university of copenhagen
Targeting glioma stem-like cell survival and chemoresistance through inhibition of
lysine-specific histone demethylase KDM2B
Staberg, Mikkel; Rasmussen, Rikke Darling; Michaelsen, Signe Regner; Pedersen, Henriette;
Jensen, Kamilla Ellermann; Villingshøj, Mette; Skjoth-Rasmussen, Jane; Brennum, Jannick;
Vitting-Seerup, Kristoffer; Poulsen, Hans Skovgaard; Hamerlik, Petra
Published in:
Molecular Oncology
DOI:
10.1002/1878-0261.12174
Publication date:
2018
Document version
Publisher's PDF, also known as Version of record
Document license:
CC BY
Citation for published version (APA):
Staberg, M., Rasmussen, R. D., Michaelsen, S. R., Pedersen, H., Jensen, K. E., Villingshøj, M., ... Hamerlik, P.
(2018). Targeting glioma stem-like cell survival and chemoresistance through inhibition of lysine-specific histone
demethylase KDM2B. Molecular Oncology, 12(3), 406-420. https://doi.org/10.1002/1878-0261.12174
Download date: 14. Jun. 2020
Targeting glioma stem-like cell survival and
chemoresistance through inhibition of lysine-specific
histone demethylase KDM2B
Mikkel Staberg1,2, Rikke Darling Rasmussen2, Signe Regner Michaelsen1,2, Henriette Pedersen2,
Kamilla Ellermann Jensen2, Mette Villingshøj1, Jane Skjoth-Rasmussen3, Jannick Brennum3,
Kristoffer Vitting-Seerup2, Hans Skovgaard Poulsen1 and Petra Hamerlik2
1 Department of Radiation Biology, The Finsen Center, Copenhagen University Hospital, Denmark
2 Brain Tumor Biology Group, Danish Cancer Society Research Center, Copenhagen, Denmark
3 Department of Neurosurgery, Copenhagen University Hospital, Denmark
Keywords
cancer stem-like cell; chemoresistance;
epigenetics; glioblastoma; histone
demethylase
Correspondence
P. Hamerlik, Brain Tumor Biology Group,
Danish Cancer Society Research Center,
Copenhagen, Denmark
Fax: +45 35 25 77 21
Tel: +45 35 25 74 05
E-mail: pkn@cancer.dk
(Received 6 September 2017, revised 18
December 2017, accepted 3 January 2018 ,
available online 12 February 2018)
Glioblastoma (GBM) ranks among the most lethal cancers, with current
therapies offering only palliation. Inter- and intrapatient heterogeneity is a
hallmark of GBM, with epigenetically distinct cancer stem-like cells (CSCs)
at the apex. Targeting GSCs remains a challenging task because of their
unique biology, resemblance to normal neural stem/progenitor cells, and
resistance to standard cytotoxic therapy. Here, we find that the chromatin
regulator, JmjC domain histone H3K36me2/me1 demethylase KDM2B, is
highly expressed in glioblastoma surgical specimens compared to normal
brain. Targeting KDM2B function genetically or pharmacologically
impaired the survival of patient-derived primary glioblastoma cells through
the induction of DNA damage and apoptosis, sensitizing them to
chemotherapy. KDM2B loss decreased the GSC pool, which was potentiated by coadministration of chemotherapy. Collectively, our results demonstrate KDM2B is crucial for glioblastoma maintenance, with inhibition
causing loss of GSC survival, genomic stability, and chemoresistance.
doi:10.1002/1878-0261.12174
1. Introduction
Glioblastoma (GBM) is the most aggressive primary
central nervous system (CNS) tumor and is particularly known for its heterogeneity, robust vascularization, and rampant genomic instability. Despite recent
advances in standard of care, the median survival of
glioblastoma patients in clinical trial remains at
approximately 12–15 months (Black et al., 2012; Gil
et al., 2005; Stupp et al., 2005). Therapeutic resistance
and high recurrence rates in GBM have been attributed to a rare population of cancer stem-like cells
(CSCs) (GBM-derived CSCs—GSCs), which can be
prospectively isolated using a number of molecular
markers with prominin-1 (CD133) being among the
most commonly used in current practice (Bao et al.,
2006; Rich, 2016; Singh et al., 2004).
The genome is under constant assault by endogenous factors—such as reactive oxygen species, metabolic intermediates, replication errors; and exogenous
factors, such as ultraviolet (UV) radiation and environmental toxins (Bartek et al., 2007; Bartkova et al.,
2005). If left unrepaired, DNA double-strand breaks
(DSBs), caused by these insults, can eventually lead to
malignant transformation. DSB repair is orchestrated
within the complex organization of chromatin, where
chromatin structure and nucleosome assembly represent a significant barrier to the efficient recognition
Abbreviations
CCNU, lomustine; CI, combination index; GBM, glioblastoma; GSC, glioblastoma stem-like cell; KDM, lysine-specific histone demethylase;
VP-16, etoposide.
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This is an open access article under the terms of the Creative Commons Attribution License, which permits use,
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M. Staberg et al.
and repair of DSBs (Price and D’Andrea, 2013). Thus,
chromatin remodeling and DNA repair are intimately
linked and their functional interplay is reflected in the
genomic stability of cells. The contribution of epigenetic changes to GBM biology has been studied mostly
in terms of aberrant promoter methylation-induced
gene silencing (Maleszewska and Kaminska, 2013);
however, emerging evidence points to the role of chromatin remodeling in genome stability maintenance,
thereby raising considerable interest in chromatinmodifying enzymes for targeted therapies (Mack et al.,
2016).
