone or in combination with TSA
caused a diminished H3K27me3 in SK-BR3 and BT-474 cells, as
anticipiated from our previous report . A striking observation
was the dramatic and synergistic increase in H3K9/14 acetylation
in cells treated with the DZNep/TSA combination compared to
cells treated with DZNep or TSA single treatment (Figure 4A).
Figure 3. Changes of CDKN1C expression in response to DZNep, TSA, Aza and their combinations. (A) SK-BR-3, BT-474, MDA-MB-231 and
MCF10A cells were treated with 5 mM DZNep (D), 100 nM TSA (T), and 5 uM 5-AzaC (A) along or in indicated combinations. Expression of CDKN
members were analyzed by quantitative RT-PCR. Shown were the folds of induction relative to the untreated cells. (B) Western blot analysis of
CDKN1C protein expression in SK-BR-3 and BT-474 cells. (C) RT-PCR results show no change of LIT1 expression upon indicated drug treatment. .
Figure 2. Histone modifications at CDKN1C locus in breast cancer cells. (A) Schematic representation of CDKN1C locus, TSS (transcription
start site). Numbered bars indicate the genomic regions analyzed for histone modifications using Chromatin immunoprecipitation (ChIP) assay. (B)
ChIP assay analysis of indicated histone marks and EZH2 binding at CDKN1C locus in SK-BR-3, BT-474 and MDA-MB-231 breast cancer cells, as well as
none-cancerous epithelial breast MCF10A cells. The enrichments of examined histone marks in the indicated regions were examined by quantitative
PCR relative to input DNA. Error bars were calculated as standard error (6s.d.). (C) Gene cluster showing the differential expression of CDKN1C and
correlated genes in H3K27me3 positive and negative breast cancer samples. The data was obtained through analyzing a breast cancer microarray
dataset in Oncomine database (www.oncomine.org).
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Although a decrease in H3K4me3 was also observed in cells
treated with DZNep alone, the combination treatment seemed to
cause a reverse of this decrease, leading to a level of H3K4me3
comparable to the untreated cells. Thus, the combination of
DZNep and TSA induced a reversal of histone modifications by
inhibiting H3K27me3 while enhancing acetated H3. This
combinatorial effect on histone modification suggests a more
permissive chromatin state overall, consistent with the robust
induction of CDKN1C expression.
We further performed ChIP analysis to determine the changes of
chromatin following the above drug treatments. As expected, SK-
BR-3 cells treated with DZNep/TSA showed an reduced EZH2
enrichment in CDKN1C, with a corresponding decrease in
H3K27me3 (Figure 4B). Concomitantly, H3K9/14ac was enhanced
after the combination treatment. Thus, taken together with the
previous results from quantitative RT-PCR, we identified a strong
correlation between the collective changes in histone modifications
This indicates that combination treatment with DZNep and TSA
creates a permissive chromatin environment for CDKN1C expression
through synergistically reversing associated chromatin marks.
To directly asses the role of EZH2 in CDKN1C expression, we
used RNA interference to deplete the EZH2 expression. SK-BR-3
cells treated with small interfering RNA (siRNA) targeting EZH2
displayed a marked decrease in EZH2 expression, and a
corresponding decrease in bulk H3K27me3 (Figure 4C). Depletion
of EZH2, albeit insufficient to induce CDKN1C expression,
resulted in a marked accumulation of CDKN1C protein in the
presence of TSA (Figure 4C). This result is consistent with the
previous pharmacology data and further indicates that effective
CDKN1C induction requires inhibition of both EZH2 and histone
deaceylation. It directly supports the model that histone
deacetylation and EZH2-mediated histone methylation cooperate
to repress CDKN1C expression.
Figure 4. Effects of DZNep/TSA combination on histone modifications. (A) Western blot results show the changes of histone modifications
in response to the indicated treatment. Histone proteins were acid-extracted from indicated whole-cell lysates, and indicated histone modifications
were analyzed with corresponding antibodies. Histone H3 was used as a loading control. (B) ChIP analysis detects the abundance of EZH2,
H3K27me3, H3K4me3 and H3K9/14ac at CDKN1C locus before and after the DZNep/TSA combination treatment in SK-BR-3 cells. (C) SK-BR-3 cells were
treated with negative control siRNA (NC) or EZH2 siRNA for 48 h, followed by TSA treatment for 24 h. Changes of CDKN1C, EZH2 and H3K27me3
protein levels were determined by Western blot analysis.
