ZEB1 limits adenoviral infectability by transcriptionally repressing the Coxsackie virus and Adenovirus Receptor
© Lacher et al; licensee BioMed Central Ltd. 2011
Received: 16 December 2010
Accepted: 27 July 2011
Published: 27 July 2011
We have previously reported that RAS-MEK (Cancer Res. 2003 May 1;63(9):2088-95) and TGF-β (Cancer Res. 2006 Feb 1;66(3):1648-57) signaling negatively regulate coxsackie virus and adenovirus receptor (CAR) cell-surface expression and adenovirus uptake. In the case of TGF-β, down-regulation of CAR occurred in context of epithelial-to-mesenchymal transition (EMT), a process associated with transcriptional repression of E-cadherin by, for instance, the E2 box-binding factors Snail, Slug, SIP1 or ZEB1. While EMT is crucial in embryonic development, it has been proposed to contribute to the formation of invasive and metastatic carcinomas by reducing cell-cell contacts and increasing cell migration.
Here, we show that ZEB1 represses CAR expression in both PANC-1 (pancreatic) and MDA-MB-231 (breast) human cancer cells. We demonstrate that ZEB1 physically associates with at least one of two closely spaced and conserved E2 boxes within the minimal CAR promoter here defined as genomic region -291 to -1 relative to the translational start ATG. In agreement with ZEB1's established role as a negative regulator of the epithelial phenotype, silencing its expression in MDA-MB-231 cells induced a partial Mesenchymal-to-Epithelial Transition (MET) characterized by increased levels of E-cadherin and CAR, and decreased expression of fibronectin. Conversely, knockdown of ZEB1 in PANC-1 cells antagonized both the TGF-β-induced down-regulation of E-cadherin and CAR and the reduction of adenovirus uptake. Interestingly, even though ZEB1 clearly contributes to the TGF-β-induced mesenchymal phenotype of PANC-1 cells, TGF-β did not seem to affect ZEB1's protein levels or subcellular localization. These findings suggest that TGF-β may inhibit CAR expression by regulating factor(s) that cooperate with ZEB1 to repress the CAR promoter, rather than by regulating ZEB1 expression levels. In addition to the negative E2 box-mediated regulation the minimal CAR promoter is positively regulated through conserved ETS and CRE elements.
This report provides evidence that inhibition of ZEB1 may improve adenovirus uptake of cancer cells that have undergone EMT and for which ZEB1 is necessary to maintain the mesenchymal phenotype. Targeting of ZEB1 may reverse some aspects of EMT including the down-regulation of CAR.
The coxsackie virus and adenovirus receptor (CAR), encoded by the CXADR gene, is localized at the apicolateral/basolateral surface of polarized epithelial cells and serves as a component of tight junctions, thus participating in the sealing of the epithelial layer. In addition to its basolateral localization, recently, an apically localized isoform (CAREx8) was described which may be responsible for initiation of respiratory adenoviral infections . Furthermore, CAR regulates cardiac conductance, as demonstrated in a mouse model in which heart-specific inducible CAR knockout resulted in impaired electrical conductance between atrium and ventricle .
CAR is the primary receptor for adenovirus serotypes 2 and 5  and thus a likely determining factor for the efficacy of adenovirus-based cancer therapy. A number of mechanisms by which CAR expression is regulated have been described, but our understanding of how to manipulate CAR expression levels in cancer is incomplete [4–11]. Learning the molecular machinery regulating CAR expression could set the stage for pharmacological interventions aimed at achieving high cell surface CAR levels to maximize virus uptake.
We previously identified RAS-MEK  and TGF-β signaling  as negative regulators of CAR expression in cancer cell lines. Down-regulation of CAR through TGF-β occurred in the context of epithelial-to-mesenchymal transition (EMT), a process that refers to the formation of mesenchymal cells from epithelial cells without the involvement of stem cells. During EMT, both tight junctions at apicolateral surfaces containing CAR, and more basolateral adherens junctions containing E-cadherin are disrupted, and cells acquire a motile phenotype. EMT has evolved as an important developmental program. However, inappropriate activation is linked to pathological conditions such as fibrosis and cancer . In the case of cancer, EMT may contribute to the formation of invasive and metastatic carcinomas by reducing cell-cell contacts and increasing cell migration [13–15]. Additionally, the EMT-associated reduction of cell surface CAR likely makes advanced malignancies with already poor prognosis less responsive to treatment with oncolytic adenoviruses [5, 9].
