Molecular Endocrinology, in press (December 2003).



            Identification of a Novel Glucocorticoid Receptor Mutati...
Kunz et al. - page 2


ABSTRACT

We developed a molecular genetic model to investigate glucocorticoid receptor (GR)

signa...
Kunz et al. - page 3


ABBREVIATIONS

Bud; budesonide

Dex; dexamethasone

DHPLC; denaturing high performance liquid chrom...
Kunz et al. - page 4


INTRODUCTION

Glucocorticoids are potent anti-inflammatory agents that have been used to treat a

v...
Kunz et al. - page 5


bioavailability (20, 21). Upon ligand activation, GR is transported to the nuclear

compartment whe...
Kunz et al. - page 6


that important cell-specific hormone responses in humans may not be recapitulated in

this single c...
Kunz et al. - page 7


may prove to be a useful biological reagent to study coactivator functions specifically in

human b...
Kunz et al. - page 8


       Since it was important to have a reliable screen for Bud-induced GFP expression

in BudR mut...
Kunz et al. - page 9


also isolated two additional BudR variants from a plating of 7 x 106 Ch-P8 cells that had

been pre...
Kunz et al. - page 10


was not the case for the two EMS-induced Budr mutants. Ch-BdE4 cells were found to

have <40% the ...
Kunz et al. - page 11


mutants, then GR-mediated transrepression of NFkB activity should also be

compromised. Figure 4B ...
Kunz et al. - page 12


      Figure 5 shows the RT-PCR strategy that was used to cover a 740 amino acid

region of the GR...
Kunz et al. - page 13


DNA sequencing reveals presence of GRg transcripts and a novel mutation at V575M

Since results of...
Kunz et al. - page 14


mutation into the cloned GRa cDNA sequence in order to directly measure the ligand

binding and tr...
Kunz et al. - page 15


GRa, however, the maximal transactivation activity was greatly reduced. Figure 8B

shows the resul...
Kunz et al. - page 16


(RAR) and the retinoid X receptor RXR. Moreover, based on recent data describing the

predicted mo...
Kunz et al. - page 17


other atoms at this long distance. Considering that both Val and Met are neutral side

chains poss...
Kunz et al. - page 18


identified. The first class of mutants is represented by Ch-Bd2 which had a decreased

amount of G...
Kunz et al. - page 19


previously shown to be involved in coactivator binding (53, 54). Molecular dynamic

simulations (f...
Kunz et al. - page 20


of GRa protein due to differences in protein stability. If this were the case, then the

observed ...
Kunz et al. - page 21


analogs or other small molecules that reverse the BudR phenotype resulting from GR

signaling defe...
Kunz et al. - page 22


Alto, CA). The plasmid pMMTV-HSVtk-Zeo was constructed by inserting the MMTV

LTR (XhoI-HindIII) p...
Kunz et al. - page 23


aspirated and replaced with RPMI growth media. Following an overnight recovery,

media was aspirat...
Kunz et al. - page 24


Quantitation of GR levels by Immunoblotting

Whole cell protein extracts were prepared from ~2x106...
Kunz et al. - page 25


(50mM NaCl, 1mM EDTA, 12% vol/vol glycerol, 1mM 2-mercaptoethanol, 10mM Na-

molybdate, 1mM PMSF a...
Kunz et al. - page 26


were treated for 18 h with 10-6 M Dex or 10-7 M Bud for the transactivation assays, or

with 10-6 ...
Kunz et al. - page 27


structure of the progesterone ligand (CAS registry number [57-83-0]) and the

crystallographic wat...
Kunz et al. - page 28


of the relative free energy of the LxxLL motif binding to the wild-type and mutant

receptor, resp...
Kunz et al. - page 29


+Bud samples during the binding and washing steps. Finally, GST proteins were eluted

from the bea...
Kunz et al. - page 30


REFERENCES

1.    Szefler SJ 2001 A review of budesonide inhalation suspension in the treatment of...
Kunz et al. - page 31


21.   Kralli A, Bohen SP, Yamamoto KR 1995 LEM1, an ATP-binding-cassette transporter,
      select...
Kunz et al. - page 32


      emergency department: a controlled comparative study with oral prednisolone. J Allergy
     ...
Kunz et al. - page 33


61.   Rogatsky I, Luecke HF, Leitman DC, Yamamoto KR 2002 Alternate surfaces of
      transcriptio...
Kunz et al. - page 34


Table 1. Characterization of Chago variants containing GR signaling defects. Three

of the cell li...
Kunz et al. - page 35


FIGURE LEGENDS

Figure 1. Flow scheme illustrating the strategy used to isolate BudR ChagoK1 cell
...
Kunz et al. - page 36


Figure 4. Complementation of the BudR phenotype in Ch-Bd1 and Ch-Bd2 cells by

transiently transfe...
Kunz et al. - page 37




Figure 7. Functional expression of GRa, GRg and GRV575M proteins in transiently

transfected COS...
Kunz et al. - page 38


view of the hydrophobic coactivator binding pocket for the wild-type complex (left)

and mutated c...
ChagoK1



                      pMMTV-GFP-neo




                       Ch-GFP.9




                    pMMTV-HSV-tk-Ze...
A                         100
                                        24 hr
                                        48 hr
...
B
                                                                                                       A
               ...
A                                         120



                  Fold-induction (MMTV)
                                 ...
0              100                     200               300                     400                 500                60...
A    GRγ (3 bp      insertion at exon 3 splice site)
     449 450        451        452 453 454
     GTG GAA        GGT AG...
A




                                           A



                                                 5M
                ...
A                        120
                                 GRα
                         100     V575M




      Fold-in...
GRV575M
A
    GR      LNMLGGRQVIAAVKWAKAIPGFRNLHLD            590
    MR      LNRLAGKQMIQVVKWAKVLPGFKNLPLE            796
...
A                                    14

                                     12


         Relative Luciferase Units
    ...
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Molecular Endocrinology, in press (December 2003 ...

