Cancer Research Annual Meeting 2010  Protein Translation and Cancer
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[Cancer Research 60, 6171-6177, November 1, 2000]
© 2000 American Association for Cancer Research


Tumor Biology

BRG1, a Component of the SWI-SNF Complex, Is Mutated in Multiple Human Tumor Cell Lines

Alexander K. C. Wong1, Frances Shanahan, Yuan Chen, Lubing Lian, Phuong Ha, Kristin Hendricks, Siavash Ghaffari, Diana Iliev, Brandon Penn, Anne-Marie Woodland, Richard Smith, Grant Salada, Arlene Carillo, Kirsten Laity, Jamila Gupte, Brad Swedlund, Sean V. Tavtigian, David H-F. Teng2,3 and Emma Lees2,4

Myriad Genetics, Inc., Salt Lake City, Utah 84108 [A. K. C. W., Y. C., L. L., P. H., S. G., D. I., B. P., A-M. W., R. S., G. S., A. C., K. L., J. G., B. S., S. V. T., D. H-F. T.], and DNAX Research Institute of Molecular and Cellular Biology, Palo Alto, California 94304 [F. S., K. H., E. L.]


    ABSTRACT
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Human BRG1 is a component of the evolutionarily conserved SWI-SNF chromatin remodeling complex. BRG1 has been implicated in growth control through its interaction with the tumor suppressor pRb and may consequently serve as a negative regulator of proliferation. Postulating that BRG1 may itself be a tumor suppressor gene, we screened a panel of tumor cell lines to determine whether the gene is targeted for mutation. We report that the COOH-terminal region of BRG1 is homozygously deleted in two carcinoma cell lines, prostate TSU-Pr1 and lung A-427. In addition, biallelic inactivations of BRG1 were observed in four other cell lines derived from carcinomas of the breast, lung, pancreas, and prostate; their mutations in BRG1 included three frameshift lesions and one nonsense lesion. Point mutations were also discovered in a number of other cell lines, however in most cases any effect of these mutations on BRG1 function remains to be established. A variety of different mutations within BRG1, in several cell lines, suggest that BRG1 may be targeted for disruption in human tumors. Significantly, reintroduction of BRG1 into cells lacking BRG1 expression was sufficient to reverse their transformed phenotype inducing growth arrest and a flattened morphology. These data strongly support the model that BRG1 may function as a tumor suppressor and strengthen the hypothesis that the regulation of gene expression through chromatin remodeling is critical for cancer progression. It will be important to confirm these observations in primary tumors.


    INTRODUCTION
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
The mammalian SWI-SNF complex is a multiprotein complex involved in chromatin remodeling during transcriptional activation. Within this complex, BRG1 or its relative BRM, provide the ATPase activity necessary for transcriptional regulation by nucleosome disruption (reviewed in Refs. 1, 2, 3 ).

The SWI/SNF apparatus has been demonstrated to play a role in hormone receptor activation and the transcriptional activation of a number of other genes (reviewed in Ref. 1 ). More recent data using microarray analysis of global gene expression in yeast have demonstrated that SWI/SNF may also be involved in transcriptional repression. Inactivation of the SWI/SNF remodeling complex altered the expression levels of 6% of all of the yeast genes and surprisingly revealed that most were negatively regulated by SWI/SNF (4) . Experiments in many systems now support a model whereby chromatin remodeling complexes facilitate both transcriptional activation and repression via nucleosome mobilization (reviewed in Ref. 3 ).

In mammalian cells it is believed that BRG1 may play an important role in growth control through its physical interaction with the pRb tumor suppressor protein (5 , 6) . Transfection of wild-type BRG1 gene into SW13 adrenal carcinoma cells that lack endogenous BRG1/BRM expression reverted the transformed phenotype of these tumor cells and induced growth arrest in a pRb-dependent fashion (5) . More recent data show that pRb and BRG1/BRM act together to repress transcription of certain E2F target genes required for entry into S phase, such as cyclin A and CDC2 (7 , 8) . Additionally, BRG1 may act to modulate the transcriptional activity of oncogenes such as c-FOS (9) . In this case the repression is believed to be E2F independent, suggesting that BRG1 may modulate transcriptional activity via a number of alternate mechanisms.