Histone methylation occurs naturally throughout
the genome, mostly at the CpG islands, a subset of
which is bound by polycomb-group proteins, including
polycomb repressive complex 1 (PRC1). KDM2B, a
Jumonji (JmjC) domain histone histone 3 lysine 36
(H3K36) di-demethylase, is highly expressed in embryonic stem cells, hematopoietic stem cells, leukemia,
and many solid cancers (Farcas et al., 2012; He et al.,
2008, 2011, 2013; Inagaki et al., 2015; Karoopongse
et al., 2014; Tzatsos et al., 2009, 2013). In addition to
its role in H3K36 and H3K4me3 demethylation,
KDM2B recruits PRC1 to CpG islands (Farcas et al.,
2012), thereby repressing the expression of genes regulating senescence, apoptosis, ribosomal RNA expression, hematopoietic stem cell self-renewal, and the
proper generation of the neural tube in vivo (Andricovich et al., 2016; Liang et al., 2012; Tzatsos et al.,
2009, 2013).
In this study, we demonstrate that KDM2B plays
an important role in GBM cell survival, DNA repair,
and maintenance of GSC pools. Importantly, the
impact of KDM2B loss or inhibition on the survival
and DNA repair capacity of GBM cells is further
potentiated when combined with either lomustine
(CCNU) or etoposide (VP-16), chemotherapeutics routinely used in therapeutic management of recurrent
disease (Taal et al., 2014; Wick et al., 2017).
2. Materials and methods
2.1. Primary cell cultures and glioma patient
tissue
About 4121 and 4302 cells were a generous gift from
J.N. Rich (University of California, San Diego, CA,
USA). IN84 cells were a generous gift from I. Nakano
(University of Alabama, Birmingham, Alabama,
USA). Primary glioblastoma cell cultures (T115, 1587,
T131, T133, T140, T143, T91, and 017) were established upon the approval by Danish Ethical Committee/Danish Data Protection Agency (2006-41-6979/KF-
KDM2B targeting sensitizes glioblastoma to chemotherapy
01-327718). Signed informed consents were obtained
24 h prior surgery for each patient. Primary patientderived glioblastoma cell cultures were cultured in
stem cell-permissive Neurobasal-A media (NB)
(Invitrogen, Taastrup, Denmark; #10888-022) supplemented with B27 (#12587-010), bFGF (10 ngmL1,
#13256-029), EGF (10 ngmL1, #PHG0311), Glutamax, penicillin (50 UmL1), and streptomycin
(50 lgmL1, #15070-063) (all from Invitrogen) with
5% CO2 at 37 °C. Glioblastoma patient tissue samples
used for protein lysate preparation were collected at
surgery and stored in liquid nitrogen before use. Normal human astrocytes (#CC-2565) were obtained from
Lonza and grown in astrocyte growth medium (AGM)
with provided supplements. Prior each experiment,
cells were dissociated using Accutase (Thermo-Fisher,
Hvidovre, Denmark, #00-4555-56) and counted using
a NucleoCounter NC-200 (ChemoMetec, Lillerød,
Denmark). Cells were seeded in appropriate media and
treated with lomustine (CCNU, #L5918), GSK-J4
(#SML0701) from Sigma-Aldrich (St. Louis, MO,
USA), etoposide (VP-16; 20 mgmL1, Meda, Denmark) or a vehicle control (DMSO).
2.2. siRNA transfection
For siRNA transfection experiments, constructs targeting KDM2B (KDM2B-1 and KDM2B-2; #1299001)
and siCTRL (si-negative control duplex, #462001)
were obtained from Thermo Fisher Scientific. Cells
were transfected with 50 nM of siKDM2B or siCTRL
using Lipofectamine RNAiMAX (#1377150) in
Opti-MEM reduced serum medium (Thermo Fischer
Scientific).
2.3. Immunoblot analysis
Cells were lysed in whole-cell lysis buffer (50 mM Tris/
HCl, 10% glycerol, 2% SDS) or modified RIPA buffer
(50 mM Tris/HCl, 1% NP-40, 0.25% Na-deoxycholate,
150 mM NaCl, 1 mM EDTA) supplemented with protease and phosphatase inhibitors, and protein concentrations were estimated by BCA protein assay (Pierce
Biotechnology, Rockford, IL, USA). Protein samples
were separated on 4–12% NuPAGE Bis/Tris gels
(NP0336BOX) (Invitrogen) and electroblotted onto
nitrocellulose membranes (Invitrogen, LC2000). The
membranes were blocked for 1 h at room temperature
(RT) and incubated with primary antibodies in 5%
nonfat milk overnight (ON) at 4 °C followed by horseradish peroxidase (HRP)-conjugated secondary antibodies for 1 h at RT. Blots were developed using
either the SuperSignal West Dura Extended Duration
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KDM2B targeting sensitizes glioblastoma to chemotherapy
Substrate (#34075) or the SuperSignal West Femto
Maximum Sensitivity Substrate (#34095) from Thermo
Fisher and developed with the Biospectrum Imaging
System (UVP, Upland, CA, USA). Primary antibodies
used are shown in Table S1.
2.4. Viability assays
The MTT assay (Sigma M-5655) was employed
(Figs 1F, 4, 5A and 6) as previously described (Staberg
et al., 2017). Cells were plated at a density of 1 9 104
cells per well in 96-well plates, transfected with siRNA
constructs, or treated with GSK-J4, lomustine, etoposide, or DMSO. After 72 h of incubation, MTT solution was administered and incubated for 4 h followed
by addition of 100 lL solubilization buffer. The following day, absorbance was measured at 570 nm with
690 nm as a background reference using a Synergy2
microplate reader with GEN5, Microplate Data Collection and Analysis Software (Biotek, Winooski, VT,
USA). CellTiter-Glo Luminescent Cell Viability Assay
(Promega, Madison, WI, USA ) was used in Figs 2E,
and 5E), where viability was calculated as relative fold
change in ATP production with each group internally
normalized to the respective vehicle control.
