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Molecular Cancer Research 1:508-518 (2003)
© 2003 American Association for Cancer Research


Cell Cycle, Cell Death, and Senescence

ARMER, Apoptotic Regulator in the Membrane of the Endoplasmic Reticulum, A Novel Inhibitor of Apoptosis1

Hannah M. Lui2, Jun Chen1, Lingli Wang1 and Louie Naumovski1

1 Department of Pediatrics, Division of Hematology/Oncology, Stanford University School of Medicine, Stanford, CA and
2 Department of Biological Sciences, Stanford University, Stanford, CA

Requests for reprints: Louie Naumovski, Department of Pediatrics, Division of Hematology/Oncology, Stanford University School of Medicine, CCSR Rm. 1215, Stanford, CA 94305-5149. Phone: (650) 723-5113; Fax: (650) 736-0195. E-mail: naumovsk{at}stanford.edu


    Abstract
 Top
 Notes
 Abstract
 Introduction
 Results
 Discussion
 Materials and Methods
 References
 
We have identified a novel protein, apoptotic regulator in the membrane of the endoplasmic reticulum (ARMER), which protects HT1080 fibrosarcoma cells from apoptosis induced by various stimuli. We demonstrate that ARMER is an endoplasmic reticulum (ER) integral membrane protein with four predicted transmembrane domains and a COOH-terminal KKXX ER retrieval motif. We used an inducible expression system (pIND) to study the effects of regulated ARMER overexpression. Cells in which ARMER was overexpressed exhibited protection from multiple apoptotic inducers including serum starvation, doxorubicin, UV irradiation, tumor necrosis factor {alpha}, and the ER stressors brefeldin A, tunicamycin, and thapsigargin. Analysis of the caspase proteolytic cascade reveals that ARMER inhibits proteolysis of the caspase-9-specific fluorogenic substrate LEHD-AFC as well as endogenous substrates downstream of caspase-9; however, it does not inhibit cytochrome c release or cleavage of caspase-9 itself. Apoptotic stimuli cause endogenous levels of ARMER protein and RNA to decrease, leading to cell death; however, sustaining ARMER protein levels through exogenous expression inhibits apoptosis. These data suggest that ARMER is a novel ER integral membrane protein which protects cells by inhibiting caspase-9 activity and reveal a possible role for ARMER in cell survival.

Key Words: apoptosis • endoplasmic reticulum • KIAA0069 • ARL6ip


    Introduction
 Top
 Notes
 Abstract
 Introduction
 Results
 Discussion
 Materials and Methods
 References
 
Apoptosis is a form of cellular suicide that typically includes plasma membrane blebbing, cellular volume contraction, and nuclear condensation, and culminates in the activation of endogenous endonucleases that degrade cellular DNA (1, 2). The well-defined loss of specific cells is crucial during embryonic development and organogenesis (3). In addition to its physiological roles, apoptosis also occurs in many types of cancer cells when they are exposed to various chemotherapeutic drugs, including antimetabolites, deoxynucleotide synthesis inhibitors, DNA topoisomerase inhibitors, anti-microtubule agents, alkylating agents, and endoplasmic reticulum (ER) stressors (4). Overexpression of proteins that inhibit apoptosis can lead to cancer cell resistance to chemotherapy drugs, resulting in an unfavorable outcome for the patient.

A central mechanism in the apoptotic pathway is the activation of caspases, a family of cysteine aspartic acid-specific proteases (5). Caspases are synthesized as zymogens which require specific cleavage for activation. Caspases involved in apoptosis can be divided into two groups: initiator caspases (caspase-8, -9, and -12); and effector caspases (caspase-3, -6, and -7) (6). Through binding specific co-factors recruited by apoptotic stimuli, initiator caspases become cleaved and thus activated, and in turn activate downstream effector caspases, which cleave an array of cellular proteins, resulting in the morphological and biochemical hallmarks of apoptosis (6). The three main apoptotic pathways identified thus far (the mitochondrial, ER stress, and death receptor pathways) are activated by caspase-9, -12, and -8, respectively (7). The mitochondrial pathway may also serve as a point of convergence for the other two pathways, since death receptor activation and ER stress can both lead to cytochrome c release from the mitochondria and subsequent caspase activation (8).

Once released, cytochrome c initiates formation of a high-molecular-weight caspase-activating complex, the apoptosome, composed of cytochrome c, an adaptor protein Apaf-1, and caspase-9. Caspase-9 is cleaved at the apoptosome and recruits and cleaves caspase-3, the primary executioner caspase, which then cleaves many cellular proteins, including poly-ADP ribose polymerase (PARP) and vimentin, a major component of intermediate filaments (7, 9). Mice deficient in caspase-9 exhibit expansion and protrusion of brain tissue caused by defective apoptosis in neural progenitor cells. In addition, caspase-9-/- thymocytes are resistant to apoptotic stimuli which signal through the mitochondrial pathway, such as dexamethasone- and {gamma} irradiation-induced death (10). Proteins which can modulate caspase-9 activity, such as inhibitor of apoptosis proteins (IAPs), can inhibit apoptosis induced by a variety of stimuli, such as tumor necrosis factor (TNF), staurosporine, taxol, and growth factor withdrawal (11). Thus, caspase-9 and proteins that can modulate caspase-9 activity may play central biological roles in the pathogenesis of diseases such as stroke, neurodegenerative diseases, and cancer.