One of the most prominent inducers of EMT is TGF-β. It is postulated that TGF-β inhibits cell cycle progression, but alters the tumor microenvironment, promotes EMT, immunosuppression and angiogenesis in advanced malignancies, thus playing both tumor suppressive and oncogenic roles during multistage carcinogenesis [16–22]. The switch from tumor suppressor to oncogene may occur upon loss of the cytostatic arm of the TGF-β pathway, for instance through genetic inactivation of tumor suppressive TGF-β downstream effectors such as p15INK4b, a cyclin-dependent kinase (CDK) inhibitor .
Mechanisms underlying TGF-β-induced EMT involve E2 box-binding transcriptional repressors, in particular Snail (SNAI1), Slug (SNAI2), SIP1 (ZEB2) and ZEB1 (ZEB1). These repressors target genes whose protein products are instrumental for the integrity of the epithelial phenotype [23–25]. Interestingly, in addition to regulating protein-encoding genes, ZEB1 and SIP1 are both targets and negative regulators of microRNA-200 (miR-200) family members. Depending on whether an extracellular stimulus up-regulates ZEB1 or SIP1, or raises miR-200 levels, the resulting positive feedback loop may stabilize either a mesenchymal (elevated ZEB1 and/or SIP1 activity) or an epithelial (increased miR-200 levels) state [26–28]. Furthermore, consistent with the proposed contribution of EMT to cancer progression, expression of E2 box-binding repressors has been observed in several malignancies [25, 29–32].
The aim of this study was to examine the mechanism by which TGF-β down-regulates CAR. By investigating how RAS-MEK  and TGF-β signaling  impact on CAR expression, we noticed similar expression patterns for CAR and E-cadherin, suggesting common underlying regulatory mechanisms. We show here that for the regulation through TGF-β this is indeed the case. Both CAR and E-cadherin promoters are structurally conserved around two closely spaced E2 boxes. We provide evidence that ZEB1, which has previously been reported to repress E-cadherin expression [25, 33–36], also down-regulates CAR. This study, in combination with the work of others [26, 27, 34, 36], identifies ZEB1 as a potential therapeutic target for strategies aimed at improving uptake of therapeutic adenoviruses and preventing or reversing cancer-associated EMT processes while leaving the tumor suppressive functions of TGF-β unaffected. As our work was in progress, a report was published demonstrating that TGF-β may repress the mouse CAR promoter through Snail in combination with Smad3/4 . Our data is consistent with a model in which both ZEB1 and Snail-Smad3/4 can simultaneously repress the human CAR promoter.
Additional methods and further details including antibodies are provided in the Additional file 1.
In silico analyses
The human pancreatic cancer cell line PANC-1 , and the human breast cancer cell line MDA-MB-231 (gift from Dr. J. Gray, Lawrence Berkeley National Laboratory) were maintained in Dulbecco's Modified Eagle Medium (DMEM; UCSF Cell Culture Facility, San Francisco, CA, USA) supplemented with 10% Fetal Bovine Serum (FBS; Valley Biomedical, Inc.; Winchester, VA, USA) and 100 units/mL penicillin "G", 100 mcg/mL streptomycin SO4 (both UCSF Cell Culture Facility), and 5 microgram/mL Plasmocin™ (InvivoGen, San Diego, CA, USA). The human non-small cell lung cancer cell line H460 (gift from Dr. D. Jablons, UCSF)  was grown in RPMI-1640 (Gibco/Invitrogen, Carlsbad, CA, USA), supplemented with 10% FBS, penicillin, streptomycin and Plasmocin (all supplemented components as above).
Various CAR [promoter]-[5'-UTR] fragments were independently PCR-amplified from human genomic DNA and cloned into pGL3Ba-DESneo3N. The sequence between the translational ATG start codons of CAR and luciferase was removed by restriction digestion, followed by ethanol precipitation and re-ligation. Mutations at the E2 boxes, ETS and CRE motifs were introduced into the -291/-1 luciferase construct. Inducible Myc-tagged ZEB1 expression constructs were generated by replacing the mSIP1 coding sequence (cds) of pUHD10.3SIP1  through PCR-amplified human ZEB1 cds. Primer sequences and cloning strategies are provided as supplemental information (Additional file 1).