2.5. Quantitative real-time PCR
Total RNA was purified from GBM patient tissue and
GBM cell pellets using the QIAshredder (79654) and
RNeasy Mini kit (#74104; Qiagen, Copenhagen, Denmark). Synthesis of cDNA and qRT/PCRs was performed using the SuperscriptTM III Platinum Two
Step qRT-PCR kit with SYBR Green (Invitrogen,
#11735-032). Gene expression levels were determined
applying the comparative Ct method and normalized
to expression of three housekeeping genes (TOP1,
EIF4A2, and CYC1) included in the human geNorm
housekeeping gene selection kit (Primerdesign). Primers used for estimation of mRNA levels were as follows: KDM2B forward; 50 -CAT GGA GTG CTC
CAT CTG CAA TG-30 , KDM2B reverse; 50 -ACT
TCG GAC ACT CCC AGC AGT T-30 . Sox2 forward;
50 -GGC AGC TAC AGC ATG ATG C-30 , Sox2
reverse; 50 -TCG GAC TTG ACC ACC GAA C-30 .
Primers were obtained from DNA Technology A/S.
M. Staberg et al.
After 48 h, cells were fixed and stained for anticH2AX Ser139 (Millipore, Copenhagen, Denmark,
#05-636). Nuclei of the cells were counterstained with
DAPI, and pictures were acquired on a Zeiss LSM 700
confocal microscope (Birkerød, Denmark). For quantification, 100 nonoverlapping images were acquired
for each condition and scored for > 5 foci per cell
using the ScanR screening station (Olympus, Ballerup,
Denmark). At least 1000 cells were scored and processed using the SCANR analysis software (Olympus).
2.7. S-phase cell quantification using ScanR
microscopy analysis
Glioblastoma cells were plated on precoated (Geltrex;
Thermo Fisher Scientific) coverslips, transfected with
respective siRNA and incubated for 72 h. Prior fixation, cells were pulse-labeled with 10 lM (5-ethyl-20 deoxyuridine; EdU) for 20 min and then processed
using Click-iT EdU Alexa Fluor 647 Flow Cytometry
Assay Kit (Invitrogen) following manufacturer’s
instructions. Nuclei of the cells were counterstained
with DAPI. For S-phase quantification, 100 nonoverlapping images were acquired for each condition and
at least 1000 cells were scored and processed using the
SCANR analysis software (Olympus). To quantify the
percentage of S-phase cells, single cells were gated
based on DAPI—area signal intensity, circularity (to
exclude cell debris and doublets), and EdU positivity.
2.8. Magnetic-activated cell sorting
Enrichment of CD133-positive GBM cells was accomplished using magnetic-activated cell sorting as per the
manufacturer’s recommendations (MACS; Miltenyi
Biotec, Bergisch Gladbach, Germany). CD133-positive
cells were maintained as neurospheres in stem cell-permissive Neurobasal-A media (NB) (Invitrogen,
#10888-022) supplemented with B27 (#12587-010),
bFGF (10 ngmL1, #13256-029), EGF (10 ngmL1,
#PHG0311), Glutamax, penicillin (50 UmL1), and
streptomycin (50 lgmL1, #15070-063) (all from
Invitrogen) with 5% CO2 at 37 °C., whereas CD133negative cells (non-GSCs) were maintained in DMEM
supplemented with 10% FBS, penicillin (50 UmL1),
and streptomycin (50 lgmL1, #15070-063) (all from
Invitrogen).
2.6. Immunofluorescence imaging
For cH2AX staining and quantification, GBM cells
were plated on precoated (Geltrex; Thermo Fisher Scientific) coverslips and either transfected with siRNA
constructs, or treated with GSK-J4 or vehicle control.
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2.9. Extreme limiting dilution assay
Glioblastoma cells were dissociated using Accutase,
counted, and plated in 96-well plates at cell densities
ranging from 1 to 50 cells/well (16 replicate wells per
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M. Staberg et al.
KDM2B targeting sensitizes glioblastoma to chemotherapy
A
B
C
D
E
F
G
Fig. 1. siRNA-mediated knockdown of KDM2B impairs glioblastoma cell viability and proliferation. (A) Immunoblot analysis of KDM2B and
GAPDH (loading control) in glioblastoma cells compared to normal human astrocytes (NHA). (B) Immunoblot analysis of KDM2B and tubulin
(loading control) in tissue extracts from glioblastoma samples compared to normal brain (NB). (C) qRT/PCR analysis of relative KDM2B
mRNA expression in glioblastoma cells 48 h post-transfection with either siCTRL or two independent siRNA constructs targeting KDM2B
(siKDM2B-1 and siKDM2B-2). Data are presented as mean SEM, n = 4. **P < 0.01; ***P < 0.001 by an unpaired Student’s t-test. (D)
Immunoblot analysis of KDM2B and GAPDH (loading control) in tumor cells 72 h post-transfection with siCTRL, siKDM2B-1, or siKDM2B-2.
(E) Immunoblot analysis of dimethylation of histone H3 at lysine 36 (H3K36me2) and tubulin (loading control) in 4121 glioblastoma cells 48 h
post-siRNA transfection. (F) Relative cell viability of glioblastoma cells over time transfected with siCTRL, siKDM2B-1, or siKDM2B-2
constructs analyzed by MTT assay. Data presented as mean SEM, n = 3. ***P < 0.001 by two-way ANOVA. (G) ScanR microscopy- and
software (Olympus)-based quantification of S-phase (%, proliferative) cells for 4121, 1587 and T115 glioblastoma lines upon transfection
with either siCTRL, KDM2B-1, or KDM2B-2 constructs. Data presented as mean SD, ***P < 0.001 by one-way ANOVA followed by
Dunnett’s post hoc test.
condition). Transfected cells or cells treated with
GSK-J4, CCNU, or VP-16 were incubated at 37 °C
for 10 days. The formation of tumor spheres was evaluated after 10 days, and each well was analyzed for
presence or absence of at least one tumor sphere. The
calculation of estimated stem cell frequency in each
condition was made by employing the extreme limiting
dilution analysis (Hu and Smyth, 2009).