In this study, we report on a novel protein, apoptotic regulator in the membrane of the endoplasmic reticulum (ARMER). We show by immunofluorescence that ARMER is localized in the ER and by membrane-partitioning assays that it fractionates with membrane proteins. Overexpression of ARMER under control of a ponasterone-inducible promoter protects HT1080 fibrosarcoma cells from apoptosis induced by all stimuli tested, including serum deprivation, doxorubicin, UV irradiation, TNF-{alpha}, brefeldin A, tunicamycin, and thapsigargin. Analysis of the caspase proteolytic cascade reveals that ARMER inhibits proteolysis of substrates downstream of caspase-9; however, it does not affect cytochrome c release or cleavage of caspase-9 itself. Apoptotic stimuli cause endogenous levels of ARMER protein and RNA to decrease, leading to cell death; however, sustaining ARMER protein levels through exogenous expression inhibits apoptosis. Thus, our results suggest that ARMER may be a novel modulator of caspase-9 activity and have possible implications in cancer and other diseases involving aberrant apoptosis.


    Results
 Top
 Notes
 Abstract
 Introduction
 Results
 Discussion
 Materials and Methods
 References
 
Expression of ARMER Inhibits Apoptosis
We initially isolated the ARMER cDNA in a yeast two-hybrid screen using Bcl-xL as bait (12). As a potential Bcl-xL interactor, we tested the ability of ARMER to modulate apoptosis in HT1080, a human fibrosarcoma cell line. Constitutive expression of a Flag-epitope-tagged ARMER (F-ARMER) inhibited serum deprivation-induced cell death in two independently derived clones (Fig. 1). We pursued the interaction of ARMER and Bcl-xL observed in yeast but found that the interaction did not occur in mammalian cells as determined by co-immunoprecipitation (data not shown). Thus, we presumed that the interaction in yeast was a false-positive, which is a notable problem with yeast two-hybrid screening, and directed our efforts toward the ability of ARMER to modulate cell death.



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FIGURE 1. ARMER inhibits apoptosis in serum-starved HT1080 cells. HT1080 cells were transfected with vector (Cep4F) or vector expressing F-ARMER (Cep4F-ARMER). A. Western blot with anti-Flag antibody demonstrates F-ARMER expression. B. Survival curve of Cep4F- and Cep4F-ARMER-expressing cells in the absence of fetal bovine serum (FBS) demonstrates enhanced survival of ARMER-expressing cells as determined by Hoescht stain for condensed and fragmented nuclei. Points, means of one experiment representative of two independent clones, each performed in triplicate (>200 nuclei counted at each time point); bars, SD. Some error bars are too small to be seen.

 
To eliminate any potential bias from analyzing constitutively expressing clones, we expressed F-ARMER from an ecdysone-regulatable promoter in the pIND vector. The advantage of a regulatable promoter is that the same cell line can be studied in the presence and absence of expression of the gene of interest, thereby eliminating clonal variation that arises when studying constitutively expressing clones. Any resultant differences in phenotype, therefore, can be attributed to expression of the target protein. Multiple clones of HT1080 pIND F-ARMER were independently isolated and two (designated clone 1 and clone 2) were chosen for further characterization because greater than 95% of the cells from each clone were expressing F-ARMER after induction with ponasterone A (ponA), an ecdysone analogue, as determined by immunofluorescence (Fig. 2A). In both clones, F-ARMER could not be detected by Western blotting in the uninduced state but was readily detectable after addition of ponA (Fig. 2B). We also constructed cells inducibly expressing LacZ to ensure that any observed changes in phenotype were specifically due to F-ARMER and not due to treatment with ponA or overexpression of any protein in general (Fig. 2B). To determine if regulated expression of F-ARMER modulated cell death, cells were induced with ponA and then deprived of serum or treated with doxorubicin or UV irradiation, and the percentage of apoptotic cells was determined by fluorescence-activated cell sorting (FACS) analysis for sub-G0 DNA content. Whereas LacZ expression did not affect cell viability, expression of F-ARMER dramatically protected cells against cell death induced by all three apoptotic stimuli in both independent clones (Fig. 3A). Because both clones acted similarly, further experiments were only performed on one (clone 1). To study the effect of F-ARMER over time, clone 1 and pIND LacZ cells were grown in the absence or presence of ponA, then treated with serum deprivation for 2, 4, and 6 days. LacZ expression did not affect cell viability, but F-ARMER expression protected cells from apoptosis at all time points (Fig. 3B). Although cells expressing F-ARMER appeared slightly flatter than cells not expressing F-ARMER, expression of F-ARMER had no effects on cell growth or cell cycle profile (data not shown).



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FIGURE 2. PonA-inducible expression of F-ARMER. A. Two HT1080 cell lines inducibly expressing F-ARMER were independently derived (clone 1 and clone 2). Cells were grown in the absence (-) or presence (+) of ponA for 3 days before processing for immunofluorescence using mouse anti-Flag antibody followed by goat anti-mouse FITC. Nuclei were stained with Hoescht stain and visualized. B. The two independently derived inducible cell lines were grown as above and analyzed by Western blot. A cell line inducibly expressing LacZ was also analyzed and used as a negative control for the ponA inducible system.

 


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FIGURE 3. Regulated expression of F-ARMER enhances survival of HT1080 cells against apoptotic stimuli. A. Two independently derived pIND F-ARMER clones were treated with ponA for 3 days to induce F-ARMER expression before removal of serum from media or addition of doxorubicin (150 ng/ml) or UV irradiation (10 J/m2). Survival was assayed 4 days after serum deprivation and 2 days after doxorubicin or UV treatment. Cells inducibly expressing LacZ served as a control. Columns, means of one representative of three independent experiments, each done in triplicate; bars, SD. ARMER's protection is statistically significant (P < 0.0001). , pIND LacZ; , pIND F-ARMER clone 1; , pIND F-ARMER clone 2. B. ARMER expression protects serum-deprived cells over time. Clone 1 was grown in the absence or presence of ponA for 3 days and treated with serum deprivation. Cells were harvested at 0, 2, 4, and 6 days. Points, means of one representative of three independent experiments, each done in triplicate at each time point; bars, SD.