Immunofluorescence and F-actin staining
PANC-1 and MDA-MB-231 cells were grown on Lab-Tek™ Chamber Slides (Nalge Nunc/Thermo Fisher Scientific, Inc., Rockford, IL, USA) and treated with 5 ng/mL platelet-derived human TGF-β1 (R&D Systems, Minneapolis, MN, USA) for four days. For E-cadherin staining, cells were fixed with a 1:1 solution of methanol and acetone at -20°C, and unspecific epitopes were blocked with 3% bovine serum albumin (BSA) (Sigma-Aldrich, St. Louis, MO, USA). Then, cells were incubated for 1 hour with 2 microgram/mL of the mouse anti-E-cadherin antibody (clone HECD-1, Invitrogen). For F-actin and vimentin stainings, cells were fixed for 15 min. with IC Fixation Buffer (Invitrogen) and permeabilized for 5 min. with 0.1% Triton X-100 (Aqua Solutions, Deer Park, TX, USA). Then, unspecific epitopes were blocked with 3% BSA and cells were incubated for 1 hour with a 1:100 dilution of phalloidin conjugated to Texas Red® (Invitrogen) or with a 1:100 dilution of the rabbit anti-vimentin antibody (D21H3, Cell Signaling Technology, Inc., Danvers, MA, USA). For E-cadherin and vimentin stainings secondary antibodies conjugated to Alexa Fluor® 488 (Molecular Probes/Invitrogen) were used. Nuclei were stained with DAPI, and samples mounted onto glass slides using Vectashield (Vector Lab, Burlingame, CA, USA). Immunofluorescence images were obtained using a Zeiss Imager Z2 microscope (Carl Zeiss, Jena, Germany) equipped with an AxioCam camera and processed with Axiovision software. Digital images were adjusted for contrast and brightness using Adobe Photoshop CS5.
PANC-1 cells were pre-treated for two days with 5 ng/mL platelet-derived human TGF-β1 (R&D Systems), then, and two days later, siRNA-transfected by using Lipofectamine RNAiMax (Invitrogen). TGF-β treatment was continued through the first, until two days after the second transfection. MDA-MB-231 cells were similarly transfected, but not stimulated with ectopic TGF-β. Cell lysis for protein harvest, flow cytometric analysis of cell-surface CAR and adenovirus infections were carried out four days after the initial transfection. Abbreviations: UT, untransfected; Ctrl #1, siControl ON-TARGETplus Non-targeting siRNA #1 (Dharmacon/Thermo Fisher Scientific, Inc.); Ctrl #2, firefly luciferase-targeting siRNA; ZEB1 siRNA #1/#2, ZEB1-targeting siRNAs. Ctrl #2 and ZEB1 siRNA sequences are provided in Additional file 1 (Table S3) and were obtained by using the siDESIGN® Center (Dharmacon/Thermo Fisher Scientific, Inc.). Detailed information is provided as supplemental information (Additional file 1).
Expression analysis by real-time RT-PCR
Total RNA was extracted with the RNeasy kit (Qiagen, Valencia, CA, USA). Reverse-transcription and real-time PCR were carried out at the UCSF HDFCCC Genome Core with the primer/probe sequences listed in Additional file 1 (Table S3) and with Expression Assays (Applied Biosystems, Foster City, CA, USA) for CDH1 (E-cadherin, Hs00170423_m1), ZEB1 (Hs00611018_m1 or Hs00232783_m1), ZEB2 (SIP1, Hs00207691_m1), SNAI1 (Snail, Hs00195591_m1), SNAI2 (Slug, Hs00161904_m1) and SERPINE1 (PAI-1, Hs01126604_m1). Data were analyzed by relative quantitation .
Immunoblotting and cell fractionation
Antibodies used include rabbit anti-phospho-Smad2 (Ser465/467, Cell Signaling Technology, Inc.), goat anti-ZEB1 (E-20, Santa Cruz Biotechnology, Inc., Santa Cruz, CA, USA), mouse anti-β-tubulin (Sigma-Aldrich), mouse anti-PARP (clone C2-10, Pharmingen/BD Biosciences, San Jose, CA, USA), mouse anti-GAPDH-Peroxidase Conjugate (Sigma-Aldrich), and mouse anti-Myc Tag (clone 4A6; Upstate/Millipore, Charlottesville, VA, USA). Cell fractionation was carried out via the NE-PER® Nuclear and Cytoplasmic Extraction Reagents kit (Pierce/Thermo Fisher Scientific, Inc.). A description of the Western blot procedure and further antibody references are provided elsewhere .
