Identification and characterization of genes expressed in normal cells and decreased in their malignant counterparts is an important method for detecting candidate tumor suppressors. Using differential display of mRNAs from nontumorigenic infinite life span human fibroblast cell strain MSU-1.1 and an isogenic fibrosarcoma-derived cell line, 6A/SB1, which was derived from chemical carcinogen transformed MSU-1.1 cells, we identified a novel gene, ST7, showing sixfold lower expression in 6A/SB1 cells compared with parental MSU-1.1 cells. Molecular cloning of a near full-length cDNA revealed that the novel gene encodes a putative transmembrane protein composed of 859 amino acids: the 492 N-terminal amino acids including a fivefold cysteine-rich repeat of 40 amino acids homologous to the ligand binding repeat of the known low density lipoprotein receptor, a 24 hydrophobic amino acid stretch spanning the plasma membrane, and a C-terminal domain of 343 residues. ST7 is located on human chromosome 8, band q22.2-23.1, the same locus as the genes involved in acute myeloid leukemia and a locus of high polymorphism in cancer biopsies. The ST7 gene is widely expressed in normal human tissues and is particularly abundant in human heart and skeletal muscle. Northern analysis of 15 tumor cell lines derived from patients and 16 cell lines established from tumors formed in athymic mice by MSU-1.1 cells transformed in culture by various methods showed that 16 of the 31 cell lines have low or undetectable levels of ST7 mRNA. Furthermore, Western blotting analysis using a specific anti-peptide antibody demonstrated that the level of ST7 protein is high in normal fibroblasts and low in 12 sarcoma-derived cell lines tested. Altered expression of ST7 appears to occur at both the transcriptional and post-transcriptional levels. These studies are a first step in characterizing a novel putative receptor protein, whose expression is downregulated in some malignantly transformed cells, and which may play an important role in the transformation process of these cells.
Cancer results from the accumulation of a series of genetic and biochemical changes in normal cells (Peto, 1977; Farber, 1984; Klein and Klein 1985; Fearon and Vogelstein, 1990). Despite the vast increase in our knowledge of oncogenes and tumor suppressor genes associated with human neoplasia over the past 15 years, the molecular events leading to the formation of most types of human tumors are still not well understood. Therefore, identification of genes that are involved in the transition of non-tumorigenic cells to malignant cells can be expected to help us understand the molecular mechanisms underlying tumor formation.
The recent introduction of several in vitro transformation systems utilizing human cells in culture (Stoner et al., 1991; Reznikoff et al., 1993; McCormick and Maher, 1994; Rhim et al., 1994; Park et al., 1995) has facilitated the investigation of the cellular and molecular mechanisms involved in the multistep carcinogenic process. In our laboratory, transfection of the v-myc oncogene into a human neonatal foreskin-derived fibroblast cell line, LG1, led to the establishment of a near-diploid, karyotypically stable, infinite life span human fibroblast cell strain MSU-1.1 (Morgan et al., 1991). MSU-1.1 cells are phenotypically normal and do not form tumors in athymic mice. Treatment of MSU-1.1 cells with chemical carcinogens such as benzo[a]pyrene diol epoxide (BPDE) (Yang et al., 1992) or gamma irradiation (Reinhold et al., 1996), followed by selection of focus-forming cells, results in cells capable of forming tumors in athymic mice. Since the focus-derived, tumorigenic cells have various properties not possessed by the parental cells, it is presumed that additional genetic alterations induced by carcinogens are required in the transformation process. However, the cellular genes responsible for the neoplastic transformation induced by these carcinogens remain poorly understood. The present study was carried out to isolate an oncogene(s), or tumor suppressor gene(s) that is involved in this neoplastic conversion.
The recently developed differential mRNA display method (Liang and Pardee, 1992; Liang et al., 1993) allows one to identify genes that are differentially expressed between closely related eukaryotic cells. In our study, we applied this method to compare the mRNA profile between the nontumorigenic parental MSU-1.1 cells and one of its malignant derivative cell lines, 6A/SB1, which was established from a fibrosarcoma formed in an athymic mouse by MSU-1.1 cells transformed by treatment with an active derivative of benzo[a]pyrene and selected for focus formation. We have identified a novel gene, designated ST7, whose mRNA is markedly downregulated in 6A/SB1 cells compared with MSU-1.1 cells. A near full-length cDNA was cloned and the deduced amino acids revealed that this novel gene encoded a putative transmembrane protein of 859 amino acids. ST7 is located on human chromosome 8, band q22.2-23.1. ST7 mRNA and protein levels were low in a large fraction of the tumor-derived cell lines tested. Further characterization of ST7 should lead to a better understanding of the carcinogenesis process in human cells.