  1. 1. Molecular Endocrinology, in press (December 2003). Identification of a Novel Glucocorticoid Receptor Mutation in Budesonide-Resistant Human Bronchial Epithelial Cells Susan Kunz § Robert Sandoval § Peter Carlsson*,# Jan Carlstedt-Duke# John W. Bloom ¥, † Roger L. Miesfeld §, ¶ From the Departments of §Biochemistry and Molecular Biophysics, ¥Pharmacology and the †Respiratory Sciences Center at the University of Arizona, Tucson, AZ 85721, *Karo Bio AB, S-141 57 Huddinge, Sweden, #Department of Medical Nutrition, Karolinska Institutet, Huddinge University Hospital, Novum, S-141 86 Huddinge, Sweden. running title: Molecular Genetics of Glucocorticoid-Resistance key words: asthma, ganciclovir, dexamethasone, mutation, GRIP1, GRg ¶ Address correspondences to: Roger L. Miesfeld Department of Biochemistry and Molecular Biophysics 1041 E. Lowell Street University of Arizona Tucson, AZ 85721, USA tel. (520) 626-2343 FAX (520) 621-9288 e-mail: RLM@u.arizona.edu
  2. 2. Kunz et al. - page 2 ABSTRACT We developed a molecular genetic model to investigate glucocorticoid receptor (GR) signaling in human bronchial epithelial cells in response to the therapeutic steroid budesonide. Based on a genetic selection scheme using the human Chago K1 cell line and integrated copies of a glucocorticoid-responsive herpes simplex virus thymidine kinase gene and a green fluorescent protein gene, we isolated five Chago K1 variants that grew in media containing budesonide and ganciclovir. Three spontaneous budesonide- resistant subclones were found to express low levels of GR, whereas two mutants isolated from ethylmethane sulfonate-treated cultures contained normal levels of GR protein. Analysis of the GR coding sequence in the budesonide-resistant subclone Ch- BdE5 identified a novel Val to Met mutation at amino acid position 575 (GRV575M) which caused an 80% decrease in transcriptional regulatory functions with only a minimal effect on ligand binding activity. Homology modeling of the GR structure in this region of the hormone binding domain and molecular dynamic simulations suggested that the GRV575M mutation would have a decreased affinity for the LXXLL motif of p160 coactivators. To test this prediction, we performed transactivation and GST pull down assays using the p160 coactivator GRIP1/TIF2 and found that GRV575M transcriptional activity was not enhanced by GRIP1 in transfected cells nor was it able to bind GRIP1 in vitro. Identification of the novel GRV575M variant in human bronchial epithelial cells using a molecular genetic selection scheme suggests that functional assays performed in relevant cell types could identify subtle defects in GR signaling that contribute to reduced steroid- sensitivities in vivo.
  3. 3. Kunz et al. - page 3 ABBREVIATIONS Bud; budesonide Dex; dexamethasone DHPLC; denaturing high performance liquid chromatography FACS; fluorescent activated cell sorting Gnc; ganciclovir GR; glucocorticoid receptor GRIP1; glucocorticoid receptor interacting protein 1 GST; glutathione S-transferase MMTV; mouse mammary tumor virus NR; nuclear receptor PMSF; phenyl-methylsulfonyl fluoride RT-PCR; reverse transcriptase polymerase chain reaction SEM; standard error of the mean
  4. 4. Kunz et al. - page 4 INTRODUCTION Glucocorticoids are potent anti-inflammatory agents that have been used to treat a variety of clinical symptoms including arthritis, respiratory disease and hemaetopoietic cancers. Inhaled glucocorticoids such as budesonide (1, 2) and fluticasone (3), have been shown to be effective in the treatment of asthma because of their high potency and reduced systemic effects compared to oral glucocorticoids (4). However, long term steroid therapy for chronic diseases can sometimes lead to complications and not all asthma patients respond similarly to the same dose of inhaled glucocorticoids (5). In the most extreme cases of steroid insensitivity, individuals are found to be functionally glucocorticoid-resistant (6). The molecular basis for steroid insensitivity in asthma treatment is poorly understood, partly due to the complexity of the disease and to the number cell types involved (7). It is known that inhaled glucocorticoids are able to mediate responses in bronchial epithelial cells (8), circulating thymocytes (9) and infiltrating eosinophils (10), all of which are present at high levels in asthmatic airways. Glucocorticoid action in each of these cell types is highly diverse, ranging from down- regulation of cytokine gene expression in bronchial epithelial cells (11) and T cells (12), to GR-mediated apoptosis in eosinophils (13). The most abundant GR isoform in cells is the 90 kDa GRa protein (14). Two alternatively spliced forms of GR have also been described, the GRb isoform which is defective in ligand binding due to a 50 amino acid deletion in the C-terminus (15) , and GRg, an exon 3 splice variant that contains an deleterious arginine insertion at position 452 (16-18). Other protein determinants required for glucocorticoid signaling include immunophilin proteins and chaperonins which sequester unliganded GR in a large multi-subunit complex in the cytoplasm (19). There is also evidence for membrane- bound steroid transport proteins that may play a role in modulating hormone
  5. 5. Kunz et al. - page 5 bioavailability (20, 21). Upon ligand activation, GR is transported to the nuclear compartment where it regulates gene expression by direct interactions with specific DNA sequences called glucocorticoid response elements (GREs), or through DNA- independent protein-protein interactions (22). Two types of GR-interacting proteins have been characterized, the p160 coreceptor proteins GRIP1/TIF2, SRC1 and RAC3/AIB1 that contain LXXLL receptor binding motifs (23), and transcription factors such as p300/CBP, CREB, AP-1, STAT-5 and NFkB which have been shown to interact with GR based on co-immunoprecipitation assays (22). Other protein determinants that could affect GR function include a variety of cellular kinases and phosphatases that have been proposed to directly or indirectly modulate transcriptional regulatory activity (24, 25). Alterations in the GRa coding sequence that affect ligand binding, DNA binding and protein-protein interactions have been shown to cause glucocorticoid insensitivity (22). It has also been reported that altered cell-specific expression of the GRb (26-29) or GRg (16-18) isoforms could contribute to steroid insensitivity, as well as elevated levels of immunophilin proteins such as FKBP51 (30). One way to investigate cell-specific signal transduction pathways is to use a molecular genetic approach to identify phenotypic variants that can be isolated and characterized. For example, mouse and human T cell lines have been used to select for resistance to the synthetic glucocorticoid hormone dexamethasone (Dex) on the basis of a failure to initiate the apoptotic pathway (31, 32). Yamamoto and colleagues have exploited yeast as a model eukaryotic cell to develop powerful genetic strategies that have led to the isolation of yeast-encoded ligand-effect modulator genes such as LEM3 and LEM4, that control intracellular concentrations of steroid (33). The advantage of using yeast is the ability to combine genetic analysis with functional genomics. A potential drawback however, is
  6. 6. Kunz et al. - page 6 that important cell-specific hormone responses in humans may not be recapitulated in this single cell organism. We are interested in cell-specific glucocorticoid signaling pathways that mediate the effects of steroid therapy, especially as they relate to the treatment of asthma (34). While complete glucocorticoid-resistance is relatively rare in asthma patients (35, 36), it has been observed that there is a broad range of glucocorticoid-sensitivity amongst asthmatics that respond to steroid therapy (37). The molecular basis for variable GC responsiveness in these patients is unknown but it could be due to altered expression of GR isoforms (16-18, 26-29), or to the activity of non-receptor determinants that control GR functions (38, 39). Since GR structure-function studies based on transient transfection assays using monkey kidney CV-1 cells may not be suitable for detecting subtle GR signaling defects, and high throughput whole genome analysis is not yet feasible for large scale studies of diverse populations, we constructed a model system using the human bronchial epithelial cell line Chago K1 that permits a genetic selection for budesonide resistant (BudR) mutants. Budesonide is a synthetic glucocorticoid that is commonly used as a therapeutic agent in asthma treatment (40, 41). In this report we describe our initial findings using this molecular genetic system and its application to the isolation and characterization of five BudR cell lines. One BudR variant called Ch-BdE5, was chosen for detailed molecular studies and found to contain a novel GR mutation (V575M) that disrupts binding of the p160 coactivator GRIP1/TIF2 without effecting receptor protein stability or ligand binding activities. The GRV575M mutation represents a GR signaling defect that would not be detected by conventional assays of human biopsy material, suggesting that this selection strategy could be a generalized approach for investigating additional cell-type selective steroid responses. Moreover, in conjunction with other BudR cell lines we isolated, the GRV575M receptor