Taken together, these data suggest that BRG may play an important role in the regulation of cellular proliferation through transcriptional regulation of key genes required for S phase entry and may therefore act as a tumor suppressor itself. In this study we show that BRG1 is homozygously deleted or mutated in several different cell lines. Reintroduction of BRG1 into these cells causes cell cycle arrest and a flat cell morphology, indicating that loss of BRG1 was important in the development of their transformed phenotype.


    MATERIALS AND METHODS
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Cell Lines.
Cell lines of various cancer types were obtained from ATCC and grown as monolayers in the appropriate medium supplemented with 10% heat inactivated FCS. Tumor cell lines investigated in this study were developed from the following tissues: bladder, breast, brain, cecum, colon, lung, ovary, pancreas, prostate, skin, and testis.

Reagents.
Polyclonal antibodies to BRG1, BAF155, and hINI1 were as described in Ref. 10 , and J1 was a gift from G. Crabtree (Stanford University, Palo Alto, CA; Ref. 11 ). To generate a specific monoclonal antibody to human BRG1 (8A11) mice were immunized with a GST5 fusion protein expressing amino acids 1–700 of BRG1 (10) . Hybridomas were generated using standard procedures. Antibodies to BRM were purchased from Santa Cruz Biotechnology (sc-6449) and Transduction Laboratories (B36320) and to pRb from Santa Cruz Biotechnology (C-20). A monoclonal antibody to cyclin E, HE172 has been previously described (10) .

RNA and DNA Isolation.
Total RNA and genomic DNA were prepared simultaneously using the TRI Reagent (Molecular Research Center). RNAs were reversed transcribed with Superscript II (Life Technologies) to generate first-strand cDNAs that were subsequently PCR amplified.

Radiation Hybrid Mapping.
Radiation hybrid mapping was performed using the Genebridge panel 4 (Human Genome Project, Sanger Center) and the following BRG1-specific STS primers: 5'-ACTGTCTGCAGCTCCCGTGAA and 5'-CAGCATGGCTCCAGGGGAAGG. These primers were developed from sequences within exon 2 of the gene and amplified a 106-bp product.

Mutation Screens.
Protocols for the homozygous deletion search and PCR-sequence-based mutation analyses were as described previously (12) . All of the amplifications were done using Platinum Taq DNA polymerase (Life Technologies). Briefly, each primer pair for STSs 1–6 (Fig. 1B)Citation was mixed with 30 ng of genomic DNA and subjected to 35 cycles of PCR amplification. The product of STS 7 (Fig. 1A)Citation was generated by two rounds of sequential PCR using in the first-round primers 5'-GTGCCCCTGGTTGACTCAAGA and 5'-TTGGGAACTGACTGGCTACAG and then, in a secondary reaction, two nested primers tailed with M13 forward or reverse sequences (underlined), 5'-GTTTTCCCAGTCACGACGCAGCCCCTCCCCGACCACCT and 5'AGGAAACAGCTATGACCATAGAGCACGGTCTGTCCACCC. Product from the secondary reaction was sequenced using a M13 forward or reverse primer. Similarly, BRG1 cDNA amplicons were produced by two rounds of sequential PCR using the primers listed in Table 1Citation . Five primary A-P amplicons (1, 2, 3, 4, 5) were developed to span the gene’s entire ORF. Each primary A-P product was diluted into secondary reactions containing corresponding nested primer pairs: B-Q, C-R, D-S, E-T, or F-U. Throughout, PCR artifacts were dispelled by sequencing independent PCR fragments.