Identification of ST7 as a gene differentially expressed between preneoplastic and malignant human cells
When we compared the MSU-1.1 cell strain and its tumorigenic derivative cell line, 6A/SB1, using mRNA differential display, we saw 8000 – 10 000 displayed cDNA fragments and found in two independent experiments that nine DNA fragments reproducibly showed differential intensities between MSU-1.1 cells and the tumor-derived cells (Figure 1a and data not shown). cDNA fragments were isolated from the sequencing gel and used as probes in Northern analysis to test for differential mRNA expression between MSU-1.1 and 6A/SB1 cells. Differential expression of mRNA was confirmed for five of the nine cDNAs. Subsequent analysis showed that four of these five corresponded to the same gene, i.e., fibulin-1D (Qing et al., 1997). The fifth, designated ST7, is shown in Figure 1b. The ST7 cDNA hybridized with a 3.7 kb transcript showing a sixfold lower expression in 6A/SB1 cells than in MSU-1.1 cells. The ST7 DNA fragment was subcloned, and the insert DNA from several individual plasmids was also found to hybridize to the same sized RNA, and the transcript exhibited differential expression in MSU-1.1 cells compared with the tumor cell line. Subsequent sequencing analysis of this partial cDNA revealed that it contained 485 bp with no significant homology with any known genes in the nucleotide sequence databases.
Expression of ST7 in multiple human tumor cell lines
To test whether the expression of ST7 mRNA is also downregulated in other tumor-derived MSU-1.1 cell lines malignantly transformed by various methods, RNA from 15 additional such cell lines was assayed by Northern blotting analysis. We also examined 15 tumor-derived cell lines from patients. The origin of these cell lines has been described previously (Qing et al., 1997). Representative data are shown in Figure 2. We found downregulation of ST7 in five out of 15 MSU-1.1 derivatives (lanes 4, 5, 8, 21 and 22). We also found that in 10 out of 15 tumor-derived cell lines from patients, the expression of ST7 was very low or undetectable, i.e., in cells from three out of five fibrosarcomas (lanes 10, 12 and 13), in cells from two out of two osteosarcomas (lanes 6 and 16), in cells from the three neurofibrosarcomas (lanes 18 – 20), in cells from a cervical carcinoma (lane 7) and in cells from a bladder carcinoma (lane 3). Collectively, of the 31 tumor-derived cell lines assayed, 16 exhibited either low or no expression of ST7.
Molecular cloning of the full-length human ST7 cDNA
To obtain the full-length cDNA of ST7, we screened a human fibroblast cDNA library (library 9 of Legerski) with an ST7 gene-specific primer and a vector-specific primer, using the High Fidelity Expand PCR method (Boehringer Mannheim, Indianapolis, IN, USA). Several specific PCR products were obtained. We sequenced the longest one (clone A), which was about 2.6 kb (Figure 3a). To recover the 5′ end of the cDNA, we screened a human skeletal muscle cDNA library with another ST7-specific primer and a vector primer using the PCR method described above. This produced a fragment we called clone B. To obtain an additional 5′ sequence, we carried out the 5′-rapid amplification of cDNA ends (RACE) reaction using a human heart Marathon-ready cDNA (Clontech, Palo Alto, CA, USA) and designated the generated fragment clone C. These three clones overlapped with each other (Figure 3a). Two forms of the cDNA differing from each other at the 5′ end were isolated. The longer form has 57 more nucleotides than the shorter one. The assembled nucleotide sequence of the longer form (total 3078 bp) and the deduced amino acid sequence are shown in Figure 3b. An open reading frame extends from nucleotide positions 43 – 2619 and encodes a protein of 859 amino acids with an estimated molecular weight of 92.8 kDa. The first ATG codon (nucleotides 43 – 45) lies in the context of the Kozak consensus initiation site of eukaryotic mRNA translation (Kozak, 1991). The ST7 cDNA contains a putative 3′ untranslated region of 450 bp followed by a poly A tail and three consensus polyadenylation signals (Wahle and Keller, 1992) at nucleotide positions 2846, 2976 and 3034. Comparison of an ST7 cDNA sequence to the Genbank and EMBO database using the FASTA and the BLAST program revealed that there is no significant homology with any known genes.