  7. 7. Kunz et al. - page 7 may prove to be a useful biological reagent to study coactivator functions specifically in human bronchial epithelial cells. RESULTS Generation of a budesonide-sensitive human bronchial epithelial cell line Chago K1 cells are a human bronchial epithelial cell line derived from the lung tissue biopsy of a 45 year old male diagnosed with bronchogenic carcinoma (42). The cells are hyperdiploid with a modal chromosome number of 52 and have been shown to express the MUC-1 and MUC-2 (mucin) genes commonly associated with cancer cells (43). The overall strategy we used to develop a Chago K1 cell line for the genetic selection of BudR variants is outlined in figure 1. The basis for the selection scheme was to isolate mutant cells that failed to activate two stably integrated glucocorticoid-responsive reporter genes; 1) pMMTV- HSVtk-Zeo which contains the glucocorticoid responsive mouse mammary tumor virus (MMTV) promoter controlling the expression of the herpes simplex virus (HSV) thymidine kinase (tk) gene, and 2) pMMTV-GFP-neo containing the MMTV promoter driving the expression of the Aequorea victoria green fluorescence protein (GFP) gene. Since the nucleotide analog ganciclovir (Gnc) is toxic to cells expressing the HSV tk protein (44), this strategy permits a genetic selection for BudR variants that grow in media containing Bud+Gnc. The purpose of stably integrating the pMMTV-GFP-neo reporter gene was to permit screening of BudR clones for independent loss of Bud- induced GFP expression. BudR clones with defects in general glucocorticoid signaling, rather than simply a defect in HSV tk expression or enzyme activity, would be expected to be GFP-negative in Bud-containing media.
  8. 8. Kunz et al. - page 8 Since it was important to have a reliable screen for Bud-induced GFP expression in BudR mutants, we first isolated neomycin-resistant Chago cell line that displayed Bud- dependent green fluorescence as judged by FACS. One such cell line, Ch-GFP.9, was shown to display a dose-dependent increase in percent GFP+ cells at both 24 and 48 hours after treatment with Bud. As can be seen in figure 2A, 10% of the Ch-GFP.9 cells were found to be GFP+ at 10-9M Bud, with a maximal response of 85% GFP+ cells at 48 hours in media containing 10-7M Bud. The lack of fluorescence in ~15% of the Ch-GFP.9 cells at 48 hours could be due to cell cycle effects on GR activity in asynchronous cultures (45). We next stably transfected Ch-GFP.9 cells with pMMTV-HSVtk-Zeo and screened zeomycin-resistant clonal isolates for growth in Bud+Gnc media. Two cell lines, Ch-P10 and Ch-P8, were found to be extremely Bud-sensitive in Gnc-containing media and were chosen as founder cell lines for the genetic selection strategy (see figure 1). A representative experiment measuring Ch-P8 cell viability in media containing 10-7 M Bud and 4 mM Gnc is shown in figure 2B. It can be seen that after 10 days in Bud+Gnc media, the number of viable Ch-P8 cells was reduced over 80% as compared to cells cultured in Gnc media lacking Bud. Isolation of budesonide-resistant (Budr) Chago cell variants Ch-P10 and Ch-P8 cells (2 x 106 ) were plated in selective media (100 nM Bud, 4 mM Gnc and 50 mg/ml Zeocin) and 36 spontaneous BudR clones were isolated and expanded 14 days later. The subclones were screened for Bud-induced GFP expression by FACS analysis to identify BudR variants with defects in glucocorticoid responsiveness. Only three of the BudR cell lines, Ch-Bd1, Ch-Bd2 and Ch-Bd3, were found to be defective in GFP expression after 48 hrs of Bud treatment, suggesting that most of the spontaneous mutants were due to defects in HSV tk or Gnc metabolism. As depicted in figure 1, we
  9. 9. Kunz et al. - page 9 also isolated two additional BudR variants from a plating of 7 x 106 Ch-P8 cells that had been pre-treated for 16 hrs with 400mM ethylmethane sulfonate (EMS). In this case, 60 BudR clones were initially isolated of which only two, Ch-BdE4 and Ch-BdE5, were found to be GFP-negative in Bud-containing media. We reasoned that if the defect in Bud-responsiveness was due to a mutation in general glucocorticoid signaling, then treatment of these cells with the glucocorticoid analog dexamethasone (Dex) should reveal a DexR phenotype. Figure 3A shows the results of transient transfection assays in these cells using a glucocorticoid-responsive MMTV-luciferase (MM-Luc) reporter gene (46). All five of the Budr cell variants were found to be defective in mediating Dex-induced luciferase activity as compared to the parental cell lines Ch-P8 and Ch-P10. We also measured GR protein levels by western blotting using whole cell extracts prepared from the parental and mutant cell lines. As shown in figure 3B, all five of the BudR variants were found to express detectable levels of GRa, however, the steady-state level of protein was variable. The Western blot was scanned and GR expression levels were quantitated relative to a loading control. As shown in Table 1, Ch-Bd1 expressed the lowest amount of GR protein (26% of the parental line Ch-P10), whereas, Ch-BdE4 and Ch-BdE5, the two EMS-treated cell lines, expressed near normal levels of GR protein compared to the parental cell line Ch-P8. To determine if the BudR phenotype in any of the mutants was due to decreased steroid binding activity, we prepared whole cell extracts and measured the amount of 3 H-Dex-specific binding activity per mg protein using a saturating concentration of Dex (10 nM). Table 1 lists the mean values obtained from triplicate assays and shows that all three of the spontaneous BudR mutants, Ch-Bd1, Ch-Bd2 and ChBd3, had a reduced 3 level of H-dexamethasone binding activity that was proportional to a decrease in GR protein expression. This association between protein levels and steroid binding activity
  10. 10. Kunz et al. - page 10 was not the case for the two EMS-induced Budr mutants. Ch-BdE4 cells were found to have <40% the level of steroid binding activity relative to Ch-P8, even though the level of GR protein in these cells (based on Western blots) was higher than in the three spontaneous mutants. In contrast, 3 H-Dex binding activity in Ch-BdE5 cells was found to be the same or higher than Ch-P8 cells, suggesting that the majority of GR protein expressed in this BudR cell line retains functional steroid binding activity (Table 1). Analysis of Bud-regulated transcription in Ch-Bd1 and Ch-Bd2 To directly determine if increasing the level of GR protein expression in the spontaneous mutants Ch-Bd1 and Ch-Bd2 could complement the BudR phenotype, we transiently transfected GRa cDNA into these two cell lines and analyzed GR transcriptional transactivation and transrepression functions. Consistent with the observed defect in Dex-induced transcription of MM-Luc in Ch-Bd1 and Ch-Bd2 cells (figure 3 and Table 1), we found that induction of this same reporter gene with Bud was reduced as much as 90% relative to the parental cell lines as shown in figure 4A. More importantly, co-transfection of a GRa cDNA expression vector (CMX-GRa) with the MM-Luc reporter gene, resulted in a 30-fold increase in Bud-dependent luciferase activity in both Ch-Bd1 and Ch-Bd2 cell lines. This result suggested that the BudR phenotype of Ch-Bd1 and Ch-Bd2 was not due to defects in steroid bioavailability or in expression of co-receptor proteins required for MM-Luc transactivation, but rather suboptimal levels of functional GR. Defects in Bud-dependent transcriptional induction of the MM-Luc reporter gene were predicted based on the dependence of our genetic screen on activation of the MMTV promoter in the pMMTV-HSVtk-Zeo gene construct (figure 1). However, if decreased levels of GR protein were the only defect in these two spontaneous Budr
  11. 11. Kunz et al. - page 11 mutants, then GR-mediated transrepression of NFkB activity should also be compromised. Figure 4B shows results from transrepression assays in which Ch-Bd1 and Ch-Bd2 cells were transfected with an NFkB-luciferase (NFkB-Luc) reporter gene and stimulated with tumor necrosis factor alpha (TNFa) in the presence or absence of Bud. Although Bud-dependent transrepression of NFkB activity in Ch-Bd2 cells was greatly reduced, inhibition of NFkB activity in Ch-Bd1 cells was normal. Co- transfecting Ch-Bd1 and Ch-Bd2 cells with the pCMX-GRa and pNFkB-Luc plasmids led to increased levels of transcriptional transrepression in both cell lines. Taken together, these data suggest that the GR signaling defects in Ch-Bd1 and Ch-Bd2 cells are not the same since the decreased activation function in Ch-Bd1 is not associated with alterations in NFkB transrepression. Use of denaturing HPLC to screen for GR sequence mutations Mutations in the GR gene coding sequence that do not effect protein expression levels can best be identified by direct sequencing of the GR gene. However, the gene is large containing nine coding exons and alternative splice variants have been reported which would not be detected by exonic sequencing. Therefore, we chose to screen for GR mutations using a combination of reverse transcriptase-mediated PCR (RT-PCR) and denaturing high-performance liquid chromatography (DHPLC). This strategy permitted us to efficiently identify base pair mismatches in DNA heteroduplexes formed between GR cDNA derived from parental cell line Ch-P8, and GR cDNA produced from the Ch-P8 related variant cell lines Ch-Bd2, Ch-BdE4 and Ch-BdE5. The basis of DHPLC is that under partially denaturing conditions, heteroduplexes containing single base pair mismatches will be eluted ahead of homoduplexes that are fully double stranded under the chosen conditions (47).