Luciferase reporter assays
All transfections involving CAR promoter constructs were carried out by using FuGENE HD (Roche, Indianapolis, IN, USA) (3 microliter per 1 microgram of DNA), and included co-transfection of the renilla luciferase-encoding pRL-SV40 plasmid (Promega, Madison, WI, USA) for normalization. Cells were subconfluent at the time of transfection. For the identification of the CAR promoter, cells were grown in 24-well plates and transfected with 750 nanogram of the pGL3Ba-DESneo3N reporter plasmids in combination with 10 nanogram pRL-SV40. To transfect equimolar amounts of each CAR promoter construct of the CAR upstream 5'-deletion series, plasmid size differences were compensated by co-transfection with the pGL3Ba-DESneo3N-EmVec empty vector plasmid. For the characterization of the ETS and CRE elements, cells were grown in 6-well plates and transfected with 3 microgram of wild-type, ETS or CRE element-mutated -291/-1 luciferase construct in combination with 50 nanogram pRL-SV40. For the characterization of the E2 boxes as binding sites for ZEB1, cells were grown in 24-well plates and transfected with 500 nanogram of wild-type and E2 box-mutated -291/-1 luciferase construct, 125 nanogram pRevTet-Off (Clontech Laboratories, Inc./Takara Bio, Inc., Otsu, Shiga, Japan), and 375 nanogram pTRE-6Myc-deltaATG-hZEB1 in combination with 10 nanogram pRL-SV40. 4-6 hours post transfection, the transfection medium was removed, and around 1.5-2 hours later, stimulation with 2 microgram/mL doxycyline hyclate (Sigma-Aldrich) was begun. Cells were lysed twenty-four (to define the minimal CAR promoter and to characterize ETS and CRE elements) or forty-eight (to assess effects of Myc-ZEB1 on the WT and mutant CAR promoter) hours post transfection with Passive Lysis Buffer (Promega). Reporter activities were measured with the Dual-Luciferase® Reporter Assay System (Promega).
Biotinylated Oligonucleotide Precipitation Assay
One day after seeding 3 × 106 PANC-1 cells per 10 cm-dish, cells were transiently co-transfected with pRevTet-Off (4.0 microgram) (Clontech Laboratories, Inc./Takara Bio, Inc.) in combination with pTRE-6Myc-deltaATG-hZEB1 (12.0 microgram) by using FuGENE HD (Roche) (3 microliter per 1 microgram of DNA). Control lysates were made from PANC-1 cells seeded at a density of 5 × 105 cells per well (6-well plate) and transfected with the same plasmids. Four hours post transfection, transfection medium was replaced by antibiotic-containing full medium. Six hours post transfection, medium was again replaced by full medium with (to repress ZEB1) or without (to induce ZEB1) 2 microgram/mL doxycycline hyclate (Sigma-Aldrich). Forty-eight hours after transfection, oligonucleotide precipitations were carried out following a modified version of the procedure described by others [39, 45]. ZEB1 was detected with the mouse monoclonal anti-Myc Tag clone 4A6 (Upstate/Millipore) antibody at 1 microgram/mL. Detailed information is provided as supplemental information (Additional file 1).
PANC-1 cells were transiently transfected with pTRE-6Myc-deltaATG-hZEB1 in combination with pRevTet-Off (Clontech) using FuGENE HD (Roche). For the control sample, six hours after addition of the plasmid DNA to the cells, expression of Myc-ZEB1 was suppressed with 2 microgram/mL doxycyline hyclate (Sigma-Aldrich). The next day, cells of both control and experimental samples were stimulated with 5 ng/mL platelet-derived human TGF-β1 (R&D Systems). Forty-eight hours after transfection, chromatin was cross-linked with paraformaldehyde and subjected to Chromatin Immunoprecipitation (ChIP) at the University of California at Davis (UC Davis) Genome Center (CA, USA), following a protocol developed by the Farnham laboratory (UC Davis, Davis, CA, USA) (http://www.genomecenter.ucdavis.edu/farnham/pdf/FarnhamLabChIP%20Protocol.pdf). In short, samples were sonicated using a BioRuptor™ Sonicator (Diagenode, Inc.; Sparta, NJ, USA), DNA was precipitated with an anti-Myc Tag antibody (clone 4A6; Upstate/Millipore), and SYBR Green I real-time PCR with the precipitated DNA as template was conducted using the iQ™ SYBR® Green Supermix (Bio-Rad Laboratories, Hercules, CA, USA) using CAR promoter-specific primers (Additional file 1, Table S3).
