BMI1, a new target of CK2α
© The Author(s). 2017
Received: 2 December 2016
Accepted: 20 February 2017
Published: 7 March 2017
The polycomb group protein, BMI1 plays important roles in chromatin modification, stem cell function, DNA damage repair and mitochondrial bioenergetics. Such diverse cellular functions of BMI1 could be, in part, due to post-translational modifications, especially phosphorylation. To date, AKT has been reported as a kinase that by site specific phosphorylation of BMI1 modulates its oncogenic functions.
Immunoprecipitation in conjunction with kinase assay and mass spectrometry was used to determine association with and site specific phosphorylation of BMI1 by CK2α. Functional implications of the BMI1/CK2α axis was examined in cancer cells utilizing siRNA and exogenous gene expression followed by biochemical and phenotypic studies. Correlations between expression of CK2α and BMI1 were determined from cell lines and formalin fixed paraffin embedded tissues representing the normal fallopian tube epithelium and high grade serous ovarian cancer samples.
Here we report that CK2α, a nuclear serine threonine kinase, phosphorylates BMI1 at Serine 110 as determined by in-vitro/ex-vivo kinase assay and mass spectrometry. In ovarian cancer cell lines, expression of CK2α correlated with the phospho-species, as well as basal BMI1 levels. Preventing phosphorylation of BMI1 at Serine 110 significantly decreased half-life and stability of the protein. Additionally, re-expression of the phosphorylatable but not non-phosphorylatable BMI1 rescued clonal growth in endogenous BMI1 silenced cancer cells leading us to speculate that CK2α-mediated phosphorylation stabilizes BMI1 and promotes its oncogenic function. Clinically, compared to normal fallopian tube epithelial tissues, the expression of both BMI1 and CK2α were significantly higher in tumor tissues obtained from high-grade serous ovarian cancer patients. Among tumor samples, the expression of BMI1 and CK2α positively correlated (Spearman coefficient = 0.62, P = 0.0021) with each other.
Taken together, our findings establish an important regulatory role of CK2α on BMI1 phosphorylation and stability and implicate the CK2α/BMI1 axis in ovarian cancer.
KeywordsPost translational modification Phosphorylation Kinase assay Protein stability Formalin fixed paraffin embedded tissues (FFPE) Fallopian tube epithelial (FTE) cells High-grade serous ovarian cancer Clonal growth
BMI1 is a member of the polycomb repressor complex 1 (PRC1) that in complex with Ring1B catalyzes mono-ubiquitination of histone H2A (H2AK119) and mediates gene silencing by regulating chromatin structure. Accumulating evidences have established important roles for BMI1 as a transcriptional repressor, a regulator of stem cell function [1, 2], a DNA damage repair protein [3–5] and recently, a mitochondrial role has been described [6, 7]. The importance of BMI1 is further underscored by the fact that it has been implicated in several different malignancies including ovarian cancer leading to the development of clinical small molecule inhibitors [8–10].
The BMI1 protein comprises of 326 amino acids with an N-terminal RING finger (RF) domain, a middle helix turn helix (HTH) domain and a C-terminal Proline-Serine rich (PS/PEST) domain . Post-translational modifications confer functional diversity to proteins and few such modifications have been described for BMI1 [3, 5, 12–14]. When phosphorylated by 3 pK (MAPKAP kinase 3), specific sites unknown, BMI1 dissociated from the chromatin resulting in de-repression of targets . Phosphorylation by AKT at Ser 316 of BMI1, triggered its dissociation from the INK4A/ARF locus resulting in inability to promote tumor growth . On the other hand, AKT-mediated phosphorylation of BMI1 at Ser 251, 253 and 255 enhanced its oncogenic potential in prostate cancer . It is notable that the described phosphorylation sites reside within the PS/PEST domain, deletion of which enhances stability of the BMI1 protein . The functional fate of phosphorylated BMI1 thus remains context and cancer specific.
Like BMI1, the Ser/Thr kinase complex, Casein Kinase 2 (CK2), is involved in various cellular processes affecting clonal growth, survival, apoptosis and DNA damage repair [16–18]. Similar to BMI1, CK2 is predominantly present in the nucleus and comprises of a hetero-tetramer of the catalytic α, α’ and two non-catalytic β subunits . Notably, expression of both CK2α and BMI1 is elevated in ovarian cancer and correlates with poor overall survival [19–21]. Together with predictive bioinformatics analysis, these evidences prompted us to evaluate CK2α as a potential kinase in phosphorylating BMI1. Here, we establish that CK2α is a novel kinase for BMI1; CK2α phosphorylates BMI1 at Ser110, and this phosphorylation imparts protein stability contributing to clonal growth. The identified CK2α-BMI1 liaison is of clinical significance as high CK2α expression strongly correlates with the elevated BMI1 protein levels in high grade serous ovarian cancer tissues. Our results implicate the CK2α/BMI1 axis in ovarian cancer, thus targeting it might be potentially beneficial.