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Addition of Aza to DZNep/TSA combination further
increases CDKN1C expression in BT-474 cells
In BT-474 cells, the upstream region of CDKN1C promoter (M1)
was detected to be hypermethylated compared to that in SK-BR-3
cells (Figure 1B). We next examined whether addition of Aza in
these cells would further enhance the level of CDKN1C induction
by DZNep/TSA. BT-474 and SK-BR-3 cells were thus treated
with DZNep/TSA in the presence or absence of Aza for 72 h and
the changes in CDKN1C expression were determined by
quantitative RT-PCR analysis. Figure 5A shows the triple
treatment in BT-474 cells induced a 27-fold induction of CDKN1C
expression compared to a 12-fold induction by DZNep/TSA. By
contrast, addition of Aza in SB-KR-3 cells did not further increase
the level of CDKN1C which is already strongly induced by
DZNep/TSA. However, MSP analysis revealed that the Aza
treatment in BT-474 cells for up to 96 h did not in fact reduce the
DNA methylation in the M1 region (Figure 5B), suggesting that
the further enhanced induction of CDKN1C in BT-474 cells upon
the triple combination treatment is not the result of DNA
It has been recently reported that Aza can act independently of
its ability to inhibit DNA methylation to reactivate gene expression
by removing H3K9me2 . Since CDKN1C is marked by
H3K9me2 in BT-474 cells, we next examined if H3K9me2 in
CDKN1C, together with other histone marks, have changed after
the above treatments. The results show that H3K9me2 level was
markedly reduced in cells treated with the three-drug combina-
tion, compared with cells treated with DZNep/TSA, while
H3K27me3 levels remained the same (Figure 5C). Thus, the
further increase in CDKN1C expression upon treatment with the
triple drug combination in BT-474 cells might be due to additional
inhibition of H3K9me2. This is consistent with the fact that Aza
treatment did not further increase CDKN1C expression in SK-BR-
3 in which CDKN1C is not marked by H3K9m2. Taken together,
we conclude that histone modifications play a predominate role in
epigenetic repression of CDKN1C in breast cancer cells.
EZH2-mediated CDKN1C repression predicts breast
cancer clinical outcome
Given the involvement of EZH2 in CDKN1C repression, we took
the advantage of Oncomine microarray database and asked
whether their expression levels are reversely correlated in human
cancer. The search results revealed that EZH2 is consistently
upregulated in multiple human cancer types including breast
Figure 5. Addition of Aza to DZNep/TSA combination further enhances CDKN1C expression in BT-474 cells. (A) Changes of CDKN1C
expression in BT-474 and SK-BR-3 cells after treatment with DZNep/TSA (D/T) or Aza/DZNep/TSA (D/T/A) were determined by quantitative RT-PCR. (B)
MSP analysis of the methylation status of M1 region in BT-474 cells treated with Aza or DZNep/TSA/Aza for indicated times. (C) ChIP analysis showing
the changes of H3K9me2, H3K27me3, and H3K9/14ac at CDKN1C locus in BT-474 cells untreated and treated with DZNep/TSA or DZNep/TSA/Aza.
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cancer, while CDKN1C is downregulated in these tumors
(Figure 6A). This data suggest that EZH2-mediated CDKN1C
repression might operate widely in human cancers, indicating the
potential broad application of pharmacological inhibition of
EZH2 for reactivating CDKN1C for cancer treatment.
Enhanced EZH2 expression has been previously shown to
correlate with poor prognosis of breast cancer [8,9]. We next
determined whether CDKN1C as an EZH2-repressed target is
reversely associated with the disease outcome. To this end, we
examined the publicly available microarray dataset from two
breast cancer cohorts with annotated clinical outcome, Uppsala
(,251 patients) and Stockholm (,159 patients) [32,33]. The Cox-
proportional hazards regression analysis of both disease free
survival (DFS) and metastasis-free survival (DMFS) in both data
sets showed that EZH2 and CDKN1C are consistently associated
with the disease outcome in a reverse manner (Table S1).