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Fig. 1. A. Homozygous deletions of BRG1. BRG1-specific primers were used for PCR amplification of fragments from either genomic DNA (Lanes 1–5) or cDNA template (Lanes 6–9) generated from the following human tumor cell lines: Lane 1, prostate DU145; Lane 2, lung A-427; Lane 3, prostate TSU-Pr-1; Lane 4, lung NCI-H1299; Lane 5, no template control; Lane 6, breast ALAB; Lane 7, lung NCI-H1299; Lane 8, prostate DU145; and Lane 9, pancreas Hs 700T. The positions of the STSs are described in B. In Lanes 6–9, nested PCRs were performed using primers listed in Table 1Citation : 2A-2P in the primary reaction and 2D-2S in the secondary reaction. Twenty µl of each reaction were fractionated on a 2% agarose gel, stained with ethidium bromide, and visualized. B, finer deletion mapping of BRG1. Filled box, the ORF of BRG1 (GenBank accession no. U29175; translation initiation ATG is defined as position +1). The base positions of STSs 1–6 in this mRNA sequence are -21–84, 2615–2711, 3753–3859, 4692–4793, 4801–4899, and 4947–5144, respectively. Diagram is not drawn to scale. C, mutations abrogating the donor splice site of exon 10 of BRG1. In the DU145 prostate carcinoma line, the canonical G (*) in the exonic portion of the splice donor junction is mutated to T. In the case of lung NCI-H1299, a 69-base deletion (underlined) completely removes the wild-type splice donor site of this exon. These two independent aberrations result in the utilization of a cryptic splice donor ({blacktriangledown}), located after nucleotide position 1676 of the BRG1 ORF. Uppercase nucleotides, the 168-base exon 10 sequence of BRG1; lowercase nucleotides, the flanking intronic sequences.

 

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Table 1 Primers for BRG1 cDNA screening

 
BRG1 Gene Structure.
The intron-exon structure of the BRG1 gene was elucidated by comparing its cDNA sequence with partial genomic DNA sequences from BAC CIT-HSPC_21504 (GenBank accession no. AC011442), the complete sequence of cosmid F24827 (GenBank accession no. AC006127), and partial sequences from BAC CIT978SKB_164O19 (GenBank accession no. AC011485). We have placed an annotated sequence covering the whole locus in GenBank as accession no. AF254822.

Immunoprecipitations and immunoblots were performed as previously described (10) . For protein analysis cell pellets were lysed in buffer (250 mM NaCl, 50 mM Tris, pH 8.0, 0.1% NP40) plus protease inhibitors (complete EDTA-free tablets, protease inhibitor cocktail, Boehringer Mannheim). For E1A binding experiments 500 µg cell lysate was mixed with 5 µg GST E1A protein and incubated for 1 h at 4°C. Fifty microliters of 50% slurry of gluthathione agarose beads (Sigma) were added, and samples were incubated for an additional 1 h. The agarose beads were then pelleted by centrifugation, washed extensively with lysis buffer, resuspended in sample buffer, and then loaded on 8% Novex SDS-PAGE gels. After electrophoresis, proteins were transferred to Immobilon poly(vinylidene difluoride) (Millipore) and probed for the presence of pRb using standard Western blotting procedures.

Flat Cell Assays.
For stable transfections ALAB or TSU-Pr1 cells were transfected with 6 µg total plasmid DNA including 2 µg pBJ5.BRG1 using 25 µl LipofectAMINE reagent (Life Technologies, Inc). pBSK was used as carrier. Forty-eight h posttransfection cells were trypsinized and counted, and cells were replated in the presence of puromycin (Sigma) at 2 µg/ml in complete medium. After 10 days of selection, cells were fixed overnight in methanol and stained in crystal violet solution (2% crystal violet in 20% methanol) for 5 h.

FACS Analysis.
Cells were transiently transfected as previously described (13) . Briefly, cells were transfected with 5 µg pBJ5.BRG1, pBJ5BRGK > R, CMVp27, CMVp16, or CMV.CDK2DN plus 1 µg CMVCD20 using 25 µl LipofectAMINE reagent. pBSK was used as carrier. Forty-eight h posttransfection, the cells were trypsinized, replated at lower density, and incubated at 37°C for 18–24 h. Cells were harvested and stained with 5 µl FITC-conjugated anti-CD20 monoclonal antibody (Leu-16, Becton Dickinson), on ice for 30 min. The cells were washed and fixed with 85% ethanol. Cells were stained with propidium iodide and analyzed by FACS.