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KDM2B targeting sensitizes glioblastoma to chemotherapy
M. Staberg et al.
A
B
C
D
E
Fig. 2. KDM2B is preferentially expressed by GBM-derived cancer stem-like cells (GSCs) and is crucial for their maintenance. (A)
Immunoblot analysis of KDM2B, SOX2, and GFAP expression in acutely dissociated and MACS-sorted GSCs and non-GSCs. Tubulin (4121,
1587, T91) or GAPDH (IN84, 4302) was used as loading control. (B) Immunoblot analysis of EZH2, SOX2, and GAPDH (loading control) in
GBM cells 72 h post-transfection with siCTRL, siKDM2B-1, or siKDM2B-2. (C) Immunoblot analysis of KDM2B, GFAP, SOX2, and GAPDH
(loading control) in GBM cells that were transfected with either siCTRL or siKDM2B-2 and subjected to a differentiation assay (exposure to
10% fetal bovine serum) over a period of 3 days. (D) Glioblastoma self-renewal was analyzed by in vitro extreme limiting dilution assay
(ELDA). **P < 0.01; ***P < 0.001 analyzed by pairwise chi-squared test. (E) Cell viability of GSCs (4121+) versus non-GSCs (4121-) upon
transfection with siCTRL or siKDM2B-2 and immunoblot analysis of KDM2B knockdown efficiency. Tubulin served as loading control.
2.10. Combination Index calculations
To assess the efficacy of combinational treatments on
cell viability (MTT), the free available COMPUSYN software for calculation of a combination index (CI) was
used (Chou, 2010). From this, a CI > 1.1 indicates
antagonism, a CI of 0.9-1.1 indicates additivity, and a
CI < 0.9 indicates synergy. The CI values calculated
410
were obtained from at least three independent experiments and presented as mean standard error of the
mean.
2.11. Statistics
Data in figures are presented as mean standard
deviation (SD) or standard error of mean (SEM). All
Molecular Oncology 12 (2018) 406–420 ª 2018 Danish Cancer Society. Published by FEBS Press and John Wiley & Sons Ltd.
M. Staberg et al.
statistical analysis and creation of figures were performed using GRAPHPAD PRISM (v. 7.02, GraphPad, San
Diego, CA, USA).
3. Results
3.1. KDM2B is required for glioblastoma cell
survival
Based on the overexpression and oncogenic function
of KDM2B in systemic cancers that contain cancer
stem cells (Kottakis et al., 2014; Tzatsos et al., 2013;
Ueda et al., 2015), we investigated KDM2B as a
molecular target in glioblastoma. First, we analyzed its
expression in a cohort of primary glioblastoma cell
cultures and tissue extracts. qRT/PCR and immunoblot analysis confirmed the expression of KDM2B
(Figs 1A and S1A). KDM2B protein levels were elevated in five of eight primary cell cultures compared to
nonmalignant control normal human astrocyte cells
(NHA). To exclude the possibility that elevated
KDM2B expression was a cell culture artifact, we performed qRT/PCR and immunoblot analysis on total
RNA and protein isolated directly from primary
tumor tissue biopsies. KDM2B expression varied
among the individual GBM patients, but was overall
higher than that of normal brain control(s) (Figs 1B
and S1B,C).
To interrogate the functional role of KDM2B in
glioblastoma biology, we selected three representative
primary cultures: KDM2B—high-expressing cells
(4121, 1587) and KDM2B—low-expressing cells
(T115). Successful siRNA-mediated knockdown of
KDM2B was confirmed by qRT/PCR and immunoblot analysis (Fig. 1C,D). In addition, KDM2B knockdown was functionally by validated by an increase in
the methylation mark inhibited by KDM2B, histone 3
lysine 36 dimethyl, H3K36me2 (Fig. 1E). KDM2B loss
impaired glioblastoma cell viability, with greater
impact in cells that express higher baseline levels of
KDM2B (Fig. 1F). Moreover, KDM2B depletion
reduced the fraction of actively proliferating cells (Sphase) (Fig. 1G).
3.2. Targeting KDM2B ablates glioblastoma
cancer stem-like cells
Widespread epigenetic reprogramming occurs during
both stem cell differentiation and malignant transformation (Amente et al., 2013). Recent findings indicate
that chromatin dysregulation is likely to play a crucial
role in GBM and the dependence of GSCs on epigenetic regulators offers an opportunity to target their
KDM2B targeting sensitizes glioblastoma to chemotherapy
self-renewal capacity (Jin et al., 2017; Miller et al.,
2017). Based on prior reports that GSCs are the most
aggressive cellular population responsible for glioblastoma recurrence (Bao et al., 2006; Rich, 2016) and the
role of numerous KDMs in stem cell maintenance
(Amente et al., 2013; Andricovich et al., 2016; He
et al., 2011, 2013), we hypothesized specific function of
KDM2B in GSCs. Prospective enrichment of GSCs
through the cell surface marker, CD133, revealed preferential expression of KDM2B in GSCs compared to
non-GSCs (Fig. 2A). To link KDM2B to stem cell
regulatory pathways, we interrogated core stem cell
regulatory pathways that have been linked to GSC
maintenance. Targeting KDM2B decreased both the
stem cell transcription factor, SOX2, and the chromatin regulatory enzyme, EZH2 (Fig. 2B). Furthermore, the loss of KDM2B led to impaired
differentiation capacity of GSCs (Fig. 2C), their selfrenewal (Fig. 2D), and viability (Fig. 2E). Validation
in a broader cohort of patients was supported by an
in silico analysis of the REMBRANDT glioma dataset, which showed a strong positive correlation
between KDM2B expression with both CD133 and
SOX2 (Fig. S2A). Collectively, these data, together
with the observed reduction in GSC frequency after
KDM2B knockdown, are consistent with a crucial role
of KDM2B in GSC maintenance.