  12. 12. Kunz et al. - page 12 Figure 5 shows the RT-PCR strategy that was used to cover a 740 amino acid region of the GR coding sequence with four overlapping DNA segments (G, H, B and E segments). For these experiments, total RNA was isolated from each of the five cell lines and RT-PCR products corresponding to the four regions were produced. Equal amounts of corresponding RT-PCR products from two cell sources were mixed and subjected to DHPLC analysis using the WAVE System from Transgenomics, Inc. (Omaha, NE). Figure 5 shows representative elution profiles of DNA duplexes formed between GR cDNA derived from Ch-P8 and from each of the four related Budr cell lines (Bd2/P8, BdE4/P8, BdE5/P8) cell lines. Results from a control P8/P8 homoduplex reaction is also shown. By comparing the elution profiles of each GR segment between the various heteroduplex combinations, it can be seen that the Bd2/P8 hybridization reactions resulted in heteroduplex products that are indistinguishable from the homoduplex P8/P8 control. This result is consistent with our data indicating that the BudR phenotype in Ch-Bd2 cells is due to decreased expression of wild-type GR (Table 1). Results of the DHPLC analyses indicated that no unique sequence alterations were present in G, H and E segments of the GR from any of the cell lines since the elution profiles from the mixed reactions were identical to that found in the P8/P8 homoduplex control (figure 5). However, significant differences were found in the DHPLC elution profiles from the B segment region of GR present in Ch-BdE4 and Ch- BdE5 cells. This region spans amino acids 373-584 and encodes the GR DNA binding domain (DBD) and the amino terminal end of the ligand binding domain. These data indicate that one or more nucleotides differ between the GR cDNA generated with RNA from Ch-P8 cells, and the GR cDNA derived from Ch-BdE4 and Ch-BdE5 RNA.
  13. 13. Kunz et al. - page 13 DNA sequencing reveals presence of GRg transcripts and a novel mutation at V575M Since results of 3H-Dex binding assays (Table 1) suggested that Ch-BdE4 cells express a GR protein with a defect in steroid binding activity, we focused our molecular analysis on the nature of the GR sequence alternation in Ch-BdE5 cells. As a control, we also characterized the B segment region of GR in the parental Ch-P8 cells and the spontaneous mutant Ch-Bd2. As shown in figure 6, DNA sequence analysis of ~20 randomly selected B segment cDNA clones obtained from T:A cloning of the RT-PCR products from these three cell lines identified two deviations from the previously reported GRa coding sequence. First, approximately 10% of the cDNA inserts obtained from the three cell lines were found to encode the previously described GRg variant (16- 18). This form of the receptor has been proposed to be the result of an alternative splicing event at the exon 3 boundary resulting in the insertion of an arginine codon between amino acids 451 and 452 (17). This single amino acid insertion lies within the spacer region between the two zinc fingers. Second, we identified a novel point mutation that converts Val-575 to Met in GR cDNA clones derived from Ch-BdE5 RNA. Based on the chemical nature of the mutation (G to A transition), and its relative frequency in random plasmid clones (60%), it is most likely the result of an EMS- induced alteration in the GR exon 5 coding sequence. The position of the GRV575M mutation corresponds to a region of the ligand binding domain that is likely a p160 coactivator interaction site based on sequence homology to the human estrogen, thyroid and peroxisome proliferator-activated receptors (see Discussion). The GRV575M receptor is defective in transcriptional regulatory activities To determine if the transcriptional regulatory functions of the GRV575M mutant receptor could account for the BudR phenotype of Ch-BdE5 cells, we introduced the V575M
  14. 14. Kunz et al. - page 14 mutation into the cloned GRa cDNA sequence in order to directly measure the ligand binding and transcriptional regulatory activity of GRV575M. We also inserted the Arg codon at position 452 of GRa to generate the GRg coding sequence. The GRa, GRV575M and GRg receptor constructs were cloned into the pCMX expression vector (48) and transfected into COS-7 cells. Forty-eight hours later, cell extracts were prepared and analyzed for GR expression by western blotting and by 3 H-Dex binding assays. The results of these studies are shown in figure 7. It can be seen that all three GR constructs produce high levels of full-length receptor. Consistent with the results reported by Ray et al. (16), we found that GRa and GRg bound 3 H-Dex with similar affinities. In addition, these data confirm that the ligand binding activity of GRV575M is not significantly different than GRa, which explained why the Ch-BdE5 whole cell binding data were comparable to that of the wild-type parental cell line Ch-P8 (see Table 1). Figure 8 shows the results from transient transfection assays in which the same receptor constructs were co-transfected into Ch-Bd2 cells with either the MM-Luc or NFkB-Luc reporter genes. Our analysis of the Ch-Bd2 phenotype indicated that this spontaneous BudR variant expressed significantly reduced levels of GR (figure 3 and Table 1), and therefore could serve as a suitable genetic background to characterize GRV575M functions within the context of a human bronchial epithelial cell. Maximal transcriptional transactivation and transrepression activities of GRa, GRV575M and GRg in transfected Ch-Bd2 cells were found to differ over a range of Bud concentrations from 10-10 M to 10-7 M. It was seen that while GRa is able to induce luciferase activity nearly 100-fold at 10-9 M Bud, maximal induction by the GRV575M mutant was only 15-fold at this same steroid concentration. In addition, we found that even at the highest Bud concentration (10-7 M), the MM-Luc reporter gene was only induced 40-fold by the GRV575M receptor. Note that the dose response profile of GRg appeared to be similar to
  15. 15. Kunz et al. - page 15 GRa, however, the maximal transactivation activity was greatly reduced. Figure 8B shows the results of NFkB transrepression assays using these same receptor constructs in Ch-Bd2 cells. These data show that both GRV575M and GRg have reduced levels of transrepression activity (50% of GRa at 10-9 M) , and that maximal transrepression function is achieved with 10-8 M Bud. Based on similar defects in Bud-regulated transcriptional activation observed in the Ch-BdE5 cell line (figure 3) and the recombinant GRV575M receptor in transfected Ch-Bd2 cells (figure 8), we propose that the GRV575M mutation is a primary determinant of the BudR phenotype in Ch-BdE5 cells. GR binding to the p160 coactivator GRIP1 is defective in GRV575M Numerous point mutations in the GR HBD have been characterized, most of which disrupt ligand binding activity (49). Recently however, Vottero et al. (50) described a human GR mutation at amino acid position 747 that was identified in a patient with familial glucocorticoid resistance. Biochemical characterization of the GRI747M mutation showed that the receptor had a 2-fold decrease in affinity for Dex but a ~25-fold reduction in transcriptional regulatory activity. Based on the location of residue 747 in the AF-2 region of GR, they tested the ability of GRI747M to functionally interact with the p160 coactivator GRIP1. They found that reduced affinity of GRI747M for GRIP1 binding in vitro was associated with decreased GRIP1 mediated transactivation in vivo. Since the GRV575M mutation we identified in Ch-BdE5 cells also maps to the AF-2 region of the GR HBD, we used molecular modeling and dynamic simulations to predict binding interactions with a p160 peptide from the coactivator TIF2 as shown in figure 9. A ClustalW alignment of amino acid residues surrounding GRV575M with the analogous AF-2 region of 16 other nuclear receptors (figure 9A), reveals that Val-575 is conserved in progesterone receptor (PR), mineralocorticoid receptor (MR), retinoic acid receptor
