Mahanine restores RASSF1A expression by down-regulating DNMT1 and DNMT3B in prostate cancer cells
- Soumik Agarwal†1,
- Karishma S Amin†1,
- Shankar Jagadeesh1, 4,
- Gokul Baishay2,
- Paruchuri G Rao2,
- Nabin C Barua2,
- Samir Bhattacharya2, 3 and
- Partha P Banerjee1Email author
© Agarwal et al.; licensee BioMed Central Ltd. 2013
Received: 22 May 2013
Accepted: 24 August 2013
Published: 30 August 2013
Hypermethylation of the promoter of the tumor suppressor gene RASSF1A silences its expression and has been found to be associated with advanced grade prostatic tumors. The DNA methyltransferase (DNMT) family of enzymes are known to be involved in the epigenetic silencing of gene expression, including RASSF1A, and are often overexpressed in prostate cancer. The present study demonstrates how mahanine, a plant-derived carbazole alkaloid, restores RASSF1A expression by down-regulating specific members of the DNMT family of proteins in prostate cancer cells.
Using methylation-specific PCR we establish that mahanine restores the expression of RASSF1A by inducing the demethylation of its promoter in prostate cancer cells. Furthermore, we show that mahanine treatment induces the degradation of DNMT1 and DNMT3B, but not DNMT3A, via the ubiquitin-proteasome pathway; an effect which is rescued in the presence of a proteasome inhibitor, MG132. The inactivation of Akt by wortmannin, a PI3K inhibitor, results in a similar down-regulation in the levels DNMT1 and DNMT3B. Mahanine treatment results in a decline in phospho-Akt levels and a disruption in the interaction of Akt with DNMT1 and DNMT3B. Conversely, the exogenous expression of constitutively active Akt inhibits the ability of mahanine to down-regulate these DNMTs, suggesting that the degradation of DNMT1 and DNMT3B by mahanine occurs via Akt inactivation.
Taken together, we show that mahanine treatment induces the proteasomal degradation of DNMT1 and DNMT3B via the inactivation of Akt, which facilitates the demethylation of the RASSF1A promoter and restores its expression in prostate cancer cells. Therefore, mahanine could be a potential therapeutic agent for advanced prostate cancer in men when RASSF1A expression is silenced.
Prostate cancer is the most common non-cutaneous malignancy in men in the Western world. The etiology of prostate cancer is not well defined; however, the inhibition of various tumor suppressor genes and concomitant activation of oncogenes is a frequent occurrence in most cancers, including prostate cancer. DNA hypermethylation of promoters at CpG sequences often sterically hinders the binding of transcription factors, thereby represses gene transcription . The transfer of a methyl group to DNA at the fifth carbon position of cytosine residues by the DNA methyltransferase (DNMT) family of enzymes is one of the most common events for the establishment of epigenetic program . Three active DNMTs have been identified so far in mammalian cells; DNMT1 (Gene ID: 1786), DNMT3A (Gene ID: 1788), and DNMT3B (Gene ID: 1789). DNMT1 is the most abundant and methylates hemimethylated CpG di-nucleotides in the mammalian genome during DNA replication in a number of different cancer types . DNMT3A and DNMT3B are methyltransferases involved in de novo methylation of DNA following replication .
Numerous reports have demonstrated the overexpression of DNMT1 in lung, hepatocellular, acute and chronic myelogenous leukemia, colorectal, gastric, breast and prostate cancers [5–11]. Gravina and associates have shown that the hormone resistant prostate cancer phenotype is associated with an increase in DNMT expression and activity . The majority of gene silencing induced by DNA hypermethylation in prostate cancer can be attributed to DNMT activity . Since promoter hypermethylation results in the silencing of several tumor suppressor genes in cancer cells, the reactivation of these genes by demethylation of their promoters is a feasible approach to cancer therapy. DNMT inhibitors, such as 5-aza-deoxycytidine and 5-aza-2’-deoxycitidine, have been used extensively in clinical trials for cancer treatment. These nucleoside analogues bind covalently to the DNMTs and irreversibly inhibit their function, leading to the demethylation of silenced promoters and subsequently, the activation of gene expression. However, studies in rodent cell lines and bacteria have indicated that these azacitidine-DNMT adducts are toxic and mutagenic if not repaired [14–16]. In addition, these compounds are unstable in neutral aqueous solution and disintegrate to yield more stable analogues such as 5, 6-dihydro-5-azacytidine and 5-fluoro-2’-deoxycytidine , that have been shown to have toxicity related issues in clinical trials [18, 19]. Therefore, there is an urgent need for the development of new drugs that will target DNMT with low toxicity.