3.3. KDM2B loss induces DNA damage and
apoptosis, and sensitizes glioblastoma cells to
chemotherapy
Open chromatin augments sensitivity to DNA damage,
and the KDM2 family regulates DNA damage repair
and correlates with treatment resistance in several cancer types (Banelli et al., 2015; Ramadoss et al., 2017).
To interrogate KDM2B in the genomic stability and
DNA repair capacity of glioblastoma, we targeted
KDM2B with two nonoverlapping siRNA species
(siKDM2B-1 and siKDM2B-2). KDM2B loss resulted
in a continuous increase in c-histone 2AX (cH2AX)
foci count over a period of 96 h, an indication of
DNA damage accumulation due to impaired DNA
repair (Fig. 3A,B). Next, we exposed GBM cells transfected with siCTRL or siKDM2B-2 to ionizing radiation (IR, 3 Gy) and assessed their DNA repair
capacity at 6 and 24 h post-IR. As shown in Fig. 3C,
in addition to baseline increase in c-histone 2AX
(cH2AX) foci count, the loss of KDM2B impaired the
ability of these cells to repair IR-induced DNA damage. Concordant with reduced proliferation and prevalence of double-stranded DNA breaks (DSBs),
KDM2B knockdown induced p21CIP1/WAF1 levels and
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KDM2B targeting sensitizes glioblastoma to chemotherapy
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increased apoptosis, measured by elevated cleavage of
PARP and caspase-3 (Fig. 3D).
The heterogeneity of GBM suggests that combination regimens exerting antitumor effects through different targets may be successful in increasing
antitumor efficacy (Qazi et al., 2017). No standard of
care is established in recurrent or progressive GBM.
As topoisomerases are involved in DNA repair mechanisms, various combinations with DNA alkylating
A
agents have been tested. This group of antineoplastic
agents is cell cycle-dependent and cycle phase-specific,
and includes irinotecan, topotecan, etoposide (VP-16),
and teniposide (Leonard and Wolff, 2013). Good
bioavailability and low toxicity make topoisomerase
inhibitors promising candidates for investigation in
phase I and II trials. Nitrosoureas, such as carmustine
(BCNU), lomustine (CCNU), nimustine (ACNU), and
fotemustine, are DNA alkylating agents and have
B
C
D
Fig. 3. KDM2B loss induces DNA damage, impairs DNA repair capacity of GBM cells, and leads to apoptosis. (A) Quantification of cH2AX
Ser139 foci count (% of cells with > 5 cH2AX foci per cell; >1000 cells were analyzed) in 4121 and 1587 cells 72 h post-transfection with
siCTRL, siKDM2B-1, or siKDM2B-2. (B) Quantification of cH2AX Ser139 foci count (% of cells with > 5 cH2AX foci per cell; >1000 cells
were analyzed) in 4121 cells at 48, 72, and 96 h after transfection with siCTRL, siKDM2B-1, or siKDM2B-2. (C) 4121 cells were transfected
with either siCTRL or siKDM2B-2, irradiated (IR, 3 Gy) or sham-irradiated, and the quantification of cH2AX Ser139 foci count (% of cells
with > 5 cH2AX foci per cell; >1000 cells were analyzed) was performed at 0, 6, and 24 h after IR. ***, P < 0.001 analyzed by one-way
ANOVA followed by Dunnett’s post hoc test. (D) Immunoblot analysis of cleaved/total PARP, p21CIP1/WAF1, cleaved caspase-3, and
GAPDH (loading control) in glioblastoma cells 72 h post-transfection with siCTRL, siKDM2B-1, or siKDM2B-2.
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M. Staberg et al.
been extensively used in glioma treatment. The use of
nitrosoureas increased for recurrent disease when
TMZ became standard of care in newly diagnosed
glioblastoma (van den Bent et al., 2017; Wick et al.,
2017). The combination of lomustine plus bevacizumab showed prolonged median PFS and OS and
higher PFS-6 than the single agents in the BELOB
phase II trial (Taal et al., 2014; Wick et al., 2017).
Therefore, we sought to evaluate to combinational
effect of KDM2B targeting KDM2B with selected
KDM2B targeting sensitizes glioblastoma to chemotherapy
chemotherapeutics, CCNU and VP-16. As shown in
Fig. 4A,B, KDM2B knockdown, in combination with
both CCNU and VP-16, was more effective at reducing cell viability than either of the monotherapies alone.
Genetic KDM2B disruption augmented chemotherapyinduced apoptosis, as measured by cleavage of PARP
and caspase-3, in all primary glioblastoma cultures tested (Fig. 4C). Collectively, our data indicate
that KDM2B promotes chemotherapy resistance in
GBM.
A
B
C
Fig. 4. siRNA-mediated knockdown of KDM2B sensitizes glioblastoma cells to CCNU and VP-16 chemotherapy. (A, B) Glioblastoma cells
were transfected with siCTRL, siKDM2B-1, or siKDM2B-2 and treated with either (A) CCNU or (B) VP-16 at indicated concentrations.