  16. 16. Kunz et al. - page 16 (RAR) and the retinoid X receptor RXR. Moreover, based on recent data describing the predicted molecular structure of the human GR HBD using x-ray crystallography (51, 52), it can be seen that Val-575 lies within helix 3. This same residue corresponds to Thr in the peroxisome proliferator-activated receptor (PPAR), and to an Ile residue in the estrogen receptor (ER) and vitamin D receptor (VDR). Importantly, the Ile-358 residue in human ERa has been shown to be part of a shallow groove adjacent to helix 3 of the ligand binding domain that binds to the LxxLL motif of coactivator proteins through van der Waals contacts (53, 54). Moreover, Thr-297 of human PPARg (55) and Val-284 of human TRb (56) have also been shown by x-ray crystallography to interact directly with LxxLL motifs in p160 coactivator peptides. Using the published x-ray structures of the human PR (57) and ER (53), we generated a molecular model of the human GR HBD shown in figure 9b. The structural features of this homology model agree very well with the recently published x-ray models of GR (51, 52) (data not shown). The homology model contains budesonide in the ligand binding pocket and includes the TIF2 Box 2 peptide with a LXXLL motif that was used in the molecular structure analysis of ERa as reported by Shiau et al. (53). This GR model predicts that Val-575 is oriented toward the surface of the receptor and is within the hydrophobic coactivator binding pocket associated with helix 3 of ERa (58). The primary effect of the larger and bulkier methionine side chain in GRV575M appears to be a constraint on the rotameric freedom of the Leu +1 side chain in the LXXLL peptide. Molecular dynamic simulations suggested that the relative free energy difference between the wild-type and the mutant would be about 0.7 kcal/mol, which translates to a ~10-fold reduction in TIF2 binding affinity. Note that the shortest distance from GR residue 575 to the budesonide ligand is approximately 15 Å according to this model. Only electrostatic forces would have a significant and direct effect on
  17. 17. Kunz et al. - page 17 other atoms at this long distance. Considering that both Val and Met are neutral side chains possessing weak partial charges, we would expect very little direct electrostatic influence of this mutation on the ligand binding. This prediction is consistent with our ligand binding data (Table 1 and figure 7). To directly test our prediction that the GRV575M mutation disrupts p160 coactivator interactions, we performed a transactivation assay in Ch-Bd2 cells using pCMX-GRa or pCMX-GRV575M and the GRIP1 expression plasmid pSG5.GRIP1 (59). The results shown in figure 10A reveal that while Bud-induction of the MMTV-Fluc reporter plasmid was enhanced over 2-fold in Ch-Bd2 cells by the co-expression of GRIP1, the transactivation activity of GRV575M was unaffected by GRIP1 expression under these same conditions. A defect in GRIP1 binding by GRV575M was confirmed using a GST pull-down assay as shown in figure 9B. These results demonstrate that GRa, but not GRV575M, displayed Bud-dependent GRIP1 binding to the NR interaction domain that includes all three NR box motifs (LXXLL) (59). Taken together, the results from molecular dynamic simulations using a TIF2 peptide (figure 9), and the in vivo and in vitro functional assays using GRIP1 expression plasmids (figure 10), suggest that the GRV575M defect in p160 coactivator interactions contributes to the BudR phenotype in Ch- BdE5 cells. In support of this conclusion, the Ch-P8, Ch-Bd2 and Ch-BdE5 subclones were found to contain a similar steady-state level of GRIP1/TIF2 protein as Jurkat cells based on Western blotting (data not shown). DISCUSSION We have developed a molecular genetic model to investigate mechanisms of glucocorticoid insensitivity in a human bronchial epithelial cell line that represents a therapeutic target in asthma treatment. At least four types of BudR phenotypes were
  18. 18. Kunz et al. - page 18 identified. The first class of mutants is represented by Ch-Bd2 which had a decreased amount of GR protein (36% of its wild-type parent Ch-P8), and contained defects in transcriptional transactivation and NFkB transrepression. Down-regulation of GR expression could account for the BudR phenotype and is consistent with earlier studies showing that GR content is rate-limiting for steroid-responsiveness (60). Ch-Bd1 is a second type of BudR mutant in that it also contained a reduced level of GR protein, however, NFkB transrepression function was found to be normal (35% compared to 31% for the wild-type parent Ch-P10). While we do not know what accounts for the difference in NFkB transrepression function between Ch-Bd1 and Ch-Bd2, we did find that ectopic expression of GR cDNA in Ch-Bd1 and Ch-Bd2 cells complemented the loss of function defects in transcriptional regulatory activity (figure 4). A third class of BudR phenotypes is represented by the EMS-induced mutant Ch- BdE4. This cell line expressed near wild-type levels of GR protein based on western blotting (figure 3B), suggesting that the BudR phenotype was not the result of reduced GR expression. However, Ch-BdE4 had the lowest level of 3 H-Dex binding activity compared to all five Budr mutants (Table 1), and GR cDNA produced an altered DHPLC elution profile in the B region (amino acids 373-584). These data indicate that Ch-BdE4 cells express a GR variant with sequence alterations that effect ligand binding. Experiments are in progress to verify this prediction (SK and RM, unpublished data). The most unusual BudR cell line we isolated was Ch-BdE5 which is characterized by normal GR protein levels and 3 H-Dex binding activity, but with defects in transcriptional regulatory functions. Sequence analysis of GR cDNA generated from Ch-BdE5 cell RNA revealed that 60% of the randomly isolated cDNA clones contained a point mutation at V575M (figure 6). A comparison of GR with other nuclear receptors showed that V575 was highly conserved and corresponded to a region in helix 3
  19. 19. Kunz et al. - page 19 previously shown to be involved in coactivator binding (53, 54). Molecular dynamic simulations (figure 9) and protein interaction assays using the p160 coactivator GRIP1/TIF2 (figure 10), confirmed that GRV575M was a poor substrate for GRIP1, suggesting that this defect may be the molecular basis for the BudR in the Ch-BdE5 cell line. Interestingly, Rogatsky et al. (61) recently reported that GRIP1 can also function as a GR corepressor to inhibit NFkB signaling though the interleukin-8 gene regulatory region. Since we found that GRV575M was defective in mediating maximal repression of NFkB signaling in transfected Ch-Bd2 cells (figure 8), it is likely that decreased transrepression functions of GRV575M are also due to altered GRIP1 binding properties. Does expression of the GRV575M mutant receptor explain the Ch-BdE5 BudR phenotype? GR transactivation functions in the BudR Ch-BdE5 cell line were only ~20% that of the parental Ch-P8 cell line (Table 1), yet about half (40%) of the GR transcripts analyzed from Ch-BdE5 cells encoded the wild-type GRa receptor based on cDNA sequence analysis (figure 6). If this crude measure of GRa and GRV575M transcript ratios were correct, then one way to explain the BudR phenotype would be if the GRV575M mutation had a inhibitory effect on GRa activity. This type of dominant negative activity would be similar to what Vottero et al. (50) found when they co-transfected the GRI747M mutant with GRa at a 1:1 ratio in CV-1 cells. To test this idea, we recently used transient co-transfection assays of GRV575M and GRa into CV-1 or Ch-Bd2 cells at various molar ratios and measured Bud-dependent transactivation using the MMTV- Luc reporter (SK and RM, unpublished data). Results from these co-transfection assays were inconclusive, however, since GRV575M inhibitory effects on GRa activity appeared to be additive, rather than synergistic, using molar ratios of up to 5:1 of pCMX-GRV575M relative to pCMX-GRa. An alternative explanation for the BudR phenotype would be that the steady-state level of GRV575M protein in Ch-BdE5 cells is much greater than that
  20. 20. Kunz et al. - page 20 of GRa protein due to differences in protein stability. If this were the case, then the observed defect in Bud-regulated GR signaling in Ch-BdE5 cells would be due to elevated levels of GRV575M protein relative to GRa protein. For example, if coactivator binding destabilizes the GRa receptor complex as a mechanism of negative feedback signaling, then the level of GRV575M protein in the cell would accumulate relative to GRa because of differences in sensitivity to such feedback mechanisms. Interestingly, transfection of equal amounts of pCMX-GRa and pCMX-GRV575M plasmid DNA into COS-7 cells resulted in higher steady-state levels of GRV575M protein than GRa protein in cell extracts as determined by Western blotting (figure 7). Therefore, it is possible that GRV575M protein is inherently more stable than GRa and constitutes a greater proportion of the total GR protein in the cell which would be consistent with the additive inhibitory effects we observed in co-transfection assays (SK and RM, unpublished data). Reconstitution experiments using stable transfections of GRa and GRV575M into the GR-deficient Ch-Bd2 variant are underway to more directly determine the role of GRV575M in mediating the BudR phenotype. In addition to identifying functional GR mutations such as GRV575M, the Chago cell system we developed could also be used to find non-GR defects that cause steroid insensitivity. While we have focused this initial analysis on identifying GR mutations, it is likely that a larger screen for BudR cells would lead to the identification of additional GR signaling variants that are GR independent. This could be facilitated by integrating multiple copies of GR cDNA into the Ch-P8 founder cell line to minimize the chance of selecting for BudR cells with GR mutations. One type of mutation we could find using this type of strategy would be defects in the coactivator proteins themselves, for example, mutations in GRIP1/TIF2, SRC1 and RAC3/AIB1. Another application of this molecular genetic model could be for high throughput screens to identify steroid