Lambda phosphatase was purchased from New England Bio labs (#P0753S). Casein Kinase II Inhibitor I, TBB was purchased from Calbiochem (#218708). CK2α-GST tagged or CK2α untagged recombinant proteins were purchased from Signalchem (#C71-10G-10) and Abcam (#90745) respectively. GST-tagged or full-length BMI1 recombinant proteins were purchased from Mybiosource.com (#MBS717171) and Origene (TP760041) respectively. GST was purchased from Abcam (#89499). Nonradioactive ATP (Adenosine triphosphate) was purchased from Thermofischer (# R1441) and radioactive ATP labeled on the gamma phosphate group with 32P was purchased from PerkinElmer (#NEG002A250UC). Cyclohexamide, MG132 and AKT inhibitor (Akti) were procured from Sigma (#R750107) and Calbiochem (#474791; 124018) respectively.
Plasmids and constructs
The plasmids FLAG-BMI1WT (wild-type) construct as previously described (Fan et. al. 2008), was used to generate S110A mutant BMI1 FLAG. Quick Change Site directed mutagenesis kit (Agilent) and the following pair of primers were used to generate the mutant. Both the plasmids were sequenced and the integrity was confirmed before performing experiments. (Forward primer: CTGATGCTGCCAATGGCGCTAATGAAG ATAGAGGA; Reverse Primer: TCCTCTATCTTCATTAGCGCCATTGGCAGCATCAG). pZW6 (CK2α) was a gift from David Litchfield (Addgene plasmid # 27086) .
Cell culture and transfection
CP20 cells (developed by sequential exposure of the A2780 parental cell line to increasing concentrations of cisplatin) and OV90 cells were kindly gifted by Dr. Anil Sood, MD Anderson Cancer Center. OVCAR4 was a kind gift from Dr. Ronny Drapkin, formerly at the Dana-Farber Cancer Institute, Boston, MA. Immortalized normal fallopian tube epithelial cells (FTE-188) were a kind gift from Dr. Jinsong Liu, MD Anderson Cancer Center. OVSAHO and TKYNU cell lines were obtained from the Japanese Collection of Research Bioresources Cell Bank (JCRB). These were routinely cultured in RPMI/DMEM/MCDB-Med199 (Sigma) supplemented with 10% FBS and 1X penicillin-streptomycin (Gibco, NY, USA) in a 5% CO2 humidified atmosphere.
Lipofectamine 3000 (Invitrogen) was used for plasmid transfection and co-transfection with siRNA as per manufacturer’s protocol. Gene silencing was performed using Hiperfect (Qiagen) and 33 picomoles siRNA (scrambled control, Dharmacon; BMI1 SASI_HS01_00175765 from Sigma and CK2α siRNA #6389, CST). All experiments were performed 48–60 h after transfection, unless stated otherwise.
Protein extraction, determination of protein concentration, and λ-Phosphatase treatment
Total Cell Lysate was prepared in RIPA (Boston Bioproducts) or Cell Lytic M (Sigma) compatible with enzymatic assay and immunoprecipitation.
For the formalin fixed paraffin embedded (FFPE) patient sample, samples were prepared as previously described with slight modification . First, samples were deparffinized with 1 ml of xylene; vortexed and stored for 10 min, followed by centrifugation at 14,000 g × 5 min and then supernatant was removed. Deparffinization process was repeated thrice following which samples were gradiently hydrated starting from 100% ethanol followed with 80% and 50% ethanol. After each step the samples were centrifuged at 14,000 g × 5 min and supernatant was removed. Samples were stored overnight at 4 °C in 1 ml of DEPC-treated water and then centrifuged at 14,000 g × 15 min and the pellet was resuspended in 2% SDS buffer with brief pulse of sonication (10 s × 3 times), centrifuged (14,000 g × 15 min) and supernatant collected for downstream assay.
Concentration of the extracted protein was determined by Bichonic acid assay (BCA) method using Pierce Kit (#23225). For most assays 10–30 μg of the lysate was used.