Following a four-day siRNA treatment period, PANC-1 cells were infected with 300 microliter/well (12-well plates) Ad-GFP  diluted in DMEM (UCSF Cell Culture Facility) supplemented with 2% FBS (Valley Biomedical, Inc.) at a Multiplicity Of Infection (MOI) of 200. Ninety minutes post-infection, virus was replaced by regular growth medium. Twenty-four hours post-infection, Ad-GFP uptake was analyzed by both flow cytometry (GFP intensities) and real-time PCR (virus copy numbers). For the latter approach genomic/adenoviral DNA was first extracted with the DNeasy® Blood & Tissue kit (Qiagen) and then subjected to ethanol precipitation to potentially improve DNA quality. Relative virus copy numbers were determined at the UCSF HDFCCC Genome Core by TaqMan PCR amplification of the adenovirus fiber gene (primer/probe sequences shown in Additional file 1, Table S3) normalized to genomic DNA amplified with a pool of primers for D1S2868, D2S385, D4S1605, D5S643, D10S586, and D11S1315 . Data were analyzed by relative quantitation .
Live cells were stained with an anti-CAR-phycoerythrin (PE) antibody (E1-1, mouse monoclonal; Santa Cruz Biotechnology, Inc.) or PE-conjugated control IgG-PE (mouse monoclonal IgG1 κ, Pharmingen/BD Biosciences) while rotating for 60 minutes at 4°C. Cells were then washed and resuspended in 1 micromolar TO-PRO®-3 iodide (TP3, for exclusion of dead cells) (Invitrogen) in PBS supplemented with 5% FBS, and analyzed by flow cytometry using FACSCalibur (BD Biosciences) or Accuri C6 (Accuri Cytometers, Inc., Ann Arbor, MI, USA/BD, Franklin Lakes, NJ, USA) flow cytometers. Cell-surface CAR was detected in the FL2 channel, non-viable cells, stained by TP3 and detected in the FL4 channel, were excluded. For the analysis of live Ad-GFP infected cells, GFP was detected in the FL1 channel. TP3-positive cells were excluded. Data analysis was carried out with Cyflogic™ software (CyFlo Ltd, Turku, Finland). Detailed information is provided as supplemental information (Additional file 1).
Defining the CAR promoter
TGF-β down-regulates CAR mRNA and protein levels . Since neither mRNA nor protein stability appeared to be affected by TGF-β , regulation of CAR expression likely occurs at the promoter level. Bowles et al. reported that the locus of the functional human CAR gene (CXADR) is on chromosome 21, 21q11.2 . However, even though 21q11 harbors CAR sequence, this locus encodes a CAR pseudogene lacking introns. The functional human CAR gene is located on 21q21.1 (Entrez Gene, Gene ID: 1525, NCBI).
To experimentally determine the CAR promoter region we cloned several fragments of CAR upstream sequence as a 5'-deletion series into pGL3Ba-DESneo3N (a luciferase reporter vector we engineered allowing recombination-based cloning of [promoter]-5'-UTR fragments in endogenous constellation, i.e. without vector sequence between the regulatory fragments and the luciferase coding sequence (Figure 1A). To identify genomic regions involved in the regulation of CAR expression, we transfected the 5'-deletion series into PANC-1 (human pancreatic cancer), H460 (human non-small cell lung cancer), and MDA-MB-231 (human breast cancer) cells. In all cell lines, reporter activities were higher for the genomic fragments -2017/-1, -1195/-1, -681/-1, -291/-1 than for -926/-1, and -890/-1 (Figure 1A). This may suggest that silencer elements are present between -1194 and -682, and that positive regulatory elements further upstream override this negative regulation. In all cell lines, maximal promoter activity was measured with the -291/-1 construct, whereas the -96/-1 fragment was only minimally active. Therefore, the CAR core promoter, which interacts with the DNA polymerase II complex, and the adjacent proximal promoter , are located within -291 and -1 relative to the translational start ATG. This is in agreement with a previous report by Pong et al. illustrating that CAR transcription is likely initiated at around -150 relative to the ATG .
Since each promoter/5'-UTR fragment was individually PCR-amplified we were able to identify a single nucleotide polymorphism (SNP) at position -579, with the base being either thymine (in the -2017/-1, -1195/-1, -926/-1 fragments) or cytosine (-890/-1 and -681/-1 fragments). It is unlikely that this SNP influences CAR expression, since the reporter activities of the -926/-1 and the -890/-1 fragments, which differ only in 36 bp, are very similar, despite the polymorphic difference (Figure 1A and data not shown).