  21. 21. Kunz et al. - page 21 analogs or other small molecules that reverse the BudR phenotype resulting from GR signaling defects. The sensitivity of such an assay could be increased by stably integrating the MMTV-Luc reporter gene into selected BudR variants. In the case of Ch- BdE5, it might be possible to screen small molecule libraries for compounds that stabilize coactivator binding to GRV575M in the presence of ligand, and thus restore normal transcriptional regulatory activity. Finally, cell-specific, and perhaps even ligand-specific, GR target genes could be identified by analyzing the RNA expression profiles of BudR variants under various conditions. This approach would exploit isogenic cell line panels that have minimal differences due to the use of founder cell lines. Moreover, by comparing RNA expression profiles generated from treating the same steroid insensitive cell line with different ligands, it should be possible to identify gene targets that track with specific hormonal responses. MATERIALS AND METHODS Cell Culture The Chago K1 cell line was obtained from the American Type Culture Collection (ATCC, Rockville, MD) and cultured in RPMI 1640 media with L-glutamine (Irvine Scientific, Santa Ana, CA), plus 10% defined calf bovine serum (CBS, Hyclone, Logan, UT), 100U/ml penicillin and 0.1mg/ml streptomycin (Sigma, St. Louis, Mo). Cultures were maintained in a 37oC incubator with 5% CO2 , at 90% humidity. COS-7 cells were grown in DMEM Low Glucose Pyruvate medium (Irvine Scientific) containing 10% CBS. Plasmids The plasmid pMMTV-GFP-neo contains a 1.4-kb fragment MMTV LTR from pMM-CAT (62) cloned into the XhoI/SalI-HindIII sites of pEGFP-1 reporter vector (Clontech, Palo
  22. 22. Kunz et al. - page 22 Alto, CA). The plasmid pMMTV-HSVtk-Zeo was constructed by inserting the MMTV LTR (XhoI-HindIII) promoter region, and the HSVtk (XbaI-BamHI) coding region into the vector pBluescript SK (Stratagene, La Jolla, CA). The zeomycin-resistance gene (Zeo) from pSV40-Zeo (Invitrogen, Carlsbad, CA) was excised with NotI and XbaI and inserted into the corresponding sites of pBluescript SK. The pMMTV-Rluc and pMMTV- Fluc plasmids used for Dual Luciferase Assay were constructed by inserting the MMTV LTR promoter into the pRL-null (Renilla) and pGL3-Basic (Firefly) vectors (Promega, Madison, WI) using XhoI and HindIII (46). pNFkB-luc was obtained from Stratagene. The pCMX-hGRa expression vector (63) was used to construct the GR V575M and GRg variants using QuikChange TM XL Site- directed mutagenesis Kit (Stratagene, La Jolla, CA) and appropriate mutagenic primers. The GRIP1 bacterial expression vector pGEX2TK/GRIP 563-1121 and eukaryotic expression vector pSG5.HA-GRIP were obtained from M. R. Stallcup and have been described (59). The GR templates for in vitro coupled transcription/translation for the GST pull-down assays were created by cloning the Kpn1/Xho1 fragments of pCMX-hGRa or pCMX-hGR V575M into the MCS of pBluescript II SK+ cloning vector (Stratagene). Generation of Isogenic Chago K1 Cell Lines Stable transfection of Chago K1 cells was done using 15 cm plates that were seeded to a density of 2 x 106 cells/plate and grown in RPMI media supplemented with 10% CBS and antibiotics for 24h. The following day, each plate was rinsed with PBS and 4 ml RPMI media (no serum or antibiotics) was added before transfection with 10mg linearized pMM-GFP plasmid DNA in DOTAP:DOPE transfection reagent (Avanti Lipids, Alabaster, AL) Lipofectamine (Invitrogen, Carlsbad, CA) using a lipid to DNA ratio of 4:1 (wt/wt). After a 6 h incubation at 37o C in 5% CO2 , the lipid mixture was
  23. 23. Kunz et al. - page 23 aspirated and replaced with RPMI growth media. Following an overnight recovery, media was aspirated and replaced with selection media containing 200mg/ml G418 (Geneticin, CalBiochem). Selection media was changed every fourth day. After 15 days, 48 Neo-resistant colonies were picked and plated in fresh media without G418. Fifteen expanded colonies were split to 10cm plates and treated with 10-7M Budesonide (AstraZeneca) for 48h. One of these cell lines, Ch-GFP.9, was stably transfected as described above with pMM-HSVtk-Zeo construct. After transfection, cells were allowed to recover for 48h before addition of RPMI selection media containing 50mg/ml Zeocin (Invitrogen) and 10% CBS. Media was changed every 3-4 days and Zeo-resistant colonies were picked and expanded in 12-well plates. Ten Zeo-resistant cell lines were screened for sensitivity to Budesonide by treating with 1mM Ganciclovir sodium (Cytovene-IV; Hoffmann-La Roche Nutley, NJ) with or without steroid (10-7M Budesonide). Two Budesonide-sensitive subclones (Ch-P8 and Ch-P10) were selected for mutational analysis. Analysis of GFP by Fluorescent Activated Cell Sorting (FACS) To screen for Bud-induced GFP expression by FACS analysis, cells were seeded at a density of 3 x 105 cells per well and allowed to attach overnight. After hormone treatment (10-7M Budesonide), cells were harvested 24 or 48 hours later with Trypsin- EDTA , washed once with PD buffer (137mM NaCl, 2.7mM KCl, 1.5 mM KH2 PO4 , 8.1 mM Na2 HPO4 , pH7.2) and fixed for 30 min in 4% paraformaldehyde. After a final wash, cells were either stored at 4o C overnight or examined immediately by FACS (Becton- Dickinson FACScan with Lysis II software).
  24. 24. Kunz et al. - page 24 Quantitation of GR levels by Immunoblotting Whole cell protein extracts were prepared from ~2x106 cells that had been harvested by trypsinization, washed with ice cold PBS, and resuspended in 200ml cold PBSTDS (1% Triton X-100, 0.5% sodium deoxycholate, 0.1% SDS), with protease inhibitors (1mg/ml leupeptin, 1mg/ml aprotinin, 1mM EDTA, and 0.5mM PMSF) in phosphate buffered saline. After 10 min on ice, the cell lysate was cleared by centrifugation at 14,000xg, for 10 min at 4oC. Cell extracts (30 mg protein) were separated by SDS-PAGE on a 7.5% polyacrylamide gel, and transferred to nitrocellulose by electroblotting in transfer buffer at 4oC for 1h at 90Volts. Non specific sites on the membrane were blocked for 1h in 3% nonfat dry milk solution in TBST (100mM Tris pH8.0, 0.9% NaCl, 0.05% Tween 20). GR was detected using anti-hGR polyclonal antibody PA1-512 (Affinity Bioreagents, Golden CO) at a 1:1200 dilution for 1h. After washes, peroxidase-labeled goat anti- rabbit IgG secondary antibody (Life Technologies, Grand Island, NY) was applied at a 1:20,000 dilution for 30 min. SuperSignal chemiluminescent substrate (Pierce, Rockford,IL) and Bio Max autoradiographic film (Kodak) were used to identify GR protein on the membrane. Hormone Binding Assay Cells were grown in RPMI media containing 10% charcoal-stripped calf bovine serum to approximately 60% confluence on 15 cm tissue culture plates. To harvest cells, plates were aspirated and washed once with PBS before addition of 10 ml PDTE ( 20mM Tris- HCl, pH 7.5;10mM EDTA in phosphate buffered saline). After 10 min at room temperature, cells were removed by repeated pipeting and centrifuged at 1500 rpm for 5 min at 4oC. Approximately 2 X 107 cells were resuspended in PBS, pelleted, quick- frozen in liquid N2 and stored at –80o C. Pellets were thawed on ice in 250 ml TEGN50
  25. 25. Kunz et al. - page 25 (50mM NaCl, 1mM EDTA, 12% vol/vol glycerol, 1mM 2-mercaptoethanol, 10mM Na- molybdate, 1mM PMSF and 10mM TRIS-HCl, pH 7.5 at 4oC). Cells were lysed by ultrasonic disruption using a Branson probe sonicator at setting 1, with a 50% cycle for 10 sec followed by centrifugation at 10,000xg for 10 min at 4o C. Soluble protein concentration was determined by colorimetric assay (BCA, Pierce). Binding assays were set up in triplicate, with each reaction containing 65ml cell extract and saturating amounts of 3 H-Dex (10nM), specific activity 81Ci/mM (Amersham, Piscataway, NJ). Non-radioactive ligand was added at 1000-fold molar excess to one tube of each set. Samples were incubated on ice for 2 hours. Unbound hormone was removed by addition of 100ml of a charcoal-dextran suspension in TEGN50 (10mg/ml activated charcoal and 1mg/ml dextran) followed by passage through a 0.45mm spin filter. Charcoal-free filtrate was added directly to scintillation cocktail and counted. Receptor- specific binding was calculated by subtracting the value of the sample containing excess cold ligand from those containing 3 H-Dex labeled ligand only. Transient Transfection Assay Cells were plated at a density of 2 X 105 cells/well in 12-well tissue culture plates in RPMI media supplemented with 10% charcoal-stripped calf bovine serum, and 100U/ml each penicillin and streptomycin. After overnight recovery, media was aspirated and cells rinsed once with PBS. One ml of serum-free RPMI media was added to each well. Plasmid DNA (2 mg reporter gene; pMMTV-Fluc and 0.5 mg control gene; pTk-Rluc/ well) was added to the cationic lipid DOTAP:DOPE (Avanti Polar Lipids, Alabaster, AL) at a lipid to DNA ratio of 2:1 wt/wt. Lipid/DNA complexes were allowed to form for 15 min at room temperature before incubation with cells for 6h at 37o C. The lipid mixture was then replaced with growth media and cells allowed to recover overnight. Cells