Viability was measured 72 h later by MTT assay. Viability measurements are normalized to siCTRL untreated (0 lM) cells (mean SEM,
n = 3). *P < 0.05; **P < 0.01; ***P < 0.001 analyzed by an unpaired t-test. (C) Immunoblot analysis of cleaved/total PARP, cleaved caspase3, and GAPDH (loading control) in glioblastoma cells transfected with either siCTRL or siKDM2B-1 constructs followed by treatment with
indicated concentrations of CCNU for additional 48 h.
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KDM2B targeting sensitizes glioblastoma to chemotherapy
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D
M. Staberg et al.
B
C
E
F
Fig. 5. GSK-J4 treatment impairs glioblastoma cell viability and self-renewal, and induces apoptosis and DNA damage. (A) Glioblastoma cells
and normal human astrocytes (NHA) were treated with increasing concentrations of GSK-J4, and cell viability was assessed 72 h later by
MTT assay. Data are presented as mean SEM, n ≥ 2. *P < 0.05; **P < 0.01; ***P < 0.001 analyzed by one-way ANOVA. (B)
Glioblastoma cells were treated with increasing concentrations of GSK-J4 for 48 h and submitted to immunoblot analysis of KDM2B,
cleaved/total PARP, EZH2, cleaved caspase-3, p21CIP1/WAF1, H3K36me2, and GAPDH (loading control) (C) qRT/PCR analysis of relative
SOX2 mRNA expression in glioblastoma cells treated with DMSO or 5 lM GSK-J4 for 48 h. Data are presented as mean SEM, n = 3.
*P < 0.05; ***P < 0.001 analyzed by an unpaired t-test. Additionally, glioblastoma cells were treated with increasing concentrations of GSKJ4 for 48 h and subjected to immunoblot analysis of Sox2 and tubulin (loading control). (D) GSC self-renewal after GSK-J4 treatment was
analyzed by in vitro extreme limiting dilution assay (ELDA). ***P < 0.001 analyzed by pairwise chi-squared test. (E) 4121 GSCs were treated
with increasing concentrations of GSK-J4 for 24 h (as used in ELDA) and the percentage of cells (%) with > 5 cH2AX foci per cell (>1000
cells were analyzed) was quantified. ***P < 0.001 analyzed by one-way ANOVA followed by Tukey’s post hoc test.
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M. Staberg et al.
3.4. Pharmacological inhibition of KDM2B targets
GSCs
Based on the efficacy of genetic targeting of KDM2B
against glioblastoma, we investigated the efficacy of
novel enzymatic inhibitors of KDM2B function. GSKJ4 is among the first highly potent small-molecule KDM
inhibitors, with efficacy against brainstem gliomas harboring histone 3.3 K27M mutations (Hashizume et al.,
2014; Heinemann et al., 2014). While GSK-J4 was originally described as a specific inhibitor of KDM6A and
KDM6B, subsequent analysis reveals that it targets a
broader spectrum of the KDM family, including
KDM2B (Heinemann et al., 2014). GSK-J4 treatment
decreased glioblastoma cell viability in a concentrationdependent manner, with two cultures expressing high
KDM2B levels (4121 and 1587) displaying higher sensitivity compared to glioblastoma cultures expressing low
KDM2B levels (T115) and normal astrocytes (Fig. 5A).
GSK-J4 reduced KDM2B expression and increased
H3K36me2, the biomarker inhibited by KDM2B, associated with induction of p21CIP1/WAF1 expression and
the cleavage of PARP and caspase-3 (Fig. 5B). Supporting a role in targeting GSCs, GSK-J4 treatment reduced
levels of GSC regulators, EZH2 and SOX2 (Fig. 5B,C),
decreased the self-renewal as well as survival of GSCs
(Figs 5D,E and S2B). Interestingly, the reduction in
GSC frequency was associated with concentrationdependent induction DSB formation (Fig. 5F).
3.5. KDM Inhibitor Sensitizes Glioblastoma to
Chemotherapy
Based on the effects of genetic targeting of KDM2B
on chemotherapy sensitivity, we interrogated the
potential of GSK-J4 to sensitize glioblastoma cells to
CCNU and VP-16, by treating cells with GSK-J4 or
chemotherapy alone or in combination with one
another, permitting calculation of the combinational
index (CI) (Fig. 6A–C). Here, both low-dose (LD) and
high-dose (HD) concentrations based on calculated
GI50 values were tested in all 3 GBM lines. Whereas
LD combinations failed to show benefit (synergy or
additive), the HD combination of GSK-J4 with either
CCNU or VP-16 showed significant synergistic inhibition (CIs < 0.9) of cell viability in only KDM2B—
high-expressing 4121 and 1587 cells (Fig. 6A–C). Supporting the functional impact of a combined treatment
strategy, treatment with GSK-J4 and either CCNU or
VP-16 decreased GSC frequencies in both 4121 and
1587 cells (Fig. 6D,E). Collectively, these results support combinatorial benefit of KDM inhibition with
KDM2B targeting sensitizes glioblastoma to chemotherapy
herein tested chemotherapeutic agents CCNU and VP16 for glioblastoma therapy.
4. Discussion
Emerging evidence suggests that epigenetic dysregulation plays fundamental roles in the onset and maintenance of cancer. Numerous studies have shown that
standard-of-care cancer therapies induce drug-resistant
phenotype that is largely reversible, strongly suggesting
benefit from interventions of epigenetic mechanisms
(Black et al., 2012; Hashizume et al., 2014; Hojfeldt
et al., 2013; Kampranis and Tsichlis, 2009; Kreth
et al., 2014; Mack et al., 2016; Maes et al., 2015). Reversible histone methylation has emerged in the last decade as an important element contributing to the
development of several diseases, especially cancer
(Hoffmann et al., 2012). Pathophysiologically, there
are strong links between the expression of certain histone demethylases, chromatin remodeling, and the initiation as well as maintenance of cancer (Hashizume
et al., 2014; Maes et al., 2015; Pedersen and Helin,
2010; Rotili and Mai, 2011).