    RESULTS
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
Genomic Localization of BRG1.
Using a STS specific for BRG1 (see "Materials and Methods"), we radiation hybrid mapped the gene to chromosome 19p13. It has been reported that human chromosome 19p13.1–13.2 harbors a gene(s) that suppresses tumorigenicity of both human TSU-Prl and rat Dunning-R3327 AT6.1 prostatic cancer cells in nude mice (14) . Given this potential correlation, we investigated directly whether BRG1 was deleted in tumors by analyzing a panel of human tumor cell lines derived from many different tissues. Observations of homozygous deletions in tumor cell lines have guided the localization of several tumor suppressor genes including p16 (15) , DPC4 (16) , and MKK4 (12 , 17) . Importantly, to date, every gene that has been found to sustain mutations at significant frequency in tumor cell lines has also been found to be aberrant in primary or metastatic tumors.

Mutation Screening.
Homozygous deletion screens were performed using BRG1 gene-specific STSs to amplify fragments from 188 human tumor cell line genomic DNAs by PCR. Two of the 188 cell lines examined, prostate carcinoma TSU-Pr1 and lung carcinoma A-427, failed to amplify a product with a STS designed from the COOH-terminal region of the BRG1 gene (Fig. 1, A and B)Citation . To ensure that failure to detect a PCR product was not because of a sequence polymorphism, we developed and tested independent flanking STSs that probed different regions of the gene (Fig. 1, A and B)Citation . Overall, three contiguous STSs (4, 5, 6) failed to amplify from TSU-Pr1 genomic DNA (Lanes 3), whereas STSs 3–6 were absent in A-427 genomic DNA (Lanes 2), indicating that the breakpoints of the deletions in the two cell lines were different.

In addition to homozygous deletions, another common mechanism for inactivating tumor suppressor genes involves microlesions, such as point mutations, in a loss-of-heterozygosity background. Using overlapping amplicons designed to cover the entire ORF of BRG1 (Table 1)Citation , we screened the BRG1 cDNAs from 92 tumor cell lines for sequence alterations. In 2 of the 92 tumor cell lines, lung NCI-H1299 and prostate DU145 (Fig. 1ACitation , Lanes 7 and 8), we observed that the PCR product of one amplicon was smaller and additionally, that no wild-type product was detected. Sequence analyses confirmed that both of these shorter cDNA fragments had eliminated the same 85 bases of the gene’s ORF (nucleotides 1677–1761), which should result in frameshift mutations. As a step toward elucidating the molecular events underlying the cDNA deletions, we mapped the genomic structure of BRG1 (see "Materials and Methods" for details). Intron-exon mapping showed that the major form of this gene contains 35 exons (GenBank accession no. AC006127) and that the 85-base deleted segment of the cDNA observed in DU145 and NCI-H1299 removes the 3' portion of the 168-base exon 10. To define the molecular cause of these deletions, primers specific to the intronic sequences flanking exon 10 were used to amplify genomic DNA fragments from the two aberrant tumor cell lines. We observed that the product from DU145 appeared to be wild type in size; however, the product from NCI-H1299 was smaller (Fig. 1ACitation , STS 7, Lane 4). On sequencing, we found a G to T mutation at the conserved splice donor site of exon 10 in DU145, whereas NCI-H1299 exhibited a 69-base deletion that deletes the same splice donor site (Fig. 1C)Citation . Both of these splice site mutations appear to result in the activation of a cryptic splice donor within exon 10 (Fig. 1Citation C, {blacktriangledown}) an event that would lead to the expression of frame-shifted BRG1 mRNA. Importantly, we found that wild-type BRG1 was not detected from either cDNA or genomic DNA template from either of these cell lines (Fig. 1A)Citation . In the screening of the rest of the tumor cell line cDNAs, another mutation was identified in the breast carcinoma cell line ALAB, where a C1630T change results in a stop codon to yield a truncated ORF (Table 2)Citation . In the Hs 700T pancreatic carcinoma cell line, deletion of a single C base at ORF position 729 was identified, which should cause a frameshift mutation. In both these cases, wild-type BRG1 mRNA was not detected, indicating loss of heterozygosity.