  26. 26. Kunz et al. - page 26 were treated for 18 h with 10-6 M Dex or 10-7 M Bud for the transactivation assays, or with 10-6 M Dex plus 1ng/ml tumor necrosis factor-a (TNF-a; R&D Systems, Minn, MN) for the NFkB transrepression studies. Forty-eight hours after transfection, cells were harvested for Dual Luciferase Assay (Promega, Madison, WI) using passive lysis buffer. Lysates were assayed for firefly and Renilla luciferase activity by addition of appropriate substrate and measurement of fluorescence using a Turner Designs Model TD-20/20 Luminometer (Sunnyvale, CA). Relative Luciferase Units (RLU) were normalized by dividing the reporter value by the control value. The COS-7 and Ch-Bd2 cell transfections were done in 10cm dishes or six well plates using Polyfect Transfection Reagent (Qiagen, Valencia, CA) following manufacturers protocol. The Ch-Bd2 cell transfections using the GRIP1 eukaryotic expression plasmid contained 300 ng of pSG5.HA-GRIP, 50 ng of pCMX, pCMX-hGRa or pCMX-hGRV575M , and the same amounts of luciferase reporter plasmids as described above. The relative luciferase units for pCMX-hGRa or pCMX-hGRV575M transfections shown in figure 10A were determined by subtracting the amount of luciferase activity in cell extracts obtained from pCMX transfections to account for the low level of endogenous GR in the Ch-Bd2 cells. Molecular Modeling A preliminary homology model of the GR was constructed using the Swiss PDB Viewer version 3.7b (64) based on the amino acid sequence of the GR (accession code P04150) retrieved from the SwissProt database (65) and the molecular structure of the progesterone receptor (accession code 1A28A) retrieved from the SwissProt ExPDB. The structures of initial GR homology model and the PR crystallographic structure were superimposed using the iterative magic fit option of the Swiss PDB Viewer. The
  27. 27. Kunz et al. - page 27 structure of the progesterone ligand (CAS registry number [57-83-0]) and the crystallographic water molecules were copied from the PR structure (PDB accession code 1A28) to the GR homology model. The GR homology was then aligned to chain A of the crystallographic structure of ERa/raloxifene core/NR Box 2 TIF2 peptide complex (PDB accession code 1GWQ) and the TIF2 peptide (chain C) was copied from the crystallographic structure to the homology model. Residues A688 to I689 (except for the backbone CA, C, and O atoms of I-689) and Q695 to D696 (except for the N and CA atoms of Q695) were deleted from the copied TIF2 peptide. Residues H691 and R692 were both mutated to alanine resulting in the capped peptide Ac-LAALL-NHMe as a simplified mimic of the LxxLL NR box. SCWRL (Sidechain placement With a Rotamer Library; University of California San Francisco, San Francisco CA 94143-0450) (66) version 2.9 was used to assign the side chain conformations of the amino acid residues in the GR/budesonide/Ac-LAALL-NHMe model complex holding fixed (-s option) conserved amino acid residues lining the ligand binding cavity (L563, L566, Q570, W600, M601, M604, L608, R611, F623, M646, L732, Y735, C736, F740, F750). The structure of progesterone ligand was converted to budesonide (CAS registry number [51333-22-3]) using the structure builder of Maestro version 4.1.012 (Schrödinger, Inc.; New York, NY 10036-4041) and minimized in the presence of the rigid receptor using the AMBER* force field. Molecular dynamics (MD) simulations with the CHARMM force field with a 600 ps equilibration phase and 1000 ps collection phase were performed on the GR/budesonide/Ac-LAALL-NHMe model complex. An explicit water sphere of radius 20 Å was centered on the peptide, and spherical boundary conditions were applied. All solvent exposed charged side chains (Asp, Glu, Arg, and Lys) outside this sphere were neutralized. Weak positional constraints were applied to all alpha carbons of the protein, while all peptide atoms were unconstrained. Estimates
  28. 28. Kunz et al. - page 28 of the relative free energy of the LxxLL motif binding to the wild-type and mutant receptor, respectively, were calculated by the LIE method (67) using parameters a = 0.18 and b = 0.33. GST Pull-down Assays GST or GST-GRIP563-1121 proteins were isolated from E. coli BL21 (DE3) pLysS cells after induction with 0.2 mM IPTG for 3 hours. Bacterial cells were harvested, resuspended in NETN buffer (100mM NaCl, 1mM EDTA, 20mM Tris-HCl, pH 8.0,) containing 0.5% NP-40 detergent plus a protease inhibitor cocktail (Sigma). Cells were then lysed using a probe sonicator (Branson) @ 60% duty cycle for 15 sec x 2 while on ice. Triton X-100 was added to a final concentration of 1 % before centrifugation at 10,000 X g in a Sorvall SA-600 rotor for 30 min at 4oC. Purification of GST proteins from these extracts was performed by incubation of the supernatant for 30 min at 4o C with gentle agitation using prewashed Glutathione Sepharose 4B (Amersham Biosciences). GST-bound beads were washed by centrifugation (500 X g for 5 min at 4o C) once with NETN Lysis Buffer (NETN buffer with 0.5% NP-40 and protease inhibitors), and then twice with cold NETN Binding Buffer (NETN buffer with 0.1% NP-40 and protease inhibitors). The [3 5S] methionine-labeled GRa, GRV575M and firefly luciferase proteins were synthesized in the presence or absence of 10-7M Bud using the TNT-T7 coupled Reticulocyte Lysate System (Promega) according to the manufacturer’s instructions. The binding assay was conducted essentially as described (59). Briefly, 40ml of bead slurry containing GST or GST-GRIP563-1121 fusion protein was incubated with 10 ml of the in vitro synthesis reaction and 50ml NETN Binding Buffer. Tubes were rotated slowly at 4oC for 2 hours and then the beads were washed four times by centrifugation and resuspended in NETN Binding Buffer at 4oC. The Bud concentration was maintained at 10-7M for all
  29. 29. Kunz et al. - page 29 +Bud samples during the binding and washing steps. Finally, GST proteins were eluted from the beads using 25 ml of 10mM reduced glutathione and protein samples were analyzed by SDS-PAGE and autoradiography using Amplify fluorographic reagent (Amersham). ACKNOWLEDGMENTS The authors wish to thank Drs. Ross Rocklin and Ralph Brattsand, formerly of Astra Draco, for supporting our initial work on developing a molecular genetic model to investigate budesonide-resistance, Dr. Ron Evans for the gift of human GRa expression plasmid, Dr. Roger Askew for the HSV tk plasmid, Dr. Michael Stallcup for the GRIP1 expression plasmids, Dr. Konrad Koehler at Karo Bio for help with the molecular modeling, Dr. Kerr Whitfield for critical comments on the manuscript, and Felisa Blackmer of the Arizona Research Labs Division of Biotechnology for help with the Denaturing HPLC analysis. This work was supported by grants to RLM from AstraZeneca, Inc., the NIH (HL-60201) and the Jack Findlay Doyle II Charitable Fund. PC was supported by the Foundation for Knowledge and Competence Development (KK-stiftelsen) and Karo Bio AB, Huddinge, Sweden.
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  34. 34. Kunz et al. - page 34 Table 1. Characterization of Chago variants containing GR signaling defects. Three of the cell lines were identified as spontaneous mutants (Ch-Bd1, Ch-Bd2, ChBd-3) and two were obtained from mutagenized cell populations (Ch-BdE4, Ch-BdE5). Ch-P8 is the parental wild-type line for Ch-Bd2, ChBd3, Ch-BdE4 and Ch-BdE5, whereas, Ch-P10 is the parental wild-type line for Ch-Bd1 (see fig. 1). The abbreviation "n.d." refers to not determined. Glucocorticoid Signaling Relative GR levels Cell Line Budesonide Fold- Percent Protein Binding a b c d e Sensitivity activation repression Level activity Ch-P10 wild-type 38.0 33% 100 2.1 Ch-Bd1 resistant 4.3 37% 26 1.4 Ch-P8 wild-type 37.6 36% 100 2.1 Ch-Bd2 resistant 3.3 3% 36 1.7 Ch-Bd3 resistant 5.2 n.d. 37 1.5 Ch-BdE4 resistant 8.5 n.d. 76 0.8 Ch-BdE5 resistant 9.2 13% 87 2.4 a Based on growth in ganciclovir + budsonide media. b MMTV-luciferase transactivation data, similar to figure 3a. c Transrepression of NFkB data, similar to figure 4b. d Quantitation of band and intensity from western blot in figure 3b. e Specific 3H-dexamethasone binding expressed as cpm/mg protein.
  35. 35. Kunz et al. - page 35 FIGURE LEGENDS Figure 1. Flow scheme illustrating the strategy used to isolate BudR ChagoK1 cell variants. ChagoK1 cells were stably transfected with the reporter gene pMMTV-GFP- neo. The cell line Ch-GFP.9 was stably transfected with the reporter gene pMMTV- HSVtk-Zeo to generate the Bud-sensitive founder lines Ch-P10 and Ch-P8. Growth of Ch-P10 and Ch-P8 cells in media containing ganciclovir, Bud and zeomycin (Zeo) led to the isolation of the BudR cell lines Ch-Bd1, Ch-Bd2 and Ch-Bd3. Two additional BudR variants, Ch-BdE4 and Ch-BdE5, were isolated following chemical mutagenesis of Ch- P8 cells with ethylmethane sulfonate (EMS). The relative proportion of GFP+ and GFP- BudR cell lines in each selection strategy is shown. Figure 2. Characterization of the Bud-sensitive phenotype in the Ch-P8 cell line. A) Budesonide induction of GFP expression in the Ch-P8 parental cell line Ch-GFP.9 measured by FACS. B) Ganciclovir killing of Ch-P8 cells in the presence of budesonide. Data for cell viability is presented as mean ± SEM. Figure 3. Characterization of GR signaling in BudR ChagoK1 variant cell lines. A) GR-mediated transcriptional activation functions in BudR variants using a transient transfection assay including the reporter plasmid pMMTV-Fluc and control plasmid pTk-Rluc. Fold-induction values were determined using the relative fluorescence units obtained from extracts prepared from cells cultured in the absence or presence of 10-6 M Dex. Data is presented as mean ± SEM. B) Western blot analysis of GR protein expression in Chago cells using an anti-GRa antibody.
