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The Burnham Institute, La Jolla, California 92037 [Y. D., T. C., W. F., Z. P., S. H.]; Endocrine Surgery Unit, Department of Surgery, Uppsala University Hospital, S-751 85 Uppsala, Sweden [T. C.]; and Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan [J-C. S.]
| ABSTRACT |
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| Introduction |
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The retinoblastoma protein-interacting zinc finger gene RIZ was isolated in a functional screening for Rb-binding proteins (4)
, also independently isolated as DNA-binding protein MTB-Zf (5)
, GATA3 transcription factor-binding protein G3B (6)
, and a coactivator of estrogen receptor (7)
. RIZ contains the canonical Rb-binding motif LXCXE and the nuclear hormone receptor-binding motif LXXLL. In addition, RIZ contains a novel protein methyltransferase domain, called the PR domain or SET domain (8
, 9)
, which is present in
50 human genes. Two products of the gene exist: (a) RIZ1, which contains the PR domain; and (b) RIZ2, which lacks the domain (10)
. RIZ1 but not RIZ2 has tumor-suppressive properties. The gene maps to chromosome 1p36, a region commonly deleted in more than a dozen different types of human cancers (11)
. RIZ1 expression, but not RIZ2 expression, is commonly silenced in many types of human tumors, including breast cancer, liver cancer, colon cancer, neuroblastoma, melanoma, lung cancer, and osteosarcoma (12, 13, 14)
. RIZ1 missense inactivating mutations also occur in human cancer tissues and cell lines, and all target the PR/SET domain (15)
. Frequent frameshift mutations of the RIZ gene are common in microsatellite instability-positive tumors and truncate a PR-interacting domain (14
, 16
, 17)
. Importantly, mouse gene knockout models show that RIZ1 inactivation can indeed cause tumor susceptibility (15)
. In keeping with its role as a bona fide TSG, RIZ1 has strong tumor-suppressive activities. Adenovirus-mediated RIZ1 expression causes G2-M cell cycle arrest and/or apoptosis in breast cancer, liver cancer, and microsatellite instability-positive colon cancer cells (12, 13, 14)
. Adenovirus RIZ1 can also inhibit growth of colon cancer xenografts (18)
. Finally, an independent line of investigation supports the notion of methyltransferases such as RIZ1 as TSGs. A methyltransferase inhibitor, MTA, is known to accumulate in many cancers due to the homozygous deletion of the MTAP gene, which encodes the enzyme MTA phosphorylase that degrades MTA (19)
.
In this study, we examined the role of DNA methylation in the loss or decrease in RIZ1 mRNA expression in human cancers. We cloned the RIZ1 promoter and found that it has characteristics of CpG island. The promoter was commonly methylated in breast and liver cancers, and methylation correlated strongly with loss of mRNA expression. Treatment with methylation inhibitors reactivated mRNA expression. Thus, DNA methylation appears to be a common mechanism of inactivating the RIZ1 TSG.
| Materials and Methods |
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RIZ1 Promoter Cloning.
To clone full-length RIZ1 cDNA, we made cDNAs from mRNA of Y79 retinoblastoma cells using primer RP99 (5'-TAGTAAATGGCTCTGTTG-3') derived from the RIZ gene 5' region and packaged the cDNAs into the
phages using the cDNA library kit from Pharmacia. The library was next screened using RIZ1 cDNA probe. One clone was isolated that has an extended 5' region with high similarity to the 5' end of the rat RIZ cDNA. We next made an oligonucleotide primer from this region, RP279 (5'-CGCGCCAGCGCCTCAGAGCACCGA-3'), and used it to screen a chromosome 1 cosmid library from the Reference Library Data base at the Max Plank Institute in Berlin, Germany (22)
. From one of the positive cosmid clones, we then isolated an
1-kb Pst1 fragment, which was next subcloned into pBSK vector and sequenced.
Promoter Reporter Assay.
To test for promoter activity, we subcloned a fragment of the CpG island amplified using primer set RP280 (5'-GCCCTAGGGTGCGGTCGGACTTGCC-3') and RP279 into luciferase reporter vector pGL3basic (Promega, Madison, WI). Plasmid pGLR1P279-280 contains a 0.315-kb fragment (330645 bp) at the middle of the Pst1 fragment. pGL3control (Promega) containing SV40 promoter and enhancer was used as positive control. Plasmid DNAs were transfected into human kidney 293 cells by standard calcium phosphate procedure, and luciferase activity was determined as described previously (10
, 23)
. The plasmid pCMVß-gal was cotransfected to serve as a control for transfection efficiency, and promoter activity was adjusted for ß-gal activity.
RNase Protection Assay.
RNA was prepared and used for RNase protection analysis as described previously (10)
. The PCR fragment amplified from primers RP280 and RP279 was subcloned into pCR script vector kit (Invitrogen). The plasmid was linearized with MscI, which was then used as a template for T3 polymerase transcription in vitro to produce the 32P-labeled antisense transcript. The antisense probe was then purified and used for hybridization with total cellular RNA.