 
ARMER Sequence Predicts a Highly Conserved Transmembrane Protein With a COOH-Terminal ER Retrieval Motif
The ARMER cDNA that we identified has been previously described as KIAA0069, a cDNA that was isolated and sequenced as part of a systematic effort to characterize complete cDNAs (13). However, no function was ascribed to KIAA0069. Our clone starts at nucleotide 3 and ends at nucleotide 924 of the KIAA0069 sequence. KIAA0069 RNA was reported to be expressed in KG-1 and HeLa cells and all human tissues tested with highest expression in brain, testis, and liver.

Full-length human and mouse sequences show extensive homology with four conservative amino acid substitutions and one less conservative change (F v. A) (Fig. 4). An almost full-length rat sequence diverges by one amino acid from the mouse (not shown). Partial ESTs derived from zebrafish, Xenopus laevis, and Brugia malayi were also found to have extensive homology. Significant but more distant homology was also found in a Drosophila melanogaster EST (Fig. 4).



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FIGURE 4. ARMER is a highly conserved predicted transmembrane protein with an ER retrieval motif. EST databases were screened for homology to ARMER protein using BLAST homology search. Full-length sequences were identified from mouse but only partial sequences from zebrafish (aa 1–154), X. laevis (aa 1–51), B. malayi (aa 70–118), and D. melanogaster (aa 1–157). Protein represented in one-letter code; identities are boxed, homologies are shaded. Black bars, location of potential transmembrane domains (15).

 
Computer program analysis of the protein sequence of ARMER revealed a 203-amino-acid protein with a predicted molecular weight of Mr 23,363 (presuming translation starts at the first ATG). Four potential transmembrane (TM) domains (indicated by bars in Fig. 4) were also predicted by several computer programs developed to analyze topology of membrane proteins (14, 15). Both the NH2- and COOH-terminal ends of ARMER are predicted to be exposed to the cytoplasm. A 55-amino-acid region between TM2 and TM3 is also predicted to be exposed to the cytoplasm. Although the exact membrane topology of ARMER is not relevant to the present work, it should be noted that these programs have had a success rate of 90% in identifying TM segments and 85% in predicting membrane topology (14). The cytoplasmically exposed regions are predicted to have four sites of potential phosphorylation by protein kinase C and casein kinase II and one site for potential N-glycosylation (NRST) at amino acids 6–9. Another notable feature of the sequence is a COOH-terminal KKNE (lysine, lysine, asparagine, and glutamic acid) which conforms to the KKXX motif commonly found in ER membrane proteins which mediates their retention in the ER (16).

ARMER Is an Integral Membrane Protein Co-Localizing With the ER Marker Calreticulin
We used biochemical methods to determine if ARMER was an ER integral membrane protein as suggested from computer analysis of the protein sequence. Fractionation of post-nuclear homogenates (H) of F-ARMER-expressing cells into membrane (M) and soluble fractions (S) showed that the vast majority of F-ARMER was present in the membrane fraction (Fig. 5A, lanes labeled fractionation). Triton X-114 partitioning studies revealed that ARMER is a hydrophobic protein because it was found in the Triton X-114 phase (L) (Fig. 5A, lanes labeled TX-114). Finally, carbonate extraction of membrane fractions demonstrated that F-ARMER was retained in the membrane (P) (Fig. 5A, lanes labeled sodium carbonate), consistent with an integral membrane protein (17). In each case, F-ARMER fractionated with calnexin, a protein known to be in the ER membrane, and not calreticulin, a protein known to be in the ER lumen.



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FIGURE 5. ARMER is an ER integral membrane protein. A. Cells expressing F-ARMER were homogenized (H) and separated into membrane (M) and supernatant (S) fractions. The membrane fraction was treated with TX-114 and separated into pellet (P), lower (L), and upper (U) phases. The membrane fraction was also treated with sodium carbonate and separated into pellet (P) and supernatant (S) fractions. Proteins were isolated from each fraction and separated by SDS-PAGE for Western blot. F-ARMER fractionates as an integral membrane protein. B. ARMER co-localizes with the ER marker calreticulin. Cells expressing Flag-tagged ARMER were examined by co-immunofluorescence using a mouse anti-Flag antibody followed by goat anti-mouse FITC to detect ARMER expression, visualized in green (left panel), and rabbit anti-calreticulin followed by goat anti-rabbit Alexa 594 to detect calreticulin, an ER marker, in red (middle panel). The merged image shows extensive overlap in yellow (right panel).

 
We also performed co-immunofluorescence using an anti-Flag antibody to detect F-ARMER and anti-calreticulin antibody to detect a known ER protein. pIND F-ARMER cells were treated with ponA to induce F-ARMER expression before they were processed for immunofluorescence. F-ARMER was seen to have a cytoplasmic reticular pattern, most prominent in the perinuclear region, which extensively overlapped the staining pattern of calreticulin (Fig. 5B). These results, in conjunction with the fractionation studies, the predicted transmembrane domains, and the COOH-terminal KKNE ER retrieval sequence, strongly suggest that ARMER is an integral membrane protein in the ER.