Specifically, as shown in the Kaplan-Meier plots of Figure 6B,
significant poorer outcome in disease free survival (DFS;
P=0.004227 and P=0.005694) were observed between Stock-
holm patients with a higher EZH2 and a lower CDKN1C,
respectively. This indicates that both EZH2 and its target gene
CDKN1C can be used to predict breast cancer outcome. In
Figure 6. Levels of CDKN1C expression predict the clinical outcome of breast cancer patients. (A) Upregulation of EZH2 and
downregulation of CDKN1C expression are shown in multiple cancer types with indicated P values by comparing the tumor (red) and the adjacent
normal (blue) tissues. The data is extracted from Oncomine microarray database (www.oncomine.org). Breast cancer patients were ranked according
to different levels of EZH2 or CDKN1C as described in Methods. (B) Kaplan-Meier survival plots of disease-free survival (DFS) from Stockholm cohort
(Miller, et. al., GEO ID GSE3494). Patients with higher EZH2 or CDKN1C expression are highlighted in red, while patients with lower EZH2 or CDKN1C
expression are highlighted in green. (C) Kaplan-Meier survival plots of disease-free survival (DFS) from Stockholm cohort. Patients with higher EZH2
but lower CDKN1C are highlighted in green, while patients with lower EZH2 but higher CDKN1C are highlighted in red.
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comparison, no other CDKN family genes could significantly
separate the patients by survival (data not shown), consistent with
the hypothesis that these genes might not be targeted by EZH2 in
breast cancer. Furthermore, we show that breast cancer expressing
both higher EZH2 and lower CDKN1C show a much poorer
disease-free survival rate (P=0.001046) compared to patients with
lower EZH2 and higher CDKN1C (Figure 6C). Thus, the
combination of both EZH2 and CDKN1C may be more predictive
of breast cancer recurrence than either one alone. This result
suggests that assessing both EZH2 and its target gene may be more
accurate to measure the activity of EZH2 pathway. This data also
has implications in patient stratification for potential clinical use of
EZH2-inhibiting agents such as DZNep. We predict that breast
cancer patients with higher EZH2 and lower CDKN1C might
receive the greatest benefit from cancer therapeutic targeting of
EZH2-mediated gene repression.
Our findings suggest that Polycomb protein EZH2-mediated
H3K27me3 might be the key chromatin mark associated with the
transcriptional repression of CDKN1C in breast cancer cells. It also
indicates that EZH2 functions through cooperation with histone
deacetylation for effective repression of its target genes. Lack of
dominate effect of DNA methylation, together with RT-PCR
analysis, indicate that CDKN1C expression in breast cancer is
maintained at low or basal levels rather than completely silenced.
Indeed, CDKN1C can be only modestly induced by Aza but
strongly induced by DZNep/TSA that targets both EZH2-
mediated histone methylation and deacetylation. This finding
indicates that DZNep/TSA might preferentially target genes
whose repression is associated with H3K27me3 but not those
completely silenced by DNA methylation. This is consistent with a
recent study showing that EZH2 functions to maintain the low
expression of target genes that lack DNA methylation but is not
required for maintaining gene silencing predominantly caused by
DNA methylation .
We show that CDKN1C carries both repressive (H3K27me3)
and activating (H3K4me3) chromatin marks, revealing a ‘‘biva-
lent’’ chromatin state. Moreover, recent studies have shown that
methylation of H3K4 is reversely associated with DNA methyl-
ation of gene promoters [35,36,37] and that DNMT only
recognizes unmethylated H3K4 to induce DNA methylation
. Thus, the detection of a strong H3K4me3 in the CDKN1C
promoter is consistent with the lack of DNA methylation in the
vicinity of the CDKN1C promoter as we observed in breast cancer
cells. A ‘bivalent’ chromatin mark (H3K27me3 and H3K4me3)
has been originally described in embryonic stem (ES) cells that is
generally associated with genes transcribed in low levels [28,39].