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Table 2 BRG1 variants in tumor cell lines

A total of 92 tumor cell lines were screened: 1 bladder, 22 breast, 1 cecum, 16 colon, 7 gliomas, 14 lung, 6 melanoma, 7 ovary, 11 pancreas, 4 prostate, and 3 testis. Comparison of our consensus sequence for the BRG1 cDNA to that reported by Khavari et al. (11) (Genbank accession no. U29175) revealed a G instead of a C at position 1706 of the ORF, resulting in an amino acid change from proline to arginine. Independent sequence data from dBEST confirmed this sequence difference. In addition to the variants tabulated, several silent alterations were observed but not listed.

 
Loss of BRG1 Protein Expression.
To establish the functional significance of the biallelic mutations of BRG1 in these tumor cell lines, we examined BRG1 protein expression. ML-1 cells were included as a positive control for BRG1 expression. Western blot analysis was performed using a specific anti-BRG1 monoclonal antibody (see "Methods). As shown in Fig. 2ACitation there is no expression of wild-type BRG1 in any of the cell lines containing homozygous mutations in BRG1, consistent with the lack of mRNA expression. The presence of biallelic inactivations affecting BRG1 in these cell lines is consistent with the Knudson two-hit model of inactivation for tumor suppressor genes during cancer progression (18) .



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Fig. 2. BRG1 expression in tumor cell lines. Cells were lysed in buffer [250 mM NaCl, 50 mM Tris (pH 8.0), and 0.1% NP40]. One hundred µg were resolved on 8% Novex SDS-PAGE gel and then transferred to Immobilon (Millipore) for Western blotting. Blots were probed with monoclonal antibody to BRG1 (8A11; 1:5), mouse monoclonal antibody to BRM (1:250; Transduction Labs), polyclonal peptide antisera to hINI1 (1:1000), and rabbit polyclonal antisera to BAF155 (1:1000). Secondary antibodies were rabbit or mouse immunoglobulin conjugated to HRP (1:5000 dilution, Amersham). Blots were developed using ECL.

 
The mutant cell lines were also screened by Western blot for expression of other components of the SWI/SNF apparatus. As shown in Fig. 2BCitation , they all express detectable levels of hINI5/SNF5 and BAF155, two other core components of the SWI/SNF complex (19 , 20) . A surprising result, however, was the pattern of BRM expression in some of the tumor cell lines. In ALAB, SW13, and A427 cells that lacked BRG1 expression, we also failed to detect expression of its close relative BRM. C33A cells, a cervical carcinoma cell line previously described to lack BRM expression, has low levels of BRM but no BRG1 expression using our reagents and methods (21) . Lastly, BRM expression levels were generally much lower in cells lacking BRG expression than those in controls. These results suggest that BRM expression may also be lost in some instances when BRG1 is mutated.

pRb Status of BRG1 Mutant Cell Lines.
Work from a number of laboratories has suggested that BRG1 may function, at least in part, through its physical interaction with the pRb tumor suppressor protein (5, 6, 7, 8) . Additionally, recent work by Zhang et al. proposed a model whereby the growth-suppressive functions of both pRb and BRG1 are strictly dependent on one another (8) . This model predicts that there may be a reciprocity in BRG1 and RB mutations in tumor cell lines, given the functional redundancy of mutation of two genes that function in the same pathway. To test the BRG1 mutant cell lines for pRb status, lysates were prepared and subjected to Western blot analysis for pRb expression. ML-1 and WERI cells were included as positive and negative controls, respectively (22) . As can be seen in Fig. 3Citation A, the major of the BRG1 mutant cell lines express apparently full-length pRb protein, with the exception of C33A cells and DU145 cells. To further confirm that the expressed pRb was indeed wild type, we used a functional assay where the ability of pRb to bind the viral oncoprotein E1A was examined. To date all spontaneously occurring RB gene mutations, which do not grossly compromise pRb stability, are inactive with respect to E1A binding (23 , 24) . Cell lysates were mixed with a GST fusion protein expressing adenovirus E1A, and then bound proteins were isolated using gluthathione agarose beads. As can be seen in Fig. 3BCitation all of the cell lines expressing pRb express a functional polypeptide that can bind E1A, confirming that RB is wild type in these cells. Thus, 6 of 8 of the BRG1 mutant cell lines are wild type for RB. The two exceptions are both unusual cases. DU145 cells are known to have microsatellite instability and contain mutations in both RB and p16 in addition to the BRG1 mutation that we have identified (25) . C33A cells do not express BRG1 protein, but we have been unable to detect any homozygous mutation in BRG1 (Ref. 21 ).6