Ras-association domain family 1A (RASSF1A; Gene ID: 11186) gene has been found to be the most frequently methylated gene described thus far in human cancers [20, 21]. Hypermethylation of the promoter of RASSF1A gene at its CpG-island has been observed in 70% of prostate cancers [22, 23]. Since the restoration of RASSF1A expression in tumor cell lines impairs tumorigenicity [22, 24], factors that restore RASSF1A expression have immense importance in preventing tumor growth. We demonstrated earlier that mahanine induces RASSF1A gene expression in a diverse range of cancer cell types, including epidermoid, lung, pancreatic, colon, breast, ovarian and prostate cancer cells . Although we showed a decline in DNMT activity upon mahanine treatment, the scope of our study did not include establishing a causative effect of DNMT inhibition on RASSF1A re-expression by mahanine, and this mechanism remains to be explored.
The cellular levels of DNMTs in mammalian cells can be regulated by transcriptional events or posttranslational modifications of enzymes which ultimately affect the catalytic activity and degradation of the DNMT proteins . DNMT1 is known to be phosphorylated at several serine and threonine residues under physiological conditions. Sun and associates have reported that Akt enhances DNMT1 protein stability by inhibition of its ubiquitin–proteasome mediated degradation . Recently it has been demonstrated that Akt1 directly interacts and phosphorylates Ser143 of DNMT1 to increase its stability .
In the present study, we sought to establish the mechanism by which mahanine inactivates DNMTs and thereby restores RASSF1A expression in prostate cancer cells. We show that mahanine induces the degradation of DNMT1 and DNMT3B via the ubiquitin-proteasome mediated pathway in both androgen-responsive LNCaP and androgen receptor-negative PC3 human prostate cancer cells. Interestingly, our data suggests that the inactivation of Akt by mahanine treatment is involved in inducing DNMT degradation, thereby restoring the expression of the epigenetically silenced tumor suppressor gene RASSF1A.
Mahanine demethylates RASSF1A promoter and restores its expression in prostate cancer cells
All three DNMTs possess the ability to silence RASSF1A expression
The over-expression DNMTs and the silencing of RASSF1A expression by hypermethylation of its promoter in prostate cancer have been well documented . In order to establish the role of the various DNMTs in mediating the methylation of the RASSF1A promoter in our system, we down-regulated the expression of DNMT1, DNMT3A and DNMT3B in PC3 cells using specific shRNA constructs. Loss of expression of either member of the DNMT family resulted in restoration of RASSF1A expression; however to a lesser extent with the DNMT3A knock-down (Figure 1C). This suggests that all three members of the DNMT family of proteins are involved in the silencing of RASSF1A expression, although the degree to which each member is involved varies. Alternatively, we transfected BPH1 cells, in which the native expression of DNMTs is almost undetectable, with expression vectors of all three types of the DNMTs (Additional file 1: Figure S1B). The exogenous expression of either member of the DNMT family completely inhibited RASSF1A expression (Figure 1D), suggesting that either one of the three DNMTs are capable of silencing RASSF1A expression in prostate epithelial cells.
Mahanine decreases nuclear localization of DNMT1 and DNMT3B
To further confirm our immunocytochemical data, PC3 cells were treated in a similar manner with mahanine for 24 hours and nuclear and cytoplasmic fractions were separated from the treated and untreated cells. Our data confirmed that while mahanine decreased DNMT1 levels from the nucleus (~2-fold), and DNMT3B levels in the cytoplasm (~1.5-fold) and in the nucleus (~2.2-fold), it left DNMT3A levels unchanged, suggesting that mahanine modulates the cellular localization and protein levels of DNMT1 and DNMT3B, without affecting DNMT3A (Figure 2B).