Recent studies have also indicated its existence in differentiated
cells [26,29]. Many tumor suppressor genes carrying a bivalent
chromatin mark in ES cells are subject to further DNA
methylation for stable gene silencing in cancer cells [40,41,42].
It has been proposed that during this malignant process DNA
methylation confers a concomitant loss of H3K4 methylation after
a bivalent chromatin is converted to a monovalent state
[17,41,43]. The retention of the bivalent domain without DNA
methylation indicates that this epigenetic mechanism also exists in
cancer cells, which might also contribute to the malignant
transformation together with the well-characterized DNA meth-
ylation. This finding has obvious therapeutic implications. As
described above, these bivalent genes that are lowly transcribed
(not completely silenced) might be most susceptible to histone
modifying compounds such as DZNep/TSA as illustrated in this
study, but not to DNA demethylating agents. These genes might
contain important tumor suppressors that have been overlooked
historically. We therefore speculate that the above described
epigenetic treatment might open a new avenue for cancer
therapeutics that aim to target this aberrant epigenetic process
that has been previously under-appreciated in cancer.
Our comprehensive epigenetic analysis of these observations
mechanisms collaborate to repress gene expression in cancer
cells. Furthermore, our results indicate that DNA methylation
and EZH2-H3K27me3 might not be mechanistically linked as
previously suggested . In fact, we did not detect methylated
DNA in EZH2-H2K27me3 enriched region in CDKN1C.
Conversely, in the CDKN1C promoter region that appears to
be methylated (such as in BT-474 cells), no EZH2-H3K27me3
was detected. This finding is consistent with the recent genomic
scale analysis showing that H3K27me3-mediated gene silencing
and DNA methylation target different set of genes [15,17].
Despite the presence of both epigenetic events in the CDKN1C
locus in BT-474 cells, EZH2-H3K27me3 appears to be the
predominate one that is in synergy with histone deacetylation to
repress CDKN1C expression. Targeting EZH2-H3K27me3 by
DZNep would presumably synergize with HDAC inhibitors
and/or Aza to maximally restore the tumor suppressor function
Finally, we show that the downregulation of CDKN1C by EZH2
in breast cancer is associated with a poor disease outcome.
Mechanistically, this finding is consistent with the previous
knowledge that overexpression of EZH2 correlates with a poor
breast cancer prognosis. Moreover, a recent report shows that
Polycomb repression signature genes can predict clinical outcome
of multiple solid tumors . These findings thus suggest the
utility of EZH2 target genes as prognostic marks. We further show
that the combination of EZH2 and CDKN1C gives a better
prediction of disease outcome that achieved through either gene
alone. This might suggest that measuring both EZH2 and its target
gene activity as the readout might be more accurate in predicting
the activity of this silencing pathway. Indeed, our data suggest that
EZH2 alone is insufficient but requires other factors such as
HDAC to assure a full functionally in repression of certain genes.
Therapeutically, this information may provide significant values in
patient stratification for potential clinical use of EZH2 inhibitors as
anti-cancer agents. Such agents may be particularly useful for
patients with breast cancer harboring EZH2-mediaed repression of
CDKN1C. Furthermore, we show that upregulation of EZH2 and
the corresponding downregulation of CDKN1C occur in multiple
human cancers. This may suggest that the pharmacological
approach we have demonstrated for inhibiting EZH2 and
reactivating CDKN1C might have broad application for cancer
that multiple epigenetic
Cells and drug treatment
Cell lines used in this study were all obtained from the American
Type Culture Collection (ATCC). Cells were maintained in
appropriate medium conditions until harvested. For drug
treatment, cells were treated with 5 mM DZNep (obtained from
National Cancer Institute of USA) or 5 mM 5-aza-29-deoxycyti-
dine (5-AzaC; Sigma) for 72 h, and trichostatin A (TSA; Sigma) at
100 nM for 24 h. For 5-AzaC treatment, the medium was
replaced with freshly added 5-AzaC for every 24 h. For co-
treatment of cells with 5-DZNep and TSA, DZNep was added for
48 h, and then treated with TSA for additional 24 h.