ARMER Protects Against Apoptosis Induced by Multiple Stimuli
Since our findings strongly suggested that ARMER localizes to the ER, we hypothesized that ARMER may also be able to protect cells against apoptosis induced by ER stressors. Brefeldin A, an inhibitor of ER-Golgi transport, tunicamycin, a specific inhibitor of N-glycosylation in the ER, and thapsigargin, an inhibitor of the ER Ca2+-ATPase, are all ER stressors as evidenced by induction of grp78 and grp94 (18). To test the ability of ARMER to inhibit apoptosis from ER stressors, we grew pIND F-ARMER and pIND LacZ cells in the presence or absence of ponA induction, then treated them with the ER stressors brefeldin A, tunicamycin, or thapsigargin, as well as the chemotherapy drug doxorubicin, TNF-{alpha} plus cycloheximide, and serum starvation. Doxorubicin is an anthracycline antibiotic used to treat a variety of malignancies through many proposed but uncertain mechanisms, including DNA synthesis inhibition and inhibition of DNA repair (19). TNF-{alpha} alone does not kill HT1080 cells (20); however, TNF-{alpha} plus cycloheximide causes apoptosis by binding to cell surface TNF receptors and activating caspase-8 (21). Serum starvation deprives cells of the necessary growth factors required to sustain cell cycle progression and viability. Cells were harvested between 1 and 4 days after apoptosis induction and analyzed for sub-G0 DNA content. F-ARMER expression significantly protected cells against each apoptotic agent (Fig. 6A). LacZ expression did not have any significant effect on cell viability (data not shown), indicating that apoptotic protection was a specific effect of F-ARMER expression.



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FIGURE 6. A. ARMER protects cells from various apoptotic stimuli. Cells were treated with ponA for 3 days to induce ARMER expression, then treated with either brefeldin A (2.5 µg/ml), tunicamycin (2 µg/ml), thapsigargin (5 mM), doxorubicin (150 ng/ml), TNF-{alpha} (10 ng/ml) plus cycloheximide (1 µg/ml), or serum deprivation. Cells were harvested after 1–4 days and analyzed for sub-G0 DNA content by FACS analysis. Columns, means of one representative of two independent experiments, each done in triplicate; bars, SD. For each treatment, ARMER's protection is statistically significant (P < 0.05). B. ARMER does not inhibit release of cytochrome c. Cells were grown in the absence and presence of ponA for 3 days, then deprived of serum. Cells were harvested and separated into membrane and cytosolic fractions. Cytosolic extracts from ARMER-expressing and non-expressing cells were analyzed by Western blotting for presence of cytochrome c and cleaved caspase-3.

 
ARMER Inhibits the Caspase Cascade Downstream of Caspase-9 Cleavage
To study the mechanism by which ARMER protects cells from apoptosis, we examined steps in the apoptotic signaling pathway. Since cytochrome c release from mitochondria is an early event in apoptosis, we examined cytochrome c content in cytosolic extracts in serum-deprived cells expressing and not expressing F-ARMER. There was no difference in levels of cytochrome c in the cytosolic extracts (Fig. 6B), indicating that F-ARMER did not inhibit release of cytochrome c. We also examined a later apoptotic event, cleavage of caspase-3, and found that caspase-3 cleavage was inhibited in F-ARMER-expressing cells (Fig. 6B). These results suggested that ARMER may act at a point in the apoptotic signaling cascade downstream of cytochrome c release but upstream of caspase-3 cleavage.

To further determine at which point ARMER inhibited the apoptotic pathway, we studied the caspase cascade. Various apoptotic inducers have been suggested to converge on mitochondrial cytochrome c release, which leads to caspase-9 activation. Having shown that cytochrome c release was unaffected by ARMER, we next measured amounts of caspase-9 cleavage by Western blotting using antibodies directed to cleaved caspase-9. pIND F-ARMER and pIND LacZ cells were grown in the absence or presence of ponA, then deprived of serum or treated with brefeldin A or doxorubicin. One to 3 days after induction of apoptosis, cells were collected for quantitative Western blotting. In addition to measuring cleaved caspase-9, we also monitored downstream events, such as cleavage of vimentin, caspase-3, and PARP. In healthy, untreated cells, cleaved caspases were not detectable (Fig. 7, Day 0). On treatment with apoptotic stimuli, cleaved caspase-9 was detectable to the same extent in both F-ARMER-expressing (ponA +) and non-expressing cells (ponA -) (Fig. 7). However, cleavage of substrates downstream of caspase-9 was inhibited by F-ARMER. Cleavage of caspase-3, a direct target of activated caspase-9, was inhibited when F-ARMER was expressed (Fig. 7). In turn, cleavage of caspase-3 substrates, including PARP and vimentin, was also inhibited in F-ARMER-expressing cells. Vimentin was recently identified as a substrate that can be cleaved by both caspase-3, yielding a Mr 47,000 fragment, and also by caspase-9, yielding a Mr 28,000 fragment (7). F-ARMER inhibited cleavage of vimentin by both caspase-3 and caspase-9 (Fig. 7). LacZ expression did not affect cleavage of any of these caspase substrates (data not shown). These data demonstrate that ARMER inhibits the caspase proteolytic cascade downstream of caspase-9 cleavage.



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FIGURE 7. ARMER inhibits cleavage of caspase-9-dependent substrates and downstream markers of apoptosis but not caspase-9 itself. Cells were grown in the absence or presence of ponA (2.5 µM) for 3 days and treated with serum deprivation, doxorubicin (150 ng/ml), or brefeldin A (2.5 µg/ml) for the times indicated. Cells were harvested and lysates were analyzed by Western blot to detect cleaved caspase-9, caspase-3, vimentin, and PARP. Blots were also probed with anti-tubulin antibody to verify equal loading. Western blots are representative of three independent experiments.

 
ARMER Inhibits Caspase-9 Activity
To determine if ARMER could inhibit caspase-9 activity in cell-free lysates, cell extracts were analyzed for ability to cleave the caspase-9-specific fluorogenic substrate, LEHD-AFC. pIND F-ARMER and pIND LacZ cells were grown in the absence or presence of ponA induction, then deprived of serum or treated with brefeldin A or doxorubicin. After 1–2 days of apoptotic induction, cells were harvested, and lysates were analyzed for caspase-9 activity. In each case, caspase-9 activity was decreased by >50% in lysates from F-ARMER-expressing cells compared to cells not expressing F-ARMER (Fig. 8A). However, the amounts of cleaved caspase-9 as detected by Western blotting in these same cell extracts were similar regardless of F-ARMER expression, whereas cleavage of the caspase-9 substrate, caspase-3, was inhibited, consistent with diminished caspase-9 activity (Fig. 8B). LacZ expression did not affect caspase-9 activity in cell extracts (data not shown). Therefore, in the presence of F-ARMER, cleaved caspase-9 is not fully active, as demonstrated by decreased cleavage of both endogenous (caspase-3 and vimentin) and exogenous (LEHD-AFC) substrates.