Mahanine down-regulates DNMT1 and DNMT3B, but not DNMT3A protein levels in prostate cancer cells
To determine if mahanine affected the total cellular levels of the DNMTs, we treated androgen receptor-negative PC3 cells and androgen-responsive LNCaP cells with 10μM and 20μM of mahanine for a period of 24 to 48 hours. We observed that while mahanine causes a dose- and time-dependent down-regulation in the protein levels of DNMT1 and DNMT3B in both cell lines, it has no effect on DNMT3A protein levels, which is in agreement with our findings from the immunocytochemical and nuclear-cytoplasmic fractionation experiments (Figure 2C and Additional file 2: Figure S2B).
Next, we sought to determine whether the observed decline in DNMT1 and DNMT3B levels was due to suppression of their gene expression upon mahanine treatment. We measured the message levels of these DNMT s as an indicator of the level of their gene expression. We did not detect a noticeable change in the message levels of DNMT1 and DNMT3B in LNCaP or PC3 cells with 20μM and 10μM mahanine treatment, respectively for a period of 24 hours (Figure 2D), suggesting that the decline in DNMT1 and DNMT3B protein levels occurs post-translationally.
Mahanine-induced depletion of DNMTs is not mediated by caspases
Mahanine degrades DNMTs via the ubiquitin-proteasomal pathway
Our data so far eliminates the possibility that transcriptional down-regulation and caspase mediated degradation might be the mechanism by which mahanine decreases the levels of DNMT1 and DNMT3B. Next, we sought to determine whether mahanine mediates DNMT depletion through the ubiquitin-proteasomal pathway. Proteasomal degradation generally occurs via three types of enzymatic activities; specifically, chymotrypsin-like, trypsin-like, and caspase-like. Among these, chymotrypsin-like activity is the rate limiting step in the proteasomal degradation process. To this end, we measured proteasomal activation in PC3 cells treated with mahanine in the absence and presence of a proteasome inhibitor, MG132. We found that while mahanine induced chymotrypsin-like proteasomal activity, it caused a decline in the trypsin-like and caspase-like activities of the proteasome (Figure 3B and Additional file 4: Figure S4B).
To determine whether the induction of chymotrypsin-like proteasome activity by mahanine could account for the decline in DNMT levels, PC3 and LNCaP cells were treated with 10μM and 20μM mahanine, respectively for 24 hours in the presence and absence of MG132 (5 μM). While mahanine treatment resulted in a decline in the levels of DNMT1 and DNMT3B in both cell lines, this effect was rescued upon inhibition of the proteasome, suggesting that mahanine causes DNMT degradation via a chymotrypsin-like proteasomal mechanism (Figure 3C). Since proteasomal degradation is preceded by ubiquitination, we immuno-precipitated DNMT1 and DNMT3B from PC3 cells that had been treated with mahanine and MG132, and found an increase in the levels of ubiquitinated DNMTs in the presence of mahanine (Figure 3D). Similarly, in mahanine-treated PC3 cells we observed an increase in total ubiquitination (Additional file 4: Figure S4C). Taken together, our data suggest that mahanine decreases the cellular levels of DNMT1 and DNMT3B by a ubiquitin-proteasome mediated pathway.
Mahanine down-regulates pAkt levels in PC3 and LNCaP cells
PI3K inhibitor, wortmannin degrades DNMT1 and DNMT3B proteins in prostate cancer cells
Phosphoinositide 3-kinase or PI3K is an enzyme which acts directly upstream of Akt and is essential for its activation. To understand the relationship between Akt activation and the stability of DNMTs in prostate cancer cells, PC3 and LNCaP cells were treated with a PI3K inhibitor, wortmannin for 24 hours. As expected, inhibition of PI3K by wortmannin reduced phospho-Akt levels significantly after 24 hours of treatment. Furthermore, the inactivation of Akt was accompanied by a significant down-regulation in DNMT1 protein levels both in PC3 (~ 2-fold) and LNCaP (~ 5-fold) cells (Figure 4B and Additional file 6: Figure S6). A similar trend was observed in the case of DNMT3B, with an approximate 40% and 60% reduction in its levels in PC3 and LNCaP cells, respectively. The decrease in the levels of DNMT1 and DNMT3B after 24 hours of wortmannin treatment was also observed upon immunocytochemical analyses in PC3 cells (Figure 4C). These data confirm that DNMT stability is mediated by Akt activity and a disruption of Akt activation decreases DNMT levels in prostate cancer cells.