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Fig. 3. pRb status of BRG1 mutant cell lines. Cells were lysed in buffer [250 mM NaCl, 50 mM Tris (pH 8.0), and 0.1% NP40]. A, 100 µg were resolved on an 8% Novex SDS-PAGE gel and then transferred to Immobilon (Millipore) for Western blotting. Blots were probed with polyconal antisera to pRb (1:250; Santa Cruz). Secondary antibodies were rabbit or mouse immunoglobulin conjugated to HRP (1:5000 dilution, Amersham). Blots were developed using ECL. B, 500 µg of cell lysates were incubated with 5 µg of GST E1A fusion protein, and bound proteins were captured using glutathione agarose beads. Samples were resolved on 8% Novex SDS-PAGE gel and analyzed as in A for the presence of pRb.

 
Reintroduction of BRG1 Induces Growth Arrest and Morphological Changes.
To test whether the tumorigenicity of the BRG1 mutant cell lines was dependent on loss of BRG1 expression, we reintroduced BRG1 into ALAB cells and monitored the effects on cellular morphology and proliferation. As shown in Fig. 4Citation stable transfection of BRG1 into ALAB induced a flat cell phenotype at high frequency. BRG1-induced growth arrest previously has been demonstrated for SW13 cells; however, the flat cell induction is dramatically more efficient in ALAB cells (Fig. 4BCitation ; Refs. 5 , 10 ). A similar flattened morphology was observed with the reintroduction of BRG1 into the prostate cell line TSU-Pr1 (Fig. 4B)Citation . These results clearly demonstrate that BRG1 can alter the transformed phenotype of these cells and suggests that loss of BRG1 may have been important for their immortalization.



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Fig. 4. Reintroduction of BRG1 induces cell cycle arrest and flat cell phenotype. ALAB and TSU-Pr1 cells were transfected with hBRG1 and plasmid carrying puromycin resistance. Twenty-four h after transfection, cells were plated at ~106/ml density and grown in the presence of puromycin for 10 days. A, representative flat cells induced by BRG1 transfection; x40; B, cells were stained with crystal violet and counted. *, total number of flat cells in 3 x 1 cm.

 
Transfection of BRG1 into wild-type cells or pRb mutant cell lines does not induce a flat cell phenotype (data not shown). However, because many cell lines are not amenable to the flat cell assay, we used FACS analysis to further investigate the effects of BRG1 reintroduction into cells. As shown in Fig. 5Citation , transient transfection of BRG1 into ALAB cells induces a substantial G1 arrest as measured by FACS analysis, comparable with that seen using the CDK inhibitor p27. The ATPase mutant version of BRG1, K798R, failed to arrest the cells significantly, suggesting that BRG1 needs to be enzymatically active to induce growth arrest (11) . To confirm that it is the reintroduction of BRG1 that induces the arrest, we also examined the effects in U20S cells that contain both wild-type BRG1 (and pRb). Growth arrest was not observed after transfection of BRG1 into U2OS cells, whereas p27 was equally effective at inducing a growth arrest as in the ALAB cells. Parallel experiments using the CDK inhibitor p16 gave us surprising results. Although p16 could induce growth arrest in U20S cells, it had no effect in the ALAB cells. Similar observations have been reported by Zhang et al. in SW13 cells (8) . These findings support the model that the RB pathway is functionally defective in BRG minus cells (8) . Consistent with this notion, when BRG1 was reintroduced into ALAB cells, addition of p16 had a slight synergistic effect, resulting in a more efficient G1 arrest. Experiments in pRb minus cells such as C33A (see Fig. 5Citation ) demonstrate that BRG1 alone is insufficient to induce growth arrest in a cell lacking pRb. Work for others has shown that reintroduction of pRb and BRG1 into these cells will induce growth arrest (8 , 26) .