λ- Phosphatase treatment was performed on 50 μg of cellular protein incubated with 200units of the phosphatase at 25 °C for 1 h as per the manufacturer’s protocol. Reaction was terminated by addition of the 4 × lamelli buffer.
Immunoblotting, immunoprecipitation and kinase reaction
Immunoprecipitation was performed using Agarose A/G beads (SCBT-2003) or the Pierce crosslink IP kit (Cat No # 26147) and cell lysates or immunoprecipitated proteins were separated by SDS-PAGE and Western immunoblotting analysis was performed using standard protocol as described previously . The cell lysate were separated on 10 or 12% glycine SDS-PAGE gel or Phos-tag™SDS-PAGE (for analysis of BMI1 phosphorylation in a panel of normal and high grade serous ovarian cancer cells; Wako Cat No # 304-93521). For Mn2+-Phos-tag SDS-PAGE, 50 μM Phos-tag™ acrylamide and 2 eq of MnCl2, when added to the resolving part of 10% acrylamide gel provided a convenient method for the simultaneous analysis of a phosphoprotein isoform(s) and its non-phosphorylated counterpart [25–27]. Gels were transferred to PVDF membrane. Membranes were blocked in 5% non-fat dry milk in TBS with 0.1% TWEEN-20 (TBST) for 1 h at room temperature followed by incubation with indicated primary antibodies in TBST with 5% BSA. Antibodies were purchased from following venders: Santa Cruz Biotechnology (CK2α #sc-373894, Akt1/2/3 #sc-8312, p-Akt1/2/3 (Ser473) #sc-7985); Proteintech (HSP60#66041-1-Ig); Life-Technologies (BMI1#375400); ABCAM (α − Tubulin #ab4074) and Sigma (FLAG #F1804, secondary antibodies conjugated with horseradish peroxidase IgG Rabbit and Mouse).
10 μg of required antibody (BMI1 or CK2a) was first crosslinked to resin using DSS following crosslinking protocol of the manufacturer (Pierce, crosslinking IP protocol). Alternately, 1 mg of precleared lysate was incubated with the antibody overnight at 4 °C in spin wheel. The beads were added to the protein/antibody homogenate on the next day and incubated at 4 °C for 1 h in a spin wheel. The beads were collected by centrifugation, washed and suspended in 15 μL IP buffer to be used for radioactive or nonradioactive kinase assay. Radioactive assay for CK2α was performed using 10 μg of BMI1/BMI1-GST with 9 μl of final immunoprecipitate bead in 15 μl reaction mix respectively containing 50 mM Tris–Cl pH 8.0, 10 mM MgCl2, 50 μM ATP and 5 μCi of [γ-32P] ATP (3000 Ci/mmol). The reactions were carried out for 15 min at 25 °C after which they were stopped by adding 4 × samples loading buffer. The samples were subjected to SDS-PAGE, the gels were dried and exposed at −80 °C as required on an X-ray film and developed. Non-radioactive assay for CK2α used similar protocol with only the radioactive ATP being replaced by 200 mM of cold ATP and BMI1/BMI1-GST being used as substrate. The films were scanned and quantified using Image J software.
Cellular RNA was isolated (Zymo RNA isolation kit, Cat No: R1050) and 1 μg of total RNA was reverse transcribed to cDNA (iScript cDNA synthesis kit, Bio-Rad). Total of 1 μl of the 40 μl reverse transcription reaction were used as template for real-time detection (Bio-Rad CFX connect) using Sybr green (Bio-Rad) and primers as described below. Gene expression was quantified for the tested genes and endogenous control gene 18 S rRNA. Relative mRNA level was calculated by normalizing the gene expression levels of tested genes to that of the control 18 S rRNA gene.
CK2α: Fwd: 5’ TAGGGGGTTGGTATCTCGTG3’; Rev: 5’ TGATGTAAGCGACCAGCAAG3’
BMI1: Fwd::5’ CCTTCATTGTCTTTTCCGCCC; Rev:5’ AAGTACCCTCCACAAAGCAC 3’
18 S rRNA: Fwd:5’ TCGATGGGCGGCGGAAAATA; Rev: 5’ TTGGTGAGGTCAATGTCTGCT3’
Clonal growth assay
48 h post transfection 200 single cells of CP20 or OV90 cells in RPMI medium containing 10% FBS were seeded in the same medium in each well of 6-well plate. After 10 days (CP20) or 14 days (OV90), the colonies were stained with the crystal violet solution (0.75% crystal violet, 50% ethanol, 0.25% NaCl, 1.57% formaldehyde), imaged using Leica EZ4HD (Buffalo Grove, IL 60089 USA). 9 images from 3 independent experiments were quantified using Image J (image processing and analysis in Java, NIH).