By aligning CAR upstream sequences from diverse species ranging from zebrafish to man, several conserved elements were recognized within the -291/-1 fragment: putative binding sites for ETS transcription factors and for c-AMP responsive element (CRE) binding protein (CREB) [41, 42, 49], as well as two closely spaced E2 boxes (Figure 1B). The latter elements are particularly interesting since they are located in a similar genetic context than the E2 boxes in the human E-cadherin promoter to which E2 box-binding repressors such as SIP1 [23, 33, 35, 39] and ZEB1 [25, 33–36] bind. To investigate whether the ETS and CRE elements are biologically relevant, we transiently transfected PANC-1 and MDA-MB-231 cells with ETS or CRE mutant -291/-1 luciferase constructs. Inactivation of either motif reduced CAR promoter activity, suggesting that both ETS and CREB factors may induce CAR expression (Figure 1C).
Down-regulation of CAR in TGF-β-induced EMT
E2 box-dependent repression of the human CAR promoter by ectopic ZEB1
The presence of the dual E2 box motif suggests that, in addition to ZEB1, also SIP1 may repress the CAR promoter. Indeed, overexpression of Myc-tagged SIP1  repressed CAR promoter activity E2 box-dependently (data not shown). However, since TGF-β neither increased SIP1 mRNA expression, nor are the SIP1 mRNA levels high in PANC-1 cells (Figure 3C) SIP1 is unlikely the main regulator of CAR in TGF-β-mediated EMT in our PANC-1 system.
ZEB1 binds to the CAR promoter
To determine whether ZEB1 indeed physically binds to the E2 boxes in the CAR promoter, we overexpressed Myc-tagged human ZEB1 in PANC-1 cells and incubated the cell extracts with biotinylated oligonucleotides composed of a region of the CAR promoter containing the two E2 boxes (Additional file 1, Table S3). A similar strategy was used to elegantly demonstrate binding of SIP1 to the E-cadherin promoter . Following pull-down with streptavidin-conjugated agarose resin, Myc-ZEB1 was detected by conventional Western blotting with an anti-Myc tag antibody. A strong signal was obtained with the oligonucleotides representing both wild-type and E2 box 2-mutant CAR promoter sequence. A mutation in either only E2 box 1 or in both E2 boxes prevented binding of ZEB1 to the oligonucleotides (Figure 4B). We conducted the same assay with Myc-tagged SIP1  and, interestingly, observed a similar binding pattern (data not shown). However, as outlined above, SIP1 is unlikely the main repressor of CAR in TGF-β-mediated EMT in PANC-1 cells. Taken together, our data indicate that ZEB1 interacts with E2 box 1 but not with E2 box 2 (see Figure 1A for the location of E2 box 1 and 2 within the CAR promoter). It is conceivable that ZEB1 might still require both E2 boxes in the CAR promoter for binding, but the point mutation in E2 box 2 was insufficient to prevent binding (Figure 4C).
To ascertain whether ZEB1 also binds to the chromosomal CAR promoter in PANC-1 cells stimulated with TGF-β, a Chromatin Immunoprecipitation (ChIP) assay was conducted with cells transiently transfected with inducible Myc-ZEB1. As demonstrated in Figure 4D, precipitation of CAR DNA with an anti-Myc Tag antibody was apparent when Myc-ZEB1 was induced, suggesting binding of ZEB1 to genomic CAR promoter sequence. Nevertheless, some binding was also observed when Myc-ZEB1 was repressed (Figure 4D). However, this latter effect is likely due to leakiness of the system allowing some Myc-ZEB1 expression even in the presence of the repressor (doxycycline) (Figure 4E and Additional file 1, Fig. S1). As determined from sample aliquots removed prior to crosslinking, total ZEB1 mRNA levels were approximately 30 fold higher in the ChIP experiment following induction of Myc-ZEB1 expression by absence of doxycycline (Figure 4E).