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Fig. 5. Analysis of BRG1-induced growth arrest. ALAB (A), U2OS (B), and C33A (C), cells were transfected with CD20 and various plasmids as listed. Cells were harvested after 72 h and stained with FITC-conjugated anti-CD20 and propidium iodide. Samples were analyzed by FACS to examine DNA content of the CD20-positive transfected cells.

 
BRG1 Point Mutations.
In addition to the mutations described above, point mutations were detected in some of the other tumor cell lines. In the colon carcinoma cell line HCT-116, a T3488C alteration is predicted to result in a substitution from leucine to proline within the DNA-dependent ATPase domain of BRG1. In the breast carcinoma cell line Hs 578T, the C589T alteration should cause a nonconservative amino acid change from proline to serine. In both of these cell lines, no wild-type BRG1 mRNA was detected. A number of other BRG1 sequence variants were observed, but in every case, approximately equal amounts of wild-type BRG1 mRNA were observed (designated as HET in Table 2Citation ). Western blot analysis revealed that Hs578T does not express BRG1 protein, whereas all of the other point mutations did not appear to affect protein expression grossly, although BRG1 levels appeared to be generally lower than other cell lines that we have examined (Fig. 6Citation and data not shown).



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Fig. 6. BRG1 point mutations. A, 100 µg of cell lysate, from a variety of cell lines as indicated, were loaded directly on 8% Novex gel and transferred to Immobilon for Western blotting with anti-BRG monoclonal antibody. B, 1 mg of cell lysate was immunoprecipitated using anticyclin E monoclonal antibody HE172, cross-linked to protein A-Sepharose. Immunoprecipitates were resolved on 8% Novex SDS-PAGE gels and transferred to Immobilon for Western blotting. Blots were probed with polyclonal rabbit antisera to BRG J1 (1:1000) or cyclin E monoclonal HE12 (1:10 dilution). Secondary antibodies were rabbit or mouse immunoglobulin conjugated to HRP (1:5000 dilution; Amersham). Blots were developed using ECL.

 
To address whether these point mutations were functionally significant, we looked at the presence of these mutated BRG1 proteins in the SWI/SNF complex. We have previously shown that cyclin E, a key cell cycle regulatory protein, can associate with the SWI-SNF complex in a BRG1-dependent manner (10) . We, therefore, assessed the ability of cyclin E to associate with components of the SWI-SNF apparatus in the tumor cell lines with point mutations in BRG1. As shown in Fig. 6BCitation , several of these cell lines appear to have defective SWI-SNF complexes. Particularly interesting was that we failed to detect a complex between BRG1 and cyclin E in HCT116 cells, the cell line that displayed apparent loss-of-heterozygosity in the mutation screen but retained BRG1 protein expression. As predicted, we failed to detect a complex between BRG1 and cyclin E in Hs578T cells. These preliminary data suggest that some of the point mutations may lead to defective BRG1, providing an additional mechanism by which BRG1 function may be altered in human cancers.


    DISCUSSION
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
In summary we have identified several different mutations affecting the BRG1 gene in human tumor cell lines, many of which result in complete loss of BRG1 expression. Our study is the first to demonstrate that BRG1 is targeted for mutation and suggests that BRG1 may function as a tumor suppressor in multiple types of tissue. To test this theory it will be important to analyze human tumors for mutation in BRG1 to confirm our observations and to assess the possible frequency at which this gene is mutated in the human population. The identification of several point mutations scattered throughout the BRG1 coding region (see Fig. 7Citation ) may provide another mechanism by which BRG1 activity can be modified in human cancers. Because the activity of BRG1 is poorly understood at the mechanistic level these point mutants may provide a useful tool in elucidating BRG1 function.