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FIGURE 8. ARMER inhibits caspase-9 activity in vitro. Cells were grown in the absence or presence of ponA (2.5 µM) for 3 days and treated with serum starvation, doxorubicin (150 ng/ml), or brefeldin A (2.5 µg/ml) for 1–2 days, respectively. A. Cells were harvested, lysed, and 150 µg of cell lysate were analyzed for caspase-9 enzymatic activity by a fluorometric LEHD-AFC protease assay. Columns, means of three independent experiments; bars, SD. ARMER's inhibition of caspase-9 activity is statistically significant, as determined by Student's paired, two-tailed, t test (P < 0.025). B. Amounts of cleaved caspase-9, cleaved caspase-3, and tubulin were determined in these cell lysates by Western blot.

 
Apoptotic Stimuli Decrease Expression of Endogenous ARMER but not Overexpressed F-ARMER
After multiple unsuccessful attempts to generate useful rabbit polyclonal or mouse monoclonal antibodies directed against full-length ARMER, an amino-terminal peptide coupled to KLH elicited an immune response in mice, and a monoclonal antibody was generated. This antibody was tested on HT1080 pIND F-ARMER cells grown in the absence and presence of ponA. Western blots were probed with the anti-ARMER antibody, then stripped and reprobed with anti-Flag antibody. The anti-ARMER antibody recognized the same protein as the anti-Flag antibody, corresponding to F-ARMER, and an endogenous protein, visualized by a band migrating at a molecular weight (Mr ~24,000) slightly lower than F-ARMER, corresponding to endogenous ARMER (Fig. 9A). Using this antibody, we determined by co-immunofluorescence that endogenous ARMER co-localized with calreticulin, indicating that ARMER resides in the ER (data not shown). We also used this antibody to monitor the expression of ARMER in response to apoptotic stimuli. On treatment with brefeldin A or thapsigargin, cells exhibited a decrease in endogenous ARMER protein (Fig. 9B). Northern blots revealed that endogenous ARMER RNA expression is also decreased in cells treated with apoptotic stress. In cells inducibly expressing F-ARMER, however, F-ARMER protein and RNA expression persisted (Fig. 9, B and C), suggesting that F-ARMER expression may be maintaining viability in the absence of endogenous ARMER. Note that F-ARMER RNA migrates at a lower molecular weight than endogenous ARMER RNA because the pIND F-ARMER plasmid contains a truncated version of the endogenous RNA lacking a portion of the 3' untranslated region.



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FIGURE 9. Endogenous ARMER expression decreases on treatment with apoptotic stimuli, but sustained expression of F-ARMER protects cells from apoptosis. A. The monoclonal anti-ARMER antibody recognizes both Flag-tagged and endogenous ARMER. HT1080 pIND F-ARMER cells were treated with ponA for 3 days to induce F-ARMER expression. Endogenous ARMER (*) is detected as a band migrating at Mr ~24,000. B and C. Cells were grown in the absence or presence of ponA for 3 days, then treated with brefeldin A (2.5 µg/ml) or thapsigargin (5 mM), and harvested after 1–2 days. NT, no treatment. Cells were analyzed for endogenous ARMER and overexpressed F-ARMER protein (B) and RNA (C) expression. The F-ARMER RNA is a truncated version of the endogenous RNA lacking a portion of the 3' untranslated region. Blots are representative of two independent experiments.

 
Regulated Overexpression of Native ARMER Protects Cells From Apoptosis
Although it was clear that F-ARMER overexpression inhibited apoptosis in HT1080 cells, it was necessary to demonstrate that native ARMER could also protect cells. As another consequence of an antibody to endogenous ARMER, it also became possible to construct and analyze cells that inducibly overexpress native ARMER. We cloned an ARMER cDNA into the pIND vector and constructed a stable inducible HT1080 pIND ARMER cell line. In the presence of ponA, ARMER protein expression increased ~6-fold compared to cells grown in the absence of ponA (Fig. 10A). pIND ARMER and pIND LacZ cells were grown in the absence or presence of ponA, then deprived of serum or treated with tunicamycin or doxorubicin, and harvested for FACS analysis for sub-G0 DNA content. Cells overexpressing ARMER exhibited less apoptosis than cells not overexpressing ARMER (Fig. 10B). These results indicate that the Flag epitope tag used in experiments described in this study does not affect the biological function of ARMER.



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FIGURE 10. Regulated overexpression of native ARMER protects cells from apoptosis. A. An HT1080 cell line inducibly expressing ARMER was derived. Cells were grown in the absence or presence of ponA for 3 days and analyzed for ARMER expression by Western blot. B. Regulated overexpression of ARMER protects cells against serum starvation, doxorubicin, and tunicamycin. Cells were grown in the absence or presence of ponA for 3 days and treated with apoptotic inducers. Cells were harvested and analyzed for sub-G0 DNA content by FACS analysis. Cells inducibly expressing LacZ served as a control. Columns, means of one representative of three independent experiments, each done in triplicate; bars, SD. ARMER's protection is statistically significant (P < 0.001). , pIND LacZ; , pIND ARMER.