DNA Methylation Analysis.
Sequence analysis of genomic DNA templates treated with bisulfite was performed according to the procedure described by Frommer et al. (24)
and modified by Clark et al. (25)
. Briefly, Genomic DNAs from tumor tissues and cell lines (50 ng) were treated with sodium bisulfite, and treated DNA was purified using the Wizard column (Promega). For DNA sequencing analysis, the DNA was used for PCR with the primer set RP294 (5'-GGTTGGGTGGTGGTTATTGGG-3') and RP295 (5'-CAAAAACCGCCCTGCGCCACTCCTTACC-3'). The PCR products were subcloned into pCR script cloning vector (Invitrogen), and individual clones were subjected to DNA sequencing analysis.
Bisulfite-treated DNA was also used for MSP analysis (26) . We generated PCR primers that distinguish between bisulfite-modified and unmodified cytosines in the RIZ1 CpG island. To amplify methylated DNA, we used the primer set RP291MF (5'-GTGGTGGTTATTGGGCGACGGC-3') and RP291MR (5'-GCTATTTCGCCGACCCCGACG-3'). The annealing temperature of the PCR reaction was 68°C. To amplify unmethylated DNA, we used primer set RP291UF (5'-TGGTGGTTATTGGGTGATGGT-3') and RP291UR (5'-ACTATTTCACCAACCCCAAGA-3'). The annealing temperature of the PCR reaction was 60°C.
Reexpression of RIZ1 by 5-Aza-dC Treatment.
Cancer cells (5 x 106 cells) were grown for 4 days in the presence of various concentrations of 5-Aza-dC. RNA was isolated, and RT-PCR was performed as described previously (12
, 13)
. Briefly, reverse transcription was performed using Moloney murine leukemia virus reverse transcriptase (New England Biolabs) and oligonucleotide primer RP217 (5'-CCTCTGAGCAGTCTTCAAGAGT-3'). The first-strand cDNA sample was then amplified using RP168 (5'-TGGCTGCGATATGTGAATTG-3') + RP217. The primers for amplification of human ß-actin are 5'-GTGGGGCGCCCCAGGCACCA-3' and 5'-CTCCTTAATGTCACGCACGATTTC-3'. PCR reactions were run for 30 cycles. The PCR products were analyzed by agarose gel electrophoresis followed by ethidium bromide staining.
| Results |
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To map the transcription start sites, we performed the RNAse protection assay using a PCR fragment of the genomic DNA as probe. This fragment was amplified using primers RP280 and RP279 (Fig. 1C)
and subcloned into pBlueScript vector. Total RNAs from hepatoma cell line Huh2 (RIZ1 negative), colon cancer cell line SW480 (RIZ1 positive), and colon cancer cell line DLD1 (RIZ1 positive) were used for hybridization with the RIZ1 antisense probe. As shown in Fig. 1D
, a protected fragment of 145 nucleotides was specifically observed in RIZ1 mRNA-positive cell lines SW480 and DLD1, but not in RIZ1-negative cell line Huh2. The result mapped the transcription start site within the CpG island as shown in Fig. 1C
.
To test for promoter activity, we subcloned a fragment of the CpG island amplified using primer set RP280 and RP279 into the luciferase reporter vector pGL3 basic. Plasmid pGLR1P279-280 contains a 0.315-kb fragment (330645bp) at the middle of the Pst1 fragment (Fig.2A)
. When transfected into human kidney 293 cells, strong promoter activity was observed for construct pGLR1P279-280, which was comparable to that of the SV40 promoter/enhancer as represented by pGL3 control plasmid (Fig.2, B and C)
. Thus, the CpG island at the 5' end of the RIZ1 gene functions as a promoter.
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We then determined the frequency of RIZ1 methylation in liver and breast tumor tissues by MSP analysis (Fig. 4, C and D)
. A total of 32 pairs of DNAs from liver cancer tissues and matched normal tissues were analyzed, and 20 tumor tissues (62.5%) showed DNA methylation. Of the 20 matched normal tissue DNAs, 4 showed DNA methylation, whereas 16 did not. In 12 cases where tumor DNA did not show methylation, 3 of the matched normal tissue DNA samples showed methylation. A total of 25 breast cancer DNAs were analyzed, and 11 (44%) showed DNA methylation. The unmethylated form was detected in all samples in both tumors and nonmalignant tissues. This was expected because the tumor specimens represented macroscopically isolated samples that contained both tumor and nonmalignant tissue. We evaluated the DNA methylation changes in the tumors and the clinical data obtained from these patients. We found no correlation between methylation and any of the clinicopathological characteristics of the patients. We also analyzed the DNA methylation changes and the 1p36 or RIZ LOH changes in these liver and breast cancers, which were characterized previously (20
, 21)
. We found no correlation between methylation and 1p36 or RIZ loss of heterozygosity.