Despite concerted worldwide efforts to tackle
glioblastoma, patient prognosis remains grim and
recurrence is inevitable (Rich, 2016; Stupp et al.,
2005). Several histone demethylases, including LSD1,
KDM5A, and KDM5B, are upregulated in malignant
gliomas, sustaining cell growth, and resistance to
chemotherapy (Amente et al., 2015; Banelli et al.,
2015; Black et al., 2013; Dai et al., 2014; Hayami
et al., 2011; Tzatsos et al., 2013). In the present study,
we examined the role of KDM2B in glioblastoma. We
found that KDM2B is expressed in glioblastoma and
critically maintains glioblastoma cell survival, genome
integrity, and stem-like tumor populations. KDM2B
dependency of glioblastoma cells is supported by the
preferential sensitivity of KDM2Bhigh tumor cells to
KDM2B inhibition compared to KDM2Blow tumor
cells. RNA interference against KDM2B led to a massive induction of genotoxic stress, cell cycle arrest, and
consequent apoptotic cell death, consistent with prior
studies in pancreatic and breast cancers (Kottakis
et al., 2014; Tzatsos et al., 2013).
In mammalian cells, double-strand DNA breaks
(DSBs) are repaired by either error-free homologous
recombination (HR) or error-prone nonhomologous
end-joining (NHEJ) repair pathways (Brandsma and
Gent, 2012). H3K36me2 methylation near DSBs is
crucial for NHEJ repair after ionizing radiation, and
according to the report by Jiang et al. (2015), this
methylation can be counteracted by the expression of
KDM2B. This study found local fumarate to inhibit
Molecular Oncology 12 (2018) 406–420 ª 2018 Danish Cancer Society. Published by FEBS Press and John Wiley & Sons Ltd.
415
KDM2B targeting sensitizes glioblastoma to chemotherapy
M. Staberg et al.
A
B
C
D
E
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Molecular Oncology 12 (2018) 406–420 ª 2018 Danish Cancer Society. Published by FEBS Press and John Wiley & Sons Ltd.
M. Staberg et al.
KDM2B targeting sensitizes glioblastoma to chemotherapy
Fig. 6. GSK-J4 treatment sensitizes glioblastoma cells to CCNU and VP-16 chemotherapy. (A) Glioblastoma cells were treated with lowdose (LD) or high-dose (HD) single therapy or a combination of GSK-J4 and CCNU, and cell viability was assessed by MTT assay. Data
presented as mean SEM, n ≥ 3. *P < 0.05; **P < 0.01; ***P < 0.001 analyzed by an unpaired t-test. (B) Glioblastoma cells were treated
with LD or HD single therapy or a combination of GSK-J4 and VI-16, and cell viability was assessed by MTT assay. Data presented as
mean SEM, n ≥ 3. *P < 0.05; **P < 0.01; ***P < 0.001 analyzed by an unpaired t-test. (C) Combination index (CI) was calculated using
the COMPUSYN software. CI values < 0.9 indicate synergy, 0.9–1.1 additivity, and >1.1 antagonism. Data presented as mean SEM, n = 3.
(D) Glioblastoma self-renewal after treatment with GSK-J4 alone or in combination with CCNU was analyzed by in vitro extreme limiting
dilution assay (ELDA). *P < 0.05; ***P < 0.001 analyzed by a pairwise chi-squared test. (E) Glioblastoma self-renewal after treatment with
GSK-J4 alone or in combination with VP-16 was analyzed by in vitro extreme limiting dilution assay (ELDA). *P < 0.05; **P < 0.01;
***P < 0.001 analyzed by a pairwise chi-squared test.
KDM2B activity, which led to enhanced recruitment
of NHEJ repair factors to DSBs, more efficient repair
and cell survival (Jiang et al., 2015). Kurt and coworkers recently proposed a novel role of KDM2B in mediating the repression of proapoptotic proteins (Kurt
et al., 2017). In line with these observations, our study
finds genetic or pharmacologic KDM2B targeting
induced DSBs, cleavage of proapoptotic proteins
PARP and caspase-3.
KDM2B contributes to PRC1 complex recruitment
to CpG islands (Farcas et al., 2012). BMI1 is a core
component of PRC1 and facilitates DSB repair (Ginjala et al., 2011). Future studies will determine whether
KDM2B loss impairs BMI1 recruitment to DSBs and
sites of DNA damage response (DDR) activation,
resulting in accumulation of deleterious DNA damage.
KDM2B-mediated recruitment of the suppressive
PRC1 complex may silence actively transcribed
regions, making these available to DNA repair
machinery (Price and D’Andrea, 2013).
KDM2B is also required for maintenance of murine embryonic stem cells and breast cancer-initiating
cells (He et al., 2013; Kottakis et al., 2014). Here,
we find KDM2B to be expressed at higher levels in
GSCs compared to their differentiated counterparts.
GSC frequency, differentiation capacity, and survival
decreased upon either KDM2B knockdown or chemical inhibition using GSK-J4, supporting its importance in GSC self-renewal and maintenance. Our
data indicate that an early induction of DNA damage (24 h post-treatment) translates into impaired
self-renewal and maintenance of GSCs (Figs 2 and
3). KDM2B loss was accompanied by the reduction
in EZH2 and SOX2 protein levels, with both EZH2
and SOX2 serving as key factors in GSC selfrenewal and maintenance (Suva et al., 2009).