 

    Discussion
 Top
 Notes
 Abstract
 Introduction
 Results
 Discussion
 Materials and Methods
 References
 
In this study, we present the cloning and characterization of a novel protein which inhibits apoptosis in HT1080 cells treated with a variety of apoptotic insults. Its localization in the ER membrane makes it the newest member of the small but growing list of ER proteins implicated in the regulation of apoptosis, including p29Bap31 (22), Bax inhibitor-1 (23), and caspase-12 (18). The ER is gaining increasing interest as an organelle capable of sensing and transducing apoptotic signals. The ER can respond to specific stress signals including calcium depletion in the lumen and inhibition of glycosylation, as seen in thapsigargin and tunicamycin treatments, respectively (24). The ER uses diverse mechanisms to signal to the nucleus, including proteolysis of ER membrane-bound transcription factors and stress-responsive kinases in the ER membrane. On activation, transcription factors stimulate the expression of numerous stress response genes, some of which code for chaperone proteins in the ER (24).

Our study shows that ARMER inhibits apoptosis, possibly by modulating the protease activity of cleaved caspase-9. Western blot analysis showed that caspase-9 is cleaved in response to serum starvation, brefeldin A, and doxorubicin, supporting the theory that various apoptotic pathways may converge at a point upstream of apoptosome formation. Although ARMER did not affect release of cytochrome c into the cytosol or cleavage of caspase-9, events downstream of caspase-9 cleavage were inhibited in cells overexpressing ARMER. These events include the cleavage of vimentin and of the primary executioner caspase, caspase-3, as well as its substrate, PARP. In addition, cleavage of the exogenous caspase-9-specific fluorogenic substrate LEHD-AFC in extracts prepared from ARMER-expressing cells was also inhibited. These results suggest that ARMER, directly or indirectly, inhibits the proteolytic capacity of cleaved caspase-9.

We tested the ability of microsomes containing F-ARMER to inhibit the cleavage activity of recombinant human active caspase-9 in a fluorogenic assay using LEHD-AFC as substrate. F-ARMER was unable to inhibit recombinant caspase-9 activity in this context (data not shown), suggesting that inhibition of caspase-9 by F-ARMER may be indirect and may require other molecular components in the cell.

Our results support the contention that cleaved caspase-9 is not necessarily proteolytically active (7). For example, IAPs can physically interact with cleaved caspase-3, -7, and -9, and block their activity (25). IAPs inhibit the activities of caspases either by directly binding to and blocking the catalytic sites of cleaved caspases or functioning as ubiquitin ligases to promote the proteolysis of caspases once bound to them (25). IAPs contain homologous domains called baculoviral IAP repeat (BIR) domains that are necessary to inhibit caspase activity. The third BIR domain of XIAP specifically inhibits caspase-9 while the second BIR domain along with some flanking sequences was sufficient to inhibit caspase-3 and -7 (11). Expression of XIAP, as well as its family members c-IAP-1, c-IAP-2, and survivin were examined in our laboratory, and levels were found to be similar in cells overexpressing F-ARMER compared to uninduced cells (data not shown). Thus, the mechanism by which ARMER protects cells from apoptosis does not appear to be through up-regulating protein expression of IAP family members. However, it remains possible that ARMER may enhance IAP function, perhaps by facilitating IAP binding and inhibition of their caspase substrates, or may function in a manner similar to the IAPs.

ER stress stimulates cleavage of caspase-12 in the mouse as detected by a specific monoclonal antibody directed against the mouse protein (18). Interestingly, the human orthologue of mouse caspase-12 remains elusive and has not been clearly defined (26). Fischer et al. (27) recently described a potential human homologue (68% identical to mouse caspase-12), but the gene contains severe mutations causing truncations in several splice variants and destruction of the SHG box, a crucial element for caspase enzymatic activity, precluding its function as an active caspase. Neither monoclonal nor polyclonal antibodies directed against the human caspase-12 have been described in the literature or are commercially available. We have attempted to use a number of different antibodies raised against mouse caspase-12 to show cleavage of the putative human caspase-12 but have been unsuccessful in detecting any cleavage products after ER stress. Therefore, analysis of caspase-12 cleavage in our experimental system will not be possible until the human gene is identified and antibody reagents are available.

Endogenous ARMER was detected by Western blotting in numerous cell lines (data not shown). By co-immunofluorescence, endogenous ARMER was determined to co-localize with the ER protein, calreticulin, indicating that endogenous ARMER localizes to the ER, as would be predicted based on its KKNE ER retrieval sequence. The finding that endogenous ARMER and overexpressed F-ARMER both co-localize with calreticulin suggests that the Flag epitope tag does not affect the localization of ARMER. The epitope tag also did not affect the function of ARMER since we demonstrated that regulated overexpression of native ARMER also protected cells against serum starvation, tunicamycin, and doxorubicin.

Our studies showing that overexpression of epitope-tagged or native ARMER inhibits apoptosis suggests but does not prove that endogenous ARMER has the same function. However, our observation that endogenous ARMER decreases when cells are challenged with apoptotic stimuli suggests that ARMER is involved in apoptosis. The first possibility is that apoptotic stimuli down-regulate ARMER, and that lack of anti-apoptotic ARMER function then contributes to cell death. However, in cells expressing F-ARMER from an exogenous promoter, viability is maintained since F-ARMER levels do not drop. The second possibility is that ARMER expression decreases as a consequence of cell death. Our results do not support this latter possibility since endogenous ARMER still decreases in F-ARMER-expressing cells that are resistant to cell death.

The high conservation of ARMER across species suggests that ARMER function will be amenable to genetic analysis. Recent studies have identified a mouse homologue of ARMER (91% identity to human ARMER), which was isolated in a yeast two-hybrid screen using ARL-6, a small ADP-ribosylation-like factor that may be involved in intracellular protein transport, as bait (28). The mouse homologue of ARMER was also recently identified as a gene down-regulated during differentiation of myeloid progenitor cells (29). Neither of these studies provided biological significance; therefore, the relevance of these findings is currently unknown.