Promoters silenced by methylation can be reactivated by treatment with 5-Aza-dC, which is a well-documented inhibitor of DNA methylation. We treated liver cancer cell lines HepG2 and Huh1 and colon cancer cell line SW48. By RT-PCR analysis, RIZ1 expression was detected after treatment with increased amounts of 5-Aza-dC (Fig. 4E)
. The data confirm that methylation plays an important role in silencing RIZ1.
| Discussion |
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The RIZ1 promoter we cloned in this study has strong promoter activity. The observation that this promoter has a CpG island is consistent with the largely ubiquitous expression of RIZ1 (4 , 10) . Most widely expressed housekeeping genes are known to contain CpG islands. By DNA sequencing analysis, we have determined the positions of many of the methylated CpGs. Whereas not all CpGs around the transcription start site are methylated, most of them are. We also developed a MSP assay to conveniently study RIZ1 methylation in primary tumor sample DNAs. Based on the analysis of 32 tumor cell lines and tissues, methylation as detected by our MSP assay is strongly associated with lost or reduced RIZ1 mRNA expression. In addition, the PCR primers in our MSP assay cover eight CpGs, all of which are commonly methylated in liver and breast cancers as shown by DNA sequencing analysis. Therefore, our MSP assay developed here represents an accurate measure of RIZ1 gene expression status.
Our results show that the RIZ1 promoter CpG island is commonly methylated in liver and breast cancer tissue samples, consistent with the results obtained from cancer cell lines. A majority of the liver tumor tissue cases showed methylation in the tumor tissues but not in the corresponding nonmalignant tissues, suggesting that in these cases, methylation is a tumor-specific event. However, several cases showed methylation in the nonmalignant liver tissues, but not in the corresponding tumor tissues. A possible explanation for detection of methylated alleles in the nonmalignant liver samples is that they represent premalignant changes. Methylation in TSGs in normal tissues but not tumor tissues has also been reported in lung cancer, colon cancer, and breast cancers (29, 30, 31) . Alternatively, it has been described that methylation of certain genes is common in aging tissues. Thus, the aging process may also be a possible explanation for detection of methylation in nonmalignant liver tissues.
Data accumulated in the past have made it notable that TSGs tend to be preferentially inactivated by a preferred mechanism. For example, p53 is mostly inactivated by point mutation, p16/CDKN2A is generally inactivated by homozygous deletion and DNA methylation, and MLH1 is inactivated by mutation in familial colon cancer but by DNA methylation in sporadic colon cancer. The implication of these observations is that there might be a group of TSGs for which the primary mechanisms of inactivation may be DNA hypermethylation (1) . Given that silencing would relieve selective pressure for mutations, these genes may rarely suffer mutations. However, in the absence of genetic mutations, it will be challenging to prove that a gene that is silenced in human cancers is in fact causally linked with carcinogenesis. Among the numerous genes that are known to be silenced in human cancers, RIZ1 is one of the few with a proven role in causing cancer as demonstrated by genetic data in both animals and humans (15) . Whereas previous studies demonstrate reduced RIZ1 gene expression to be common in cancers, this study confirms that RIZ1 is commonly silenced by DNA methylation. RIZ1 methylation is found in 62% of liver cancers and 44% of breast cancers. However, RIZ1 mutation has not been detected in these cancers (20 , 21) . Thus, DNA methylation may represent the preferred mechanism of RIZ1 inactivation in these cancers. Furthermore, because many types of human cancer cell lines exhibit reduced RIZ1 expression, we predict that RIZ1 gene methylation will be commonly found in many types of human cancer tissues. Finally, the MSP assay we developed here can conveniently assay RIZ1 expression status in primary tissues. Our small sample-size study here was not informative with regard to a correlation between RIZ1 silencing and specific stages/characteristics of cancer. However, definitive conclusions on this issue will require future investigations of large sets of tumor samples, which would also address whether RIZ1 methylation may prove to be useful in cancer diagnosis/prognosis.
| FOOTNOTES |
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1 Supported by NIH Grant R01-CA76146 (to S. H.) and by grants (to S. H.) from the Tobacco Related Disease Research Program (TRDRP-7RT0026) and Cancer Research Program of California (CCRP-1I0023). T. C. was supported in part by the Swedish Society of Medical Research, the Swedish Medical Research Council, and the Wennergren Foundation. ![]()
2 To whom requests for reprints should be addressed, at The Burnham Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037. Phone: (858) 646-3120; Fax: (858) 646-3192; E-mail: shuang{at}burnham.org ![]()
3 The abbreviations used are: TSG, tumor suppressor gene; MTA, methylthioadenosine; MSP, methylation-specific PCR; 5-Aza-dC, 5-aza-2'-deoxycytidine; RT-PCR, reverse transcription-PCR; ß-gal, ß-galactosidase. ![]()
Received 7/10/01. Accepted 10/ 4/01.
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