Mahanine treatment disrupts the interaction of pAkt with DNMT1 and DNMT3B in prostate cancer cells
Constitutively active Akt (CA-Akt) rescues mahanine mediated DNMT1 and DNMT3B degradation in BPH1 cells
To determine whether mahanine induced DNMT1 and DNMT3B degradation occurs via the inhibition of Akt activation, BPH1 cells were transfected with a constitutively active Akt expression construct (CA-Akt) or empty vector following which the cells were treated with or without mahanine (10μM) for 24 hours. BPH1 cells are known to natively express low levels of DNMT1, DNMT3B and Akt. The presence of CA-Akt expectedly induced DNMT1 and DNMT3B levels compared to the control and empty vector transfected. Surprisingly, this induction was maintained in the presence by mahanine, indicating that when Akt is constitutively active, mahanine cannot carry out proteasomal degradation of DNMTs (Figure 5C). This clearly demonstrates that the degradation of DNMTs by mahanine stems from its ability to inactivate Akt.
The silencing of the RASSF1A gene has been associated with advanced stages of prostate cancer . Our prior work demonstrated that mahanine possesses the ability to restore RASSF1A expression in several different cancer cell lines, including androgen-responsive LNCaP and androgen-receptor negative PC3 prostate cancer cells, which have been derived from metastases to the lymph node and bone, respectively . However, the scope of that report did not include defining a molecular mechanism to explain the re-expression of RASSF1A upon mahanine treatment, although it did show a decline in total DNMT activity in the presence of mahanine . Our current work stems from these findings, and in this report we establish a molecular mechanism for the inhibition of DNMT signalling by mahanine; furthermore, we delineate the correlation between DNMT and RASSF1A expression in prostate cancer cells.
Our data demonstrate that the re-expression of RASSF1A upon mahanine treatment is a time sensitive event; while the demethylation of the RASSF1A promoter is apparent after 24 hours of mahanine treatment, RASSF1A expression can only be detected after 72 hours of mahanine treatment. This shows that the partial de-methylation of the RASSF1A promoter which occurs after 24 hours of mahanine treatment is not enough to restore its expression; the promoter region must be demethylated to a greater extent, which is only achieved approximately 72 hours following mahanine treatment. This suggests that mahanine could modulate the activities of certain factors involved in the maintaining the methylation pattern of the RASSF1A promoter region, which accounts for the time lag between mahanine treatment and RASSF1A re-expression. Since DNMT1, DNMT3A and DNMT3B are known to be involved in de novo methylation and the maintenance of methylation patterns of genes, we investigated the levels of expression of all three members of the DNMT family. Our data clearly indicates that mahanine treatment causes a decline in the levels of DNMT1 and DNMT3B, without affecting the levels of DNMT3A, in both LNCaP and PC3 prostate cancer cells. Interestingly, the time frame within which mahanine down-regulates DNMT1 and DNMT3B in LNCaP and PC3 cells correlates well with the re-expression of RASSF1A in these cell types, suggesting that mahanine could mediate RASSF1A re-expression via DNMT inhibition. Furthermore, these results indicate that mahanine selectively modulates the cellular levels of certain DNMTs, without ubiquitously down-regulating the levels of all members of the DNMT family. This data is further supported by our findings that the knock-down or over-expression of either member of the DNMT family is sufficient to restore or inhibit the expression of RASSF1A in PC3 or BPH1 cells, respectively; however to a lesser extent with DNMT3A. Therefore, mahanine selectively degrades the two DNMTs which appear to most strongly inhibit RASSF1A expression in PC3 prostate cancer cells. The ability of mahanine to selectively target DNMT1 and DNMT3B clearly differentiates it from other known DNMT inhibitors like 5-aza cytidine and 5-aza-2′-deoxycitidine, which ubiquitously bind to and irreversibly inhibit all members of the DNMT family. Therefore, anti-cancer agents like mahanine which selectively targets DNMT1 and DNMT3B could be beneficial in prostate cancer therapy.