ZEB1 represses CAR in mesenchymal cells
TGF-β does not affect ZEB1 protein levels or subcellular localization
While TGF-β only minimally up-regulated ZEB1 mRNA in PANC-1 cells (Figure 3D and Additional file 1, Fig. S1), effects at the protein level varied: some (Figure 5A) but not all (Figure 5B) experiments suggested that stimulation by TGF-β increases the total ZEB1 protein levels. To address this question systematically, we measured ZEB1 protein levels over time, with harvests of the total protein fractions in twenty-four hour intervals. Indeed, while CAR was down-regulated at every time point in the TGF-β-treated samples, ZEB1 levels remained unchanged throughout the time-course (Figure 5B). To investigate whether TGF-β promotes nuclear entry of ZEB1 as a mechanism to increase the latter protein's activity as a transcriptional repressor of CAR, we measured ZEB1 protein levels in both nuclear and cytoplasmic fractions. Interestingly, ZEB1 appears to be exclusively localized in the nucleus, both in the presence and absence of TGF-β. In agreement with the total ZEB1 protein data, TGF-β stimulation for forty-eight hours did not increase the nuclear ZEB1 levels (Figure 5C).
ZEB1 is necessary for TGF-β-induced EMT in PANC-1 cells
ZEB1 knockdown facilitates adenovirus uptake
In agreement with the total CAR protein (Figure 5A) and cell-surface CAR (Figure 7A) data, PANC-1 cells with silenced ZEB1 expression were more susceptible to infection with a green fluorescence protein (GFP)-encoding adenovirus (Ad-GFP)  than the TGF-β treated non-silencing controls. This effect was apparent both at the level of GFP signal intensity (Figure 7C) and virus copy number (Figure 7D). For both methods, cells were harvested twenty-four hours post infection and were either analyzed by flow cytometry (GFP signal) or by TaqMan PCR (copy number) using adenoviral DNA (extracted together with cellular genomic DNA) as template. This data indicates that knockdown of ZEB1 might be a suitable approach to improve cellular uptake of therapeutic adenoviruses.
Up-regulation of CAR may be achieved by treatment with pharmacological inhibitors of RAS-MEK , of TGF-β signaling , or with HDAC inhibitors [6, 7]. Here, we have demonstrated that ZEB1 plays a prominent role in the TGF-β-induced down-regulation of CAR, and that knockdown of ZEB1 is sufficient to improve adenovirus uptake.
We have previously noticed similar expression patterns for CAR and E-cadherin, and thus hypothesized that the underlying regulatory mechanisms are related. Here, we have functionally defined the minimal human CAR promoter and have shown that it contains four orthologously conserved motifs: putative ETS and CRE elements, and two closely spaced E2 boxes. Particularly the latter elements caught our attention, since they were reported to interact with E2 box transcriptional repressors such as ZEB1 [25, 33–36] and SIP1 [23, 33, 35, 39] in the E-cadherin promoter. Furthermore, the genetic context of the E2 boxes in the CAR (Figure 1B) and E-cadherin  promoters is similar. Indeed, overexpressed ZEB1 repressed the activity of the -291/-1 CAR promoter, and bound to CAR promoter oligonucleotides and chromatin. It is of note that Pong et al. suggested that the functional CAR promoter is located between -585 and -400 . However, since the latter study did not address the role of the E2 boxes and primarily focused on CAR upstream sequence mediating positive regulation of promoter activity, it does not contradict our findings. Indeed, we have shown that the -681/-1 CAR upstream fragment, containing the proposed -585/-400 promoter, is associated with high promoter activity (Figure 1A).
Our ZEB1 knockdown experiments provide evidence that ZEB1 is a physiological repressor of CAR expression in PANC-1 and MDA-MB-231 cells. However, even though knockdown of ZEB1 was sufficient to antagonize the TGF-β-induced down-regulation of CAR and E-cadherin (Figure 5A), we did not observe consistent changes of the ZEB1 protein levels in PANC-1 cells neither in total nor nuclear fractions as consequence of the TGF-β stimulation (Figure 5A-C). Therefore, in our PANC-1 EMT model, TGF-β may activate ZEB1 rather than up-regulate its expression. Underlying mechanisms have not been described yet but may include posttranslational modification of ZEB1 or physical binding to TGF-β downstream effectors. For instance, TGF-β may enhance ZEB1's repressor activity by up-regulating expression and/or activity of ZEB1-associated co-repressors such as CtBP-1/-2 and/or BRG1. In support, TGF-β stimulation increased both ctbp1 and brg1 mRNA levels in NMuMG cells (, supplementary table I), a murine cell line for which we and others reported a TGF-β-mediated down-regulation of CAR [9, 37]. However, in contrast to our data obtained with (human) PANC-1 cells, NMuMG cells responded to TGF-β stimulation with increased ZEB1 (δEF1) expression . Nevertheless, BRG1 was shown to physically associate with ZEB1 to repress the E-cadherin promoter .