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Fig. 7. Schematic representation of BRG1 and location of point mutations. Mutations in TSU-Pr1 and A427 were not included as large homozygous deletions, therefore yielding no product.

 
In support of a role for BRG1 as a tumor suppressor, reintroduction of the BRG1 gene into ALAB and TSU-Pr1 cells was sufficient to revert their transformed phenotype by inducing growth arrest and morphological flattening. The discovery of a homozygous deletion affecting BRG1 in TSU-Pr1, combined with our radiation hybrid mapping of the gene to human chromosome 19p13.1, is consistent with the notion that this gene is responsible for the tumor-suppressive effect observed by Gao et al. (14) .

In addition to loss of BRG1 expression, we also observed loss of BRM expression in a concordant fashion in some tumor cell lines. It is of interest to note that in mice homozygously deleted for BRM, BRG1 is up-regulated and may substitute for some functions allowing for viability (27) , whereas loss of BRG1 is believed to be lethal (28) . It will be interesting to learn whether this loss in viability is attributable to the additional loss of BRM expression in these knockout cells.

It is tempting to speculate that the role of BRG1 in cancer progression is primarily executed through its regulation of tumor suppressors such as pRb. Our data suggest that there may be a certain amount of reciprocity between mutations in BRG1 and RB, because pRb is wild type in the major of BRG1 mutant cell lines. Again, analysis of a larger number of samples will provide confirmation of this model. It will be important to fully elucidate the relationship of BRG1 with the p16/pRb pathway. Our initial experiments show that p16 is unable to arrest a BRG1 mutant cell line, suggesting that these two molecules may function in the same pathway. Work from the Dean laboratory strongly supports this model (8) . Despite these correlations, it remains to be established whether all of the BRG1 functions are mediated by pRb and vice versa.

Recently, another component of the SWI-SNF complex, hSNF5/INI1, localized on human chromosome 22q11.2, has been found to be mutated at significant frequency in malignant pediatric rhabdoid tumors (29) and chronic myeloid leukemias (30) . Taken together, these results indicate that transcriptional regulation through ATP-dependent chromatin remodeling by the SWI-SNF complex is critical in tumorigenesis. Additional studies will be needed to establish whether other components of the SWI-SNF complex are mutated during cellular transformation.


    ACKNOWLEDGMENTS
 
We thank Ali Fattaey for the gift of GST E1A fusion protein; the Myriad Genetics sequencing core, led by David Fritzinger and Jeff Mitchell, for excellent technical assistance; and members of the Cell Signaling Department at DNAX Research Institute for their help and advice throughout the course of this project. DNAX Research Institute is owned by Schering-Plough Corporation.


    FOOTNOTES
 
The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

1 Present address: Sankyo Pharma Research Institute, 4250 Executive Square, Suite 420, La Jolla, CA 92037. Back

2 D. H-F. T. and E. L. contributed equally to this work. Back

3 Present address: Arcaris, Inc., 615 Arapeen Drive, Suite 300, Salt Lake City, UT 84108. Back

4 To whom requests for reprints should be addressed, at DNAX Research Institute, 901 California Avenue, Palo Alto, CA 94304-1104. Phone: (650) 496-1257; Fax: (650) 496-1200; E-mail: lees{at}dnax.org Back

5 The abbreviations used are: GST, glutathione S-transferase; STS, sequence tagged-site; FACS, fluorescence-activated cell sorter; ORF, open reading frame; HRP, horseradish peroxidase; ECL, enhanced chemiluminescence. Back

6 Unpublished observations. Back

Received 7/12/00. Accepted 9/ 8/00.


    REFERENCES
 Top
 ABSTRACT
 INTRODUCTION
 MATERIALS AND METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 

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C. J. Guidi, A. T. Sands, B. P. Zambrowicz, T. K. Turner, D. A. Demers, W. Webster, T. W. Smith, A. N. Imbalzano, and S. N. Jones
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H. R. Moinova, W.-D. Chen, L. Shen, D. Smiraglia, J. Olechnowicz, L. Ravi, L. Kasturi, L. Myeroff, C. Plass, R. Parsons, et al.
HLTF gene silencing in human colon cancer
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