  36. 36. Kunz et al. - page 36 Figure 4. Complementation of the BudR phenotype in Ch-Bd1 and Ch-Bd2 cells by transiently transfected GR cDNA. A) Defects in transcriptional activation functions in Ch-Bd1 and Ch-Bd2 could be complemented by transfection of GRa cDNA. B) The defect in transrepression of NFkB function following TNFa stimulation could be corrected in Ch-Bd2 cells by expression of GRa cDNA. Ch-Bd1 cells had no loss of transrepression function relative to the parental line Ch-P10. Data is presented as mean ± SEM. Figure 5. Detection of sequence variations in the GR coding sequence using RT-PCR and Denaturing High Performance Liquid Chromatography (DHPLC). Location of RT- PCR primers used in the DHPLC analysis are shown relative to the location of GR Activation Function 1 sequence; AF-1, DNA binding domain; DBD, and Ligand Binding domain. Traces of the elution profile of partially denatured heteroduplexes derived from equimolar mixtures of RT-PCR products from the indicated cell lines. P8/P8 is the homoduplex control. Samples were analyzed using the WAVE TM DNA Fragment Analysis System (Transgenomic Inc., Omaha, NE). Figure 6. Sequence analysis of GR coding sequences spanning the B region. A) DNA and inferred protein sequence of the two sequence alterations (GRg and GRV575M) identified in cloned GR sequences obtained from the B region RT-PCR reactions (see figure 5). B) Functional map of the B region showing the location of the GRg and GRV575M mutations relative to the DBD and exon boundaries. C) Summary of DNA sequence data from independent plasmid isolates of the GR cDNA B region of the Ch- P8, Ch-Bd2 and Ch-BdE5 cell lines. The total number of random cDNA isolates with the indicated sequence organization are shown in parentheses.
  37. 37. Kunz et al. - page 37 Figure 7. Functional expression of GRa, GRg and GRV575M proteins in transiently transfected COS-7 cells. A) Western blot of GR protein levels in COS-7 cells that were transfected with pCMX expression plasmids containing the full-length GRa, GRg and GRV575M coding sequences. The relative levels of a-tubulin expression in the COS-7 extracts was determined using an a-tubulin specific antibody. B) Specific 3 H-Dex binding activity in the same COS-7 extracts shown in "A." Binding assays were performed as described in Materials and Methods except that total Dex concentration was varied between 10-10 and 10-8 M as indicated. Data is presented as mean ± SEM. Figure 8. Transcriptional activation and transrepression functions of GRa, GRg and GRV575M coding sequences in transiently transfected Ch-Bd2 cells. A) Fold-induction of the MM-Luc reporter gene using increasing amounts of Bud. B) Percent transrepression of an NFkB reporter gene following treatment with TNF-a and Bud. Data is presented as mean ± SEM. Figure 9. Molecular modeling predicts that GRV575M is defective in p160 coactivator binding. A) ClustalW alignment of amino acid residues in the region of GRV575 from a variety of intracellular receptors. This 28 residue stretch corresponds to most of helix 3 and all of helix 4 of the human GR (51), ERa (53), PPARg (55), and TRb (56) ligand binding domains as defined by x-ray crystallography. The "*" identifies the corresponding residues in hERa (I358), hPPARg (T297) and hTRb (V284) that have been shown by these same studies to make van der Waals contacts with Box II peptides of p160 coactivators. The "•" denotes residues that contribute to a shallow groove within the p160 coactivator binding site. B) Molecular modeling of the GRV575M mutation. Top
  38. 38. Kunz et al. - page 38 view of the hydrophobic coactivator binding pocket for the wild-type complex (left) and mutated complex (right). The GR surface is shown as a green mesh. The coactivator peptide is indicated by a blue tube, having the C-terminus to the right. The LxxLL leucines are shown as ball-and-stick models, and the mutated residue at position 575 is shown as space-filling atoms under the mesh. Residue 575 directly interacts with the Leu +1 and Leu +4 side chain residues in the coactivator peptide. Both pictures are representative snapshots of the equilibrated complexes after 1600 ps of simulation. Figure 10. Functional interactions between GRV575M and the p160 coactivator GRIP1 are defective in vivo and in vitro. A) Results of transactivation assays in which Ch-Bd2 cells were transfected with pCMX-GRa or pCMX-GRV575M, pMMTV-Fluc, pTk-Rluc, with or without pSG5.GRIP1 in the presence or absence of 10-7M Bud. The relative luciferase units for these experiments were determined as described in Materials and Methods. B) GST pull-down assays using in vitro synthesized [3 5S] methionine-labeled GRa, GRV575M or luciferase proteins, incubated with glutathione coupled sepharose beads bound with GST or GST-GRIP563-1121 protein produced in E. coli. Binding experiments were performed in the presence or absence of 10-7M Bud as indicated and eluted proteins were separated by SDS PAGE and visualized by autoradiography. The input radiolabeled proteins present in 2 ml of reticulocyte lysate were loaded in lanes 1, 2 and 9, whereas, all other lanes show the eluted proteins recovered from GST (lane 5) and GST-GRIP563-1121 (lanes 3, 4, 6-8) binding reactions containing 10 ml of reticulocyte lysate.
  39. 39. ChagoK1 pMMTV-GFP-neo Ch-GFP.9 pMMTV-HSV-tk-Zeo Ch-P10 BudS founder Ch-P8 cell lines EMS mutagenesis Select colonies in 4 µM ganciclovir, 0.1 µM budesonide, 50 µg/ml Zeo Screen for GFP fluorescence in 0.1 µM budesonide by FACS Ch-Bd1 Ch-Bd2 Ch-Bd3 Ch-BdE4 Ch-BdE5 Isolation of 36 BudR cell lines of which 3 were GFP- Isolation of 60 BudR cell lines of which 2 were GFP- Kunz et al., Figure 1
  40. 40. A 100 24 hr 48 hr 80 %GFP Positive 60 40 20 0 10-10 10-9 10-8 10-7 10-6 Budesonide (M) B 8 7 Viable Cells/ml (x 104) 6 -Bud 5 4 3 2 1 +Bud 0 1 2 3 4 5 6 7 8 9 10 Days in Culture Kunz et al. figure 2
  41. 41. B A Fold-Induction 0 10 20 30 40 Ch Ch -P -P 8 8 Ch Ch -B -B d2 d2 Ch Ch -B -B d3 d3 Ch Ch -B -B dE dE 4 4 Ch Cell Line Ch -B -B dE dE 5 5 Kunz et al. Figure 3 Ch Ch -B -P d1 10 Ch Ch -P -B 10 d1 - GRα
  42. 42. A 120 Fold-induction (MMTV) 100 80 60 40 20 Ch-P10 Ch-Bd1 Ch-Bd1 Ch-P8 Ch-Bd2 Ch-Bd2 + GRα + GRα Cell Line B 90 Percent Repression (NFkB) 80 70 60 50 40 30 20 10 Ch-P10 Ch-Bd1 Ch-Bd1 Ch-P8 Ch-Bd2 Ch-Bd2 + GRα + GRα Cell Line Kunz et al. Figure 4
  43. 43. 0 100 200 300 400 500 600 700 777 AF-1 DBD Ligand Binding G B H E P8/P8 Bd2/P8 BdE4/P8 BdE5/P8 3.0 3.5 4.0 4.5 5.0 5.5 3.0 3.5 4.0 4.5 5.0 5.5 3.0 3.5 4.0 4.5 5.0 5.5 2.5 3.0 3.5 4.0 4.5 5.0 Kunz et al. Figure 5
  44. 44. A GRγ (3 bp insertion at exon 3 splice site) 449 450 451 452 453 454 GTG GAA GGT AGA CAG CAC AAT V E G R Q H N V575M (G to A transition) 573 574 575 576 577 GCA GCA ATG AAA TGG A A M K W B Exon 3 Exon 4 Exon 5 373 584 DNA Binding Domain Hinge + Ligand Binding Region R (GRγ) V575M C wild type GR (18) Ch-P8 GRγ (2) wild type GR (17) Ch-Bd2 GRγ (2) V575M (11) wild type GR Ch-BdE5 (8) GRγ V575M (1) Kunz et al Figure 6
  45. 45. A A 5M DN α γ V57 GR GR No kDa 121 GR 79 53 Tubulin B 600 GRα Binding Activity (cpm/µg) 500 V575M GRγ 400 300 200 100 0 10-10 M 10-9 M 10-8 M [3H-Dexamethasone] Kunz et al. Figure 7
  46. 46. A 120 GRα 100 V575M Fold-induction GRγ 80 60 40 20 0 10-10 M 10-9 M 10-8 M 10-7M [Budesonide] B 70 GRα Percent Repression 60 V575M 50 GRγ 40 30 20 10 0 10-10 M 10-9 M 10-8 M 10-7M [Budesonide] Kunz et al. Figure 8
  47. 47. GRV575M A GR LNMLGGRQVIAAVKWAKAIPGFRNLHLD 590 MR LNRLAGKQMIQVVKWAKVLPGFKNLPLE 796 PR LNQLGERQLLSVVKWSKSLPGFRNLHID 745 TRa FTKIITPAITRVVDFAKKLPMFSELPCE 245 TRb FTKIITPAITRVVDFAKKLPMFCELPCE 299 RARa FSELSTKCIIKTVEFAKQLPGFTTLTIA 255 RARb FSELATKCIIKIVEFAKRLPGFTGLTIA 255 RARg FSELATKCIIKIVEFAKRLPGFTGLSIA 257 RXRa ICQAADKQLFTLVEWAKRIPHFSELPLD 295 RXRb ICQAADKQLFTLVEWAKRIPHFSSLPLD 366 RXRg ICHAADKQLFTLVEWAKRIPHFSDLTLE 296 PPARa CQCTSVETVTELTEFAKAIPGFANLDLN 303 PPARb CQCTTVETVRELTEFAKSIPSFSSLFLN 276 PPARg CQFRSVEAVQEITEYAKSIPGFVNLDLN 340 VDR LADLVSYSIQKVIGFAKMIPGFRDLTSE 257 ERb LTKLADKELVHMISWAKKIPGFVELSLF 325 ERa LTNLADRELVHMINWAKRVPGFVDLTLH 373 • • * • • • • • Helix 3 Helix 4 B GRα V575M Kunz et al. Figure 9
  48. 48. A 14 12 Relative Luciferase Units 10 8 6 4 2 0 Bud - - + + - - + + GRIP-1 - + - + - + - + GRα V575M B M M M cif. cif. 75 75 75 α α α α 35 GR GR GR GR S Protein V5 V5 V5 Lu Lu GST - - - - + - - - - GST-GRIP - - + + - + + + - Bud + + - + + - + - - MW (kDa) - 120 - 84 - 66 - 50 - 39 1 2 3 4 5 6 7 8 9 Kunz et al. Figure 10

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