Even though ZEB1 is necessary for the TGF-β-induced inhibition of CAR expression, TGF-β may activate factors other than co-repressors that physically interact with ZEB1 to down-regulate CAR. In such a model, ZEB1 would play a role as a constitutive repressor of CAR and thereby counteract activating factors such as those interacting with the ETS and CRE elements (Figure 1). siRNA-mediated depletion of ZEB1 would ease repression and consequentially increase CAR levels. Such a model appears attractive (Figure 6): Snail-Smad3/4 was shown to repress the mouse CAR promoter by a mechanism that involves interactions with E2 boxes and adjacent Smad-binding elements (SBE s) . Intriguingly, similarly to the mouse CAR promoter, E2 box 2 in the human CAR promoter contains an adjacent SBE (5'-CAGA-3') as well (Figure 1B). This may indicate that the human CAR promoter can also potentially be inhibited by Snail-Smad3/4 . Therefore, ZEB1 may regulate the basal CAR levels by mediating a certain degree of promoter inhibition when bound to E2 box 1. However, further repression through binding of Snail-Smad3/4 to E2 box 2 may occur upon stimulation with TGF-β (Figure 6). The assumption that the mesenchymal factor ZEB1 is bound to the CAR promoter even in the absence of TGF-β may be regarded as a discrepancy to the epithelial features of PANC-1 cells (Figure 2, 3 and 5). However, even though these cells undergo TGF-β-induced EMT, they may not be prototypical epithelial cells as they express some mesenchymal/stem cell markers and can be brought into a more typical epithelial state by inhibiting Cyr61 . Furthermore, even though functional characterization of the role of Snail-Smad3/4 on the CAR promoter was conducted in mouse cells, in invasive human ductal breast carcinoma, nuclear expression of Snail, Smad3 and Smad4 correlated with loss of CAR expression at the invasive front . This data is consistent with our model which postulates that Snail-Smad3/4 may also negatively regulate the human CAR promoter (Figure 6).
Our work identifies ZEB1 as a negative regulator of cell-surface CAR expression and adenovirus uptake and thus as a candidate therapeutic target in treatment strategies with oncolytic adenoviruses. Responsive tumor types may include moderately to poorly differentiated gastrointestinal tumors with low CAR expression . However, whether or not this approach is successful does not solely depend on how efficiently the virus is taken up by the respective target cells, but also how effectively it replicates once taken up. We and others recently demonstrated that p21WAF1 acts as a negative regulator of adenovirus replication [7, 11]. For instance, even though the HDAC inhibitor valproic acid (VPA) up-regulated CAR, and facilitated adenovirus uptake, it additionally increased p21WAF1 levels and reduced virus replication . Therefore, if such a scenario also applies to approaches targeting ZEB1, it might be necessary to engineer a replication-competent adenovirus able to silence p21 expression to improve replication and cell killing.
In summary, we have shown that ZEB1 negatively regulates CAR expression and adenovirus uptake in the context of TGF-β-mediated EMT, and that inactivation of ZEB1 may induce some form and degree of MET. We have demonstrated that knockdown of ZEB1 antagonized the TGF-β-mediated EMT process and the down-regulation of CAR in PANC-1 cells.
Our findings may suggest that carcinoma cells in vivo, stimulated by stroma-derived TGF-β, might respond to ZEB1 inactivation with MET resulting in reduced invasiveness and CAR up-regulation, and in improved adenovirus uptake. The latter effect may translate into more effective therapies utilizing oncolytic adenoviruses.
We are grateful to Drs. Tanja Tamgüney, David Dankort, Madhu Macrae and Walter Lacher for critical reading of the manuscript and suggestions, to Drs. Mike Fried, Stephan Gysin and Rosemary Akhurst for helpful discussions, and to Céline Sabatier Lacher for editing the manuscript. We are thankful to Dr. Kirsten Copren, Jennifer Dang, and Kathryn Thompson from the UCSF HDFCCC Genome Analysis Core, to Dr. Charles Nicolet and Heather Witt from the UC Davis Genome Center, and to Kristina Zumer for their excellent technical contribution. The pUHD10.3SIP1 construct is a generous gift from Dr. Frans van Roy. This work was supported by NIH grants R01 CA095701, R01 CA118545 (W.M.K), UCSF Discovery Grant 02-10242 (W.M.K), the Hellman Family Award (W.M.K), and the P30 CA82103 Cancer Center Support Grant.
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