Data analysis and statistics
All the experiments were repeated independently at least 3 times and in triplicate where applicable. Data are expressed as mean ± standard deviation (SD). Comparisons between two groups were evaluated using Student’s t-test with equal/unequal variances. For comparisons among multiple groups, we performed ANOVA. If the overall test was significant, we compared each treatment to control with Dunnett's method for multiple comparisons. For densitometry analysis of immunoblots, Image J software (NIH) was used. BMI1 expression levels were compared between normal and primary tumor samples using Wilcoxon rank-sum test. The CK2α detection rates were compared between the groups (normal vs. primary tumor) using Fisher’s exact test. Spearman correlation coefficient was used to assess the correlation between CK2α and BMI1 expression levels among primary tumor samples. P < 0.05 was considered statistically significant. All tests were two-sided.
Identification of Casein Kinase 2α, a candidate BMI1 kinase
Bioinformatics analysis of the potential phospho sites on BMI1 protein sequence
CK2 is a serine-threonine kinase comprising of two catalytic (α, α') and two regulatory (β) subunits. CK2 is upregulated in major lethal malignancies where its expression correlates with poor overall survival [16, 18, 19]. Interestingly of these subunits, high levels of CK2α correlated with poor overall survival in ovarian cancer . Using immunoblotting, we determined that CK2α levels were significantly elevated in ovarian cancer cell lines compared to the non-malignant Fallopian Tube Epithelial (FTE188) cells (Fig. 1b). Since BMI1 is reportedly phosphorylated by AKT, we determined the expression of active AKT (Phospho AKT-S473) in these cell lines. With the exception of OV90, AKT was significantly phosphorylated in all the cancer cell lines compared to FTE188 (Fig. 1b). Interestingly, the phosphorylated species of BMI1 was present in all the cancer cell lines including OV90 that expressed minimal phospho-AKT, thereby implicating other kinases in phosphorylation of BMI1. Since the expression of CK2α correlated with the phospho-species of BMI1, we next determined if altering cellular levels of CK2α affected phosphorylation of BMI1. Silencing CK2α by siRNA significantly reduced both phospho-species as well as basal BMI1 levels in CP20 and OV90 cells (Fig. 1c). However the PRC1 complex partner of BMI1, RING1A levels remained unchanged (Fig. 1c). Subsequently we confirmed that in CK2α silenced cells, reduction in basal BMI1 level was not due to decreased transcription thus implicating post-translational events (Fig. 1d). These observations were further complemented by expressing CK2α in FTE188 cells that resulted in enhanced basal expression as well as phosphorylation of BMI1 (Fig. 1e). Together these results suggest that CK2α might potentially phosphorylate BMI1 and directly or indirectly regulate its post translational expression.
CK2α phosphorylates BMI1
To confirm these observations, we performed an in vitro kinase assay using purified CK2α, GST-tagged BMI1 and [γ − 32P] ATP. The autoradiograph clearly demonstrated that BMI1 was phosphorylated by CK2α (Fig. 2b). Additionally, as previously reported , autophosphosphorylation of CK2α was also observed (Fig. 2b). To further confirm these observations we first immunoprecipitated CK2α from cellular lysates of CP20 cells using antibody-conjugated agarose beads (Fig. 2c-left panel). Equal amount of these agarose beads were incubated with recombinant BMI1 and [γ − 32P] ATP either in presence or absence of different concentrations of the CK2 inhibitor, TBB (4,5,6,7-tetrabromobenzotriazole) . The autoradiograph clearly demonstrated that BMI1 was phosphorylated by CK2α and the signal significantly diminished with TBB (Fig. 2c-right panel). Together these results demonstrate that CK2α phosphorylates BMI1.
CK2α phosphorylates BMI1 at S110
Mutation at S110 residue decreases half-life of BMI1
Importance of the CK2α/BMI1 axis in ovarian cancer
Based on these results we posited that if CK2α mediated BMI1 phosphorylation led to protein stability, then a correlation between CK2α and BMI1 protein levels would be expected in ovarian cancer clinical specimens. Therefore, we analyzed BMI1 and CK2α levels in a panel of twenty high-grade serous ovarian tumors and two normal fallopian tube epithelial (FTE) tissues  by immunoblotting. BMI1 expression was significantly higher in primary tissues (p = 0.0398) and CK2α was detected in a significantly higher proportion of primary tissues (p = 0.013). Remarkably within the tumor samples, significant correlation between CK2α and BM11 expression was observed (Fig. 5d, Spearman correlation coefficient is 0.62, p = 0.0021). While patients with higher expression of both BMI1 and CK2α showed a trend towards shorter progression free survival, the data did not reach statistical significance likely due to the limited sample size (Additional file 1: Figure S2). Together, these results demonstrate that phosphorylation of BMI1 at Ser110 by CK2α is important for both stability and functionality of the protein.