While mahanine causes degradation of DNMT1 and DNMT3B by inducing the chymotrypsin-like activity of the proteasome, it is interesting to note that it does not potentiate the trypsin- and caspase-like activities of the proteasome. The decline in these particular enzymatic activities of the proteasome upon mahanine treatment could be to compensate for the significant induction of the chymotrypsin-like activity upon mahanine treatment and thereby ensure that the overall proteasomal activity is balanced and cellular homeostasis is undisturbed.
The activity of survival kinases such as Akt is known to be highly up-regulated in prostate cancer, which correlates with the high abundance of DNMTs in prostate cancer cells, as Akt is involved in the stabilization of DNMT1, and possibly other DNMTs, via site-specific phosphorylation on Ser/Thr residues. Interestingly, the degradation of DNMTs by mahanine is dependent on its ability to inhibit Akt activity; when Akt is constitutively active mahanine treatment does not result in proteasomal degradation of DNMT1 and DNMT3B. A recent report demonstrated that Akt phosphorylates the Ser143 residue of DNMT1 and thereby increases its stability . However, no such stabilizing phosphorylation events have been described to date for DNMT3B. Our data clearly indicates that Akt is involved in stabilizing not only DNMT1, but also DNMT3B, since constitutively active Akt renders both DNMTs resistant to proteasomal degradation induced by mahanine. The mechanism by which Akt imparts increased stability to DNMT3B remains to be explored. In addition, our immunoprecipitation data shows that mahanine causes a striking decrease in the overall serine phosphorylation of DNMT1, suggesting that mahanine might modulate the phosphorylation status of DNMT1 on more than one serine residue, via the inactivation of other Ser/Thr kinases, in addition to Akt. It will be interesting to further explore specific phospho-sites involved in imparting stability to DNMT1 and DNMT3B and the kinases responsible for this phosphorylation.
Mahanine purification, cell culture, and cell transfection
Mahanine was purified from the leaves of Murraya koenigii as described in our previous published report . Human prostate cancer cell lines, PC3 and LNCaP were obtained from American Type Culture Collection (Manassas, VA). Cells were grown in IMEM (Gibco Life Technologies, Grand Island, NY) containing 10% fetal bovine serum (FBS), 2 mM glutamine, 100 u/ml penicillin G sodium, and 100 mg/ml streptomycin sulfate at 37°C and 5% CO2. BPH1 cells were obtained from Dr. Simon W. Hayward of Vanderbilt University and cultured in the same medium as mentioned above.
PC3 cells were transfected with DNMT shRNAs (OriGene Technologies Inc., Rockville, MD) and RASSF1A expression vector . BPH1 cells were transfected with 1μg/ml of DNMT expression vectors (OriGene) or constitutively active Akt (CA-Akt) #17-254 (Upstate Biotechnology, Lake Placid, NY) plasmids using Genjet vII reagent (Signagen, Gaithersburg, MD). Forty-eight hours after transfection, cells were harvested for RT-PCR analyses.
Live and dead cells were determined according to the manufacturers’ instructions (Cell Viability/Cytotoxicity Assay kit, Biotium Inc. Hayward, CA)
Western blot analysis
Western blot analysis was performed according to our earlier published report . In brief, After 24 hours of mahanine, wortmannin, and MG132 treatment, cellular protein extracts were prepared from PC3 and LNCaP cells after various treatments of mahanine, wortmannin, and MG132. Fifty micrograms of proteins were resolved on 8% SDS–PAGE and transferred onto nitrocellulose membranes (Amersham Hybond-ECL), and immunoblotted with primary antibodies (DNMT1 #2788-1, DNMT3A #3116-1, DNMT3B #2601-1 and poly-Ubiquitin #6686-1 antibodies were purchased from Epitomics, Burlingame, CA; phosphorylated-Akt S473 #4060 and total Akt #4685 were purchased from Cell Signaling Technologies, Beverly, MA; β-actin #Sc47778 antibody was purchased from Santa Cruz Biotechnology, Inc., Santa Cruz, CA; and phospho-serine #612546 antibody was obtained from BD Biosciences, San Jose, CA), overnight at 4°C. Immunoreactive protein bands were detected with horseradish peroxidise-conjugated secondary antibodies (Santa Cruz) and with enhanced chemiluminescence system (Santa Cruz) according to the manufacturer's instructions. Band intensities (pixel densities) were quantified by ImageJ software (National Institutes of Health, Bethesda, MD). The preparation of nuclear extracts and immunoprecipitations were performed according to our previously published methods .