KDM2B silencing is also reported to increase levels
of tumor-suppressing miRNA let-7b, thereby downregulating EZH2 and reducing the entry into S-phase
and thus cancer growth (Karoopongse et al., 2014;
Tzatsos et al., 2011). We observed induction of
p21CIP1/WAF1 expression, as well as impaired the
entry of glioblastoma cells into S-phase after
KDM2B loss. As several KDMs, including LSD1
and KDM5B, have been reported to regulate
p21CIP1/WAF1 expression, KDM2B may share control
of cell cycle kinetics and induction of senescence
(Amente et al., 2015; Fasano et al., 2007; Wong
et al., 2012).
A common issue in cancer is the rapid emergence
of resistant clones after initial therapy leading to
recurrence. Recently, two KDMs, KDM3A in ovarian cancer and KDM5A in glioblastoma, were
shown to confer resistance to chemotherapy (Banelli
et al., 2015; Ramadoss et al., 2017). Thus, we speculated that KDM2B may contribute to chemoresistance in glioblastoma. GSK-J4 was originally
thought to be a highly specific inhibitor of the
H3K27me3/me2-demethylases, JMJD3 (KDM6B)
and UTX (KDM6A). Hashizume and coworkers
reported GSK-J4 as a promising drug candidate in
the treatment of pediatric brainstem glioma harboring an oncogenic K27M mutation in histone H3.3
(Hashizume et al., 2014), concluding that there was
no efficacy against wild-type H3K27 glioblastoma.
This is in contrast to our findings, which showed
high sensitivity of glioblastoma cells to GSK-J4. In
addition, both siRNA-mediated KDM2B loss as
well as chemical inhibition using GSK-J4 significantly sensitized tumor cells to chemotherapeutics
used in clinical management of glioblastoma (Taal
et al., 2014; Wick et al., 2017): lomustine and
etoposide. GSCs have been reported to be resistant
to several chemotherapies, and GSK-J4 monotherapy targeted GSC frequency and molecular regulators. This effect was potentiated in combination
with both lomustine and etoposide. In agreement to
our findings of H3K27 wild-type tumor cell sensitivity to GSK-J4, ovarian cancer and non-small-cell
lung cancer are killed by GSK-J4, irrespective of
H3K27 mutational status (Sakaki et al., 2015;
Watarai et al., 2016). Heinemann et al. (2014)
showed that GSK-J4 also inhibits the catalytic
activity of the other demethylases (KDM2B,
KDM3B, KDM4A, KDM4B, KDM4C, KDM5A,
KDM5B, KDM5C, and PHF8) with similar
Molecular Oncology 12 (2018) 406–420 ª 2018 Danish Cancer Society. Published by FEBS Press and John Wiley & Sons Ltd.
417
KDM2B targeting sensitizes glioblastoma to chemotherapy
potency. Hence, it cannot be excluded that in addition to KDM2B, the antineoplastic effects reported
in our study may be in part mediated through inhibition of other KDMs.
In conclusion, we now report that KDM2B is preferentially expressed therapeutically resistant pool of
GSCs, creating a dependency for which inhibition
leads to accumulation of DNA damage, which if left
unrepaired induces apoptosis and significantly reduces
the pool of stem-like tumor cells. Further, KDM2B
inhibition sensitizes this highly resistant tumor to
chemotherapy, suggesting a potential clinical paradigm
combined with standard therapies.
Acknowledgements
We thank Dr. Jeremy N. Rich (University of California San Diego, USA) for constructive comments and
manuscript editing. We are grateful to Linea Melchior
(Copenhagen University Hospital, Denmark) for performing H3K27 mutational analysis. This work was
supported by the Danish Cancer Society Foundation
(R146-A9511/R148-A10151), Novo Nordisk Foundation (NNF16OC0023146/NNF17OC0026056), Bjarne
Saxhoff, and Dansk Kræftforsknings Fond.
Author contributions
MS, SRM, RDR, HP, KEJ, and MV conducted
in vitro studies. KVS assisted with data analysis. JSR,
JB, and HSP contributed to patient material collection
and cell line derivation; and PH is responsible for
study design, data collection/analysis, and manuscript
writing.
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Supporting information
Additional Supporting Information may be found
online in the supporting information tab for this
article:
Table S1. Overview of primary antibodies used for
western blotting (WB).
Fig. S1. (A) qRT-PCR analysis of KDM2B mRNA
expression in GBM cell cultures compared to normal
human astrocytes (NHA), (mean SD, technical
replicates = 2, n = 1). Bar graph (B) and scatter plot
graph (C) showing the results of qRT-PCR analysis of
surgical GBM patient samples normalized and compared to the mean of two normal brain samples (NB)
(technical replicates = 2), (n = 2 for NB, n = 1 for
each GBM patient; P-value = 0.12).
Fig. S2. (A) KDM2B expression is positively correlated
to PROM1 (CD133) and SOX2, both markers of
stemness in GBM. The analysis was performed using
the REMBRANDT data set via GlioVis online tool
(http://gliovis.bioinfo.cnio.es/). (B) GSK-J4 reduces the
fraction of CD133-positive GBM cells in vitro. GBM
cells (4121 and 1587) were plated and treated with
increasing concentrations of GSK-J4 for 72 h. After
incubation, cells were stained with an anti-CD133FITC antibody (Miltenyi Biotec #293C3). Dead cells
were excluded using 7-AAD staining. FACS Verse Cell
Sorter (BD Biosciences) was used for acquisition and
FLOWJO software for data analysis. Representative
FACS plots from one experiment are shown.
Molecular Oncology 12 (2018) 406–420 ª 2018 Danish Cancer Society. Published by FEBS Press and John Wiley & Sons Ltd.