In summary, our studies describe a novel ER membrane protein, ARMER, which protects human HT1080 fibrosarcoma cells from apoptosis induced by various agents. ARMER inhibits the ability of cleaved caspase-9 to cleave its substrates, both endogenous and exogenous, suggesting that ARMER may, directly or indirectly, inhibit the activity of cleaved caspase-9. The mechanism by which ARMER inhibits cleaved caspase-9 activity is the subject of current investigation in our laboratory. Although ARMER inhibits events downstream of caspase-9 cleavage, that may not be its only mechanism of action in inhibiting apoptosis. We have not definitively identified the mechanism of ARMER action; however, we note that the mechanism of action of another anti-apoptotic protein, Bcl-2, remains controversial even after more than 15 years of intense study (30).

Proteins with anti-apoptotic activity, such as ARMER, may contribute to the etiology of cancer or our inability to treat the disease with cytotoxic therapy. Since ARMER has anti-apoptotic activity, we would expect to find ARMER up-regulated in malignancies either at presentation or after relapse. Indeed, the gene for ARMER (KIAA0069) is more highly expressed in colon adenocarcinomas than in adenomas or normal colon tissues (31) and is highly expressed in highly proliferating breast tumors (32). The significance of these findings, suggesting a potential role for ARMER in cancer, is being investigated. Further characterization of ARMER will provide valuable insight with potential implications in malignant, neurodegenerative, and ischemic disorders.


    Materials and Methods
 Top
 Notes
 Abstract
 Introduction
 Results
 Discussion
 Materials and Methods
 References
 
Expression Plasmids, Cell Culture, and Generation of Cell Lines
Cep4Flag (Cep4F) is an epitope tagging vector that contains a cytomegalovirus promoter driving expression of Flag-epitope tagged proteins and a hygromycin selectable marker (12). Cep4F-ARMER was constructed by cloning a BglII fragment containing ARMER into the Cep4F vector. pIND (containing five modified ecdysone response elements upstream of a minimal heat shock promoter) and pVgRXR (expressing the heterodimeric ecdysone receptor) were obtained commercially from Invitrogen, Carlsbad, CA. pIND F-ARMER expresses Flag-tagged ARMER, whereas pIND ARMER expressed non-tagged ARMER from an ecdysone inducible promoter. Plasmid constructs were confirmed by DNA sequencing. HT1080 is an adherent human fibrosarcoma cell line that is sensitive to apoptosis-inducing stimuli. Cells were cultured in DMEM supplemented with 100 units of penicillin, 100 µg/ml of streptomycin, 300 µg/ml of L-glutamine, and 10% (v/v) heat-inactivated FBS at 37°C in a humidified atmosphere of 95% air 5% CO2 (v/v).

To establish inducible cell lines, HT1080 cells were co-transfected with pIND F-ARMER or pIND ARMER and pVgRXR receptor plasmid using calcium phosphate precipitation of DNA. The media were changed the next day. The following day, transfected cells were serially diluted into 10-cm tissue culture plates and selected with G418 (1.0 mg/ml) and Zeocin (0.5 mg/ml). Colonies that formed after 2 weeks were transferred into individual wells of a 24-well plate for further expansion (33). Some cells from each well were transferred to another 24-well assay plate and incubated for 48 h in media containing 2.5 µM ponA, an ecdysone analogue. Cells were solubilized with SDS loading buffer and expression of F-ARMER or native ARMER was detected by Western blotting using an anti-Flag antibody or an anti-ARMER antibody. Purity was assessed by immunofluorescence. As a control, a cell line inducibly expressing ß-galactosidase was constructed in a similar manner using the pIND LacZ and pVgRXR plasmids (Invitrogen). Colonies expressing ß-galactosidase were screened using X-gal as a substrate.

Survival Assays
Cells were grown in the presence of ponasterone (2.5 µM) or ethanol alone for 3 days and then treated with apoptotic stimuli as specified in the text. Survival was assayed at the times indicated by combining media and cells harvested using trypsin/EDTA. Cell pellets were washed with PBS with 5 mM EDTA and fixed with 70% ethanol. Cell pellets were treated with RNaseA (0.2 mg/ml for 30 min) and stained with propidium iodide (40 µg/ml) before analysis on a Becton Dickinson FACScan (Becton Dickinson, Franklin Lakes, NJ). Ten thousand cells were assayed for sub-G0 DNA. Hoechst staining of treated cells and immunofluorescence analysis revealed condensed and fragmented nuclei consistent with apoptosis (not shown).

For statistical analysis, percentages of non-apoptotic cells were compared between cells expressing and not expressing F-ARMER using Student's independent two-tailed t test to determine statistical significance. Each experiment was performed in triplicate.

Homogenization, Triton X-114, and Sodium Carbonate Extraction
Cells were collected and resuspended in 1.5 ml of homogenizing buffer (HB: 0.25 M sucrose, 10 mM Tris-HCl (pH 7.4), 1 mM DTT, 1 mM EDTA, and protease inhibitors). A Dounce homogenizer with a tightly fitting pestle was used for homogenization, and cell disruption was evaluated by phase contrast microscopy. The homogenate was separated into membrane fraction (M) and supernatant (S) by centrifuging at 100,000 x g for 1 h. The membrane fraction (120 µg of protein) was suspended in 1 ml of ice-cold Tris-buffered saline. Pre-condensed Triton X-114 (0.2 ml) was added and the suspension was incubated on ice for 30 min with occasional mixing. The suspension was centrifuged at 16,000 x g for 15 min at 4°C, and the pellet (P) was collected. The supernatant was transferred to a fresh tube and incubated in a 37°C water bath until the solution became cloudy. It was centrifuged at 16,000 x g for 10 min at room temperature. The upper aqueous phase (U) and the lower detergent phase (L) were collected and the proteins were precipitated with TCA (final concentration 10%). After incubation on ice for 30 min, the precipitated proteins were pelleted by centrifuging at 10,000 x g for 5 min. The pellets were washed twice with acetone and dissolved in protein loading buffer.