Given the important role of BMI1 in cancer biology it is important to investigate its post-translational modifications because they confer functional diversity to proteins and few such modifications of BMI1 have been previously described. Here we report that CK2α by phosphorylating at the Ser110 residue regulates stability of the BMI1 protein.
Interestingly, all of the previously reported phosphorylation sites of BMI1 lie within the C-terminal PS/PEST domain (236–326 amino acids) and involve AKT [3, 12]. Though bioinformatics analysis predicted a number of potential kinases that could phosphorylate BMI1, we focused on CK2α because the hetero-tetrameric CK2 complex with constitutive kinase activity is predominantly present in the nucleus like BMI1. Also, ovarian cancer cells that expressed CK2α but minimally activated AKT maintained phosphorylated species of BMI1. Following prediction, we showed that CK2α reciprocally co-precipitated with BMI1. Using in vitro kinase assays and Mass spectrometry we confirmed that CK2α phosphorylates BMI1 at the Ser110 residue.
Prior reports indicate that protein turnover of BMI1 is regulated by βTrCP recognizing a degron motif within the PS/PEST domain, where all the previously described phosphorylation sites reside . Deletion of the PS/PEST domain thus increases the half-life and stability of the protein . Other mechanisms of BMI1 stability include direct association with the FAL1 long noncoding RNA resulting in increased clonogenicity and tumorigenicity in an ovarian cancer model . Phosphorylation can differentially regulate proteosomal degradation [35–38]. Our results suggest that phosphorylation at Ser110 by CK2α stabilizes BMI1 because mutation to non-phosphorylatable alanine significantly reduces half-life of the protein resulting in increased accumulation upon addition of MG132 indicating proteasomal degradation. Phosphorylation-mediated alteration in protein conformation resulting in reduced ubiquitination or enhanced interaction with other stabilizing proteins, akin to many other cellular proteins [39, 40] may be envisioned.
Our results, generally, demonstrate a correlation between expression of CK2α and phosphorylated BMI1 in ovarian cancer cell lines and patient tissues. Interestingly previous reports suggest that expression of both CK2α and BMI1 is elevated in ovarian cancer and correlates with poor overall survival (19, 20). Also, in vivo studies in mice bearing A2780-xenografts, confirmed that antitumor efficacy could be enhanced by combining the CK2 inhibitor with cisplatin, carboplatin, or gemcitabine . However, in these studies, the expression of BMI1 was not determined. We find that re-expression of phosphorylatable but not non-phosphorylatable BMI1 rescues clonal growth in endogenous BMI1 silenced ovarian cancer cells leading us to speculate that CK2α-mediated phosphorylation stabilizes BMI1 and promotes its oncogenic function.
B lymphoma Mo-MLV insertion region 1 homolog
Casein kinase 2 alpha subunit
Formalin Fixed Paraffin Embedded
Fallopian Tube Epithelial
Polycomb repressor complex 1
Reverse Transcription and Polymerase Chain reaction
We thank the Taplin Biological Mass Spectrometry Facility for their excellent assistance. We thank the Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number P20 GM103639 for the use of Histology and Immunohistochemistry Core at Stephenson Cancer Center which provided processing and embedding/tissue staining/immunohistochemistry service.
This study was supported by the National Institutes of Health (NIH) CA 157481 (RB) and HL120585 (PM), the funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Availability of data and materials
All data generated or analyzed during this study are included in this published article [and its supplementary information files].
SBM, PKC, PM and RB designed the experiments; SBM, PKC and SKDD, performed the experiments; SBM, PKC, KM, KD and RB analyzed the data; SBM, PKC and RB wrote the manuscript. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
Consent for publication
Ethics approval and consent to participate
For experiments that involve the use of human subjects, the work described has been carried out in accordance with The Code of Ethics of the World Medical Association (Declaration of Helsinki). Informed consent was obtained for experimentation with human subjects. The privacy rights of human subjects were also observed.
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