Immunofluorescence staining was performed according to our previously published report . PC3 cells were plated onto ECL-coated chamber slides and were treated with mahanine, wortmannin, or DMSO as controls. The cells were fixed in −20°C methanol, air-dried, and re-hydrated in PBS. After blocking (0.2% BSA) cells were incubated with the primary antibodies (DNMT1, DNMT3A or DNMT3B #Sc376043 from Santa Cruz Biotechnology) overnight at 4°C, followed by incubation with the Alexa Fluor 488 or 594 conjugated secondary antibodies (Molecular probes/Invitrogen, Carlsbad, CA) for 1 hour. Slides were washed, counterstained with DAPI or with propidium iodide, mounted and viewed under a fluorescent Olympus BX microscope (Olympus Corp, Tokyo, Japan). Images were captured at the same magnification (20X) and then imported into Adobe Photoshop.
RASSF1A promoter methylation assay
The methylation status of RASSF1A promoter (Amplicon location: 17881–18115) was determined by Methylation specific primers according to the previously published protocol [38, 39] with some modifications. In brief, PC3 cells were treated with or without mahanine, and the bisulfite modified DNA was isolated using EZ DNA Methylation™ Kit procured from Zymo research (Irvine, CA). The PCR reaction was conducted with 4μl of bisulfite-modified DNA with methylated-specific primers for RASSF1A (forward primer 5’- GGG TTT TGC GAG AGC GCG -3’, reverse primer 5’- GCT AAC AAA CGC GAA CCG -3’) at the annealing temperature of 54°C. For unmethylated RASSF1A (forward primer 5’- GGT TTT GTG AGA GTG TGT TTA G -3’, reverse primer 5’- CAC TAA CAA ACA CAA ACC AAA C -3’) annealing temperature was 47.5°C. After amplification, PCR products were separated on agarose gel and visualized by ethidium bromide fluorescence using the Fuji LAS-1000 Imager.
Reverse transcriptase-polymerase chain reaction (RT-PCR)
RNA was extracted from PC3 and LNCaP cells with TRIzol solution as suggested by the manufacturer (Invitrogen, Carlsbad, CA) and genes of interest were amplified using 0.5-1 μg of total RNA using Verso 1-Step RT-PCR kit purchased from Thermo Scientific (Waltham, MA). Human-specific primers were designed using the Primer Quest program and purchased from Integrated DNA Technologies, Inc (Coralville, IA). The primer sequences are: DNMT1 forward primer 5- GTGAGGACATGCA GCTTTCA −3, reverse primer 5- TGCTGCCTTTGATGTAGTCG-3, DNMT3A forward primer 5’-TGAGAGTG ACACTGCCAAGC-3’, reverse primer 5’- CAGCAGATGGTG CAGTAGGA-3’; DNMT3B forward primer 5’-TTTGGCCACCTTCAATAAGC-3’, reverse primer 5’- GGCAACATC TGAAGCCATTT-3’; GAPDH forward primer 5-CCACCCATGGCAAATT CCATGGCA-3, reverse primer 5-TCTAGACGGCAGGTCAGGTCCACC-3’. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and RASSF1A primer sequences have been previously published . PCRs were initiated at 47°C for 30 min then 95°C for 1min followed by 30 cycles of 95°C for 1 min, 1 min annealing temperature, 72°C for 1 min, and final extension at 72°C for 3 min. After amplification, PCR products were separated on 1.5% agarose gels and visualized by ethidium bromide fluorescence using the Fuji LAS-1000 Imager.
All data were derived from at least three independent experiments and statistical analyses were conducted by using one-way analysis of variance (ANOVA) followed by the Dunnett’s post-test with an assigned confidence interval of 95%. Values were presented as means ± SEM. p-value < 0.05 was considered significant.
This work was supported by National Institutes of Health R01 CA131123 to Dr. Partha P. Banerjee. We thank Dr. Simon W. Hayward of Vanderbilt University, Nashville, TN for his generous gift of BPH1 cells. We also thank Dr. Gerd P. Pfeifer, Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA for providing us RASSF1A expression vector.
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