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The siRNA targeting EZH2 and non-targeting control were
purchase from from 1st BASE Pte Led (Singapore) as following
sequence: 59-GACUCUGAAUGCAGUUGCU -39. SK-BR-3
cells were transfected with 100 nM final concentration of siRNA
duplexes using Lipofectamine 2000 (Invitrogen) following the
Histone extraction and immunoblot analysis
Whole cell extract was prepared as previously . Histone
proteins were acid extracted following Upstate protocol. Western
blots were probed with the following antibodies: anti-H3K27me3
(07-449), anti-H3K9me3 (07-442), anti-H3K9/K14ac (06-599),
anti-H3K4me3 (07-473), and anti-EZH2 (AC22) were purchased
from Upstate. Anti-H3 (3H1) was from Cell Signaling and anti-
EZH2 and anti-p57 were from Santa Cruz Biotechnology.
Quantitative real-time PCR and RT-PCR
Total RNA was isolated from cell lines using Trizol (Invitrogen)
and purified with the RNAeasy Mini Kit (Qiagen). Reverse
transcription was performed using an RNA Amplification kit
(Ambion). Quantitative real-time PCR was performed on a
PRISM 7900 Sequence Detection System (Applied Biosystems)
using TaqMan probes (Applied Biosystems). Samples were
normalized to the levels of GAPDH mRNA. For PCR 100 ng of
cDNA was used and the primer sequences are shown in Table S2.
DNA methylation analysis
analysis after bisulfited modification (EZ DNA Methylation-Gold
Kit, Zymo Research,) and followed by methylation-specific PCR
(MSP). Primer sequences are shown in Supplementary Table 2.
Chromatin Immunoprecipitation (ChIP) assays
ChIP assay was performed as previously with a modified
protocol that uses QIAquick PCR purification kit (Qiagen) to
purify precipitated DNA. The immunoprecipitapted DNA was
quantitated by real-time quantitative PCR using PRISM 7900
Sequence Detection System (Applied Biosystems). Primer sets are
designed to amplify approximately 200 bp around the indicated
region. The following antibodies were used in this study: anti-
H3K27me3 (Upstate), anti-H3K9me3 (Abcam), anti-EZH2 (Up-
Quantification of ChIP results was performed relative to the input
amount. The sequences of the PCR primers are shown in Table
Data set and survival analysis
The breast cancer data set from Uppsala and Stockholm
cohorts with relevant clinical information have been described
previously [32,33]. The expression of probes of each CDKN gene
was averaged and transformed to z-score. The positive z-score was
treated as higher expression and the negative z-score was treated
lower expression. Using the survival event status and time
information, we computed the survival association of expression
status (high/low expression) using Cox-Proportional Hazards
model implementation (coxph) available in R-library ‘‘survival’’.
Kaplan-Meier survival analysis was used for the analysis of clinical
outcome. For the combination of EZH2 and CDKN1C, the average
expressions of both EZH2 and CDKN1C genes were separately
transformed to z-score. The tumors with opposite signs of z-scores
of the EZH2 and CDKN1C were included in the analysis and the
tumors with same signs of z-scores were left out of the analysis.
Tumors in which EZH2 up or positive EZH2 z-score and CDKN1C
down or negative CDKN1C z-score were classified as class with
label ‘‘0’’. Tumors in which EZH2 down or negative EZH2 z-score
and CDKN1C up or positive CDKN1C z-score were classified as
class with label ‘‘1’’. Similar survival analysis was carried out using
cox proportional hazards model fitting and Kaplan-Meier plots.
Found at: doi:10.1371/journal.pone.0005011.s001 (0.02 MB
Found at: doi:10.1371/journal.pone.0005011.s002 (0.03 MB
Conceived and designed the experiments: XY RGS QY. Performed the
experiments: XY MA. Analyzed the data: XY RKMK. Contributed
reagents/materials/analysis tools: RKMK FS KY LDM PT. Wrote the
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