The integral membrane and non-integral membrane proteins in the membrane fraction were separated with sodium carbonate (17). Specifically, 60 µg of membrane proteins were diluted 50-fold in 100 mM sodium carbonate (pH 11.5) and incubated on ice for 30 min or longer. The suspension was centrifuged at 240,000 x gmax for 1 h at 4°C. The pellet (P) was directly dissolved in 1x protein loading buffer. The supernatant (S) was precipitated with TCA as described above.

Immunofluorescence Localization of Protein Expression
Cells were plated in chamber slides and grown in the presence or absence of ponA (2.5 µM) for 3 days. Cells were fixed in 2% paraformaldehyde in PBS for 15 min and permeabilized for 15 min with 0.5% Triton X-100 in PBS. After washing with PBS, slides were blocked with 5% BSA in PBS for 30 min at room temperature. F-ARMER was visualized with mouse anti-Flag monoclonal antibody, and endogenous ARMER was visualized with mouse anti-ARMER monoclonal antibody followed by goat anti-mouse FITC (green fluorescence). In co-immunofluorescence experiments, calreticulin was visualized with rabbit anti-calreticulin polyclonal antibodies followed by goat anti-rabbit Alexa 594 (red fluorescence). Coverslips were mounted to slides with an aqueous anti-fade mounting solution. A Nikon ECLIPSE E800 microscope with a VFM epi-fluorescence attachment was used to visualize cells. Images were captured using a Spot RT Slider camera and Spot RT v3.0 software.

Preparation of Cytosolic Fractions
For cytochrome c releasing assays, cells were homogenized as described above. After removing nuclei by centrifuging at 800 x g for 8 min, the homogenate was separated into the mitochondria-containing membrane fraction and cytosolic fraction by centrifuging at 100,000 x g for 1 h. Cytosolic fractions were analyzed by Western blotting for cytochrome c and cleaved caspase-3. Purity of fractions was confirmed by Western blotting for cytochrome c oxidase II (data not shown).

Quantitative Western Blotting
Cells were lysed in triple-detergent lysis buffer [50 mM Tris-Cl (pH 8.0), 150 mM NaCl, 0.1% SDS, 0.5% deoxycholic acid, 1.0% NP40, and a cocktail of protease inhibitors] on ice for 10 min. After centrifugation at 15,000 x g for 5 min, supernatants were quantitated and equal quantities of protein were resolved on the appropriate percentage SDS-polyacrylamide gels. Gels were transferred to polyvinylidene difluoride membrane using a Bio-Rad Semi-dry Transfer Cell (Bio-Rad, Hercules, CA). Western blotting was performed using primary and horseradish peroxidase-conjugated secondary antibodies specified in the text. Anti-Flag and -vimentin antibodies were purchased from Sigma Chemical Co., St. Louis, MO. Anti-cytochrome c antibody was purchased from Santa Cruz Biotechnology, Santa Cruz, CA. Antibodies to caspases and PARP specifically recognized the cleaved forms (Cell Signaling Technologies, Beverly, MA). Anti-ARMER antibodies were generated against a KLH-coupled peptide containing the first 20 amino acids of ARMER by Antibody Solutions (Palo Alto, CA). Protein bands were detected using SuperSignal Chemiluminescent Substrate (Pierce, Rockford, IL). All membranes were blotted with an anti-tubulin antibody (Sigma) to control for loading and transfer. Bands were imaged and quantitated in the linear range and normalized to tubulin using the Bio-Rad Fluor-S MultiImager.

Quantitation of Caspase-9 Enzymatic Activity
Caspase-9 activity was assayed using the Caspase-9/Mch6 Fluorometric Protease Assay Kit (MBL, Japan). Cells were harvested, rinsed in cold PBS, and lysed, and supernatants were quantitated. One hundred fifty micrograms cell lysate were analyzed according to the manufacturer's protocol. Reactions were incubated in a reaction mixture containing LEHD-AFC (0.1 mM) at 37°C for 2 h, and fluorescence levels were determined at 2-min intervals at an excitation of 400 nm and emission of 512 nm using a fluorescence plate reader. The Vmax was obtained using 30 data points in the linear range of the reaction.

Northern Blotting
Total RNA was isolated using TRIzol reagent (Life Technologies, Inc., Carlsbad, CA) and dissolved in diethyl pyrocarbonate-treated H2O. Using standard techniques, 15 µg total RNA were resolved on a 1% formaldehyde-agarose gel, transferred to nylon membrane, and hybridized with a 32P-labeled ARMER cDNA probe using Rapid-hyb buffer (Amersham, Piscataway, NJ). The probe was prepared by isolating and purifying a BglII fragment containing ARMER from the pIND ARMER plasmid. The probe was labeled with random primers extended by Klenow fragment in the presence of deoxynucleotide triphosphates and [32P]dCTP using Ready-To-Go DNA Laddering Beads (Amersham). Blots were imaged and in the linear range of X-ray film and reprobed with 18S cDNA as a control.


    Notes
 Top
 Notes
 Abstract
 Introduction
 Results
 Discussion
 Materials and Methods
 References
 
1 Lund Family American Cancer Society Grant (#RPG-98-044-01-CCG). Back

Received November 15, 2002; revised March 20, 2003; accepted April 3, 2003.


    References
 Top
 Notes
 Abstract
 Introduction
 Results
 Discussion
 Materials and Methods
 References
 

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