Primary structure suggests a novel transmembrane protein
Comparison of the deduced amino acid sequence of ST7 with a nonredundant protein sequence database revealed that overall there was no significant homology with other proteins. A striking feature of this protein is that the aminoterminus is composed of five imperfect repeats of a 40-amino acid cysteine-rich repetitive sequence homologous to that found in the human low density lipoprotein (LDL) receptor (Südhof et al., 1985) (Figure 4) and complement protein C9 (Stanley et al., 1985). The similarity also includes the highly conserved, negatively charged Ser-Asp-Glu triad, which occurs near the COOH-terminal end of each repeat. Hydropathy analysis (Kyte and Doolittle, 1982) revealed that the coding sequence contained a stretch of 24 hydrophobic amino acids extending from residues 493 – 516 (underlined in Figure 3b), which is flanked at both ends by positively charged residues. This hydrophobic sequence resembles the membrane-spanning region of other transmembrane proteins (Sabatini et al., 1982). The predicted protein also contains other putative functional domains, including nine putative N-linked glycosylation sites, a number of potential phosphorylation sites for protein kinase C and casein kinase II and several N-myristoylation sites. The importance of these putative domains of the ST7 protein under physiological conditions remains to be determined.
Chromosomal mapping of ST7
To determine the precise chromosomal location of the human ST7 gene, we carried out fluorescent in situ hybridization using an ST7 genomic DNA probe as described in Materials and methods. Following hybridization with the ST7 genomic DNA fragments, a total of 20 metaphase cells were examined. All of these cells exhibited a hybridization signal on chromosome 8, band q22.2-23.1 (data not shown). No significant background was noted at any other chromosomal location. These results indicate that the ST7 gene is localized on human chromosome 8, band q22.2-23.1.
Pattern of expression of ST7 mRNA in various human tissues
Northern analysis using a human normal tissue blot (Clontech) revealed that the ST7 cDNA hybridized to a single transcript of 3.7 kb. The ST7 mRNA was found to be most abundant in heart and skeletal muscle, expressed at moderate levels in brain, lung, placenta and pancreas, and barely detectable in tissues containing a large number of epithelial cells, such as liver and kidney (Figure 5).
Western blotting analysis of ST7 protein in human tumor cell lines
A rabbit anti-ST7 polyclonal antibody (designated B250) was raised against a synthetic peptide as described in Materials and methods. This antibody recognized a protein with an apparent molecular mass of 85 kDa, which is lower than the estimated molecular mass. The reason for this anomalous migration of ST7 protein in SDS-polyacrylamide gel is not clear. The specificity of this antibody for ST7 protein was tested by determining the extent of inhibition with antigen peptide. After preincubation of the antibody with the antigen peptide (60 μM), the signal for the ST7 protein band in immunoblots was dramatically reduced (Figure 6). Using this antibody, the expression level of ST7 protein in normal cells and tumor-derived cell lines was analysed by Western blotting analysis. As shown in Figure 7, MSU-1.1 cells and normal human fibroblast cell line SL89 exhibited high levels of ST7 protein, whereas the six malignant MSU-1.1 derivatives (lanes 3 – 8) and three cell lines derived from human fibrosarcomas (lanes 9 – 11) showed low levels of ST7 protein, which was consistent with the levels of ST7 mRNA transcripts in these cells (Figure 2). Interestingly, human fibrosarcoma-derived cell lines HT1080 and VIP:FT and rhabdomyosarcoma-derived cell line RD showed an mRNA level of ST7 comparable to that in MSU-1.1 cells (Figure 2, compare lanes 9 and 11, 14 and 15), whereas the protein was undetectable (Figure 7, compare lanes 1 and 12 – 14). This result suggests that downregulation of the ST7 gene product occurs at both transcriptional and post-transcriptional levels.
We have cloned and identified a novel gene, ST7, that encodes a 3.7 kb mRNA. Our analysis of ST7 expression in multiple human tumor-derived cell lines revealed that 10 out of 15 tumor-derived cell lines from patients, including sarcomas and carcinomas, exhibit low or no expression of ST7 mRNA. Without the normal cells from which these tumor cell lines were derived, we cannot be certain that the low expression resulted from downregulation. However, because we found that ST7 is widely expressed in normal human tissues, including heart, skeletal muscle, brain, lung, pancreas and placenta, but not in tissues consisting of a large number of epithelial cells, such as liver and kidney, and that a series of normal human fibroblast cell lines in culture expressed relatively constant levels of ST7 mRNA and protein (data not shown), we conclude that ST7 is ordinarily expressed at least in most cells of mesenchymal origin. Because six out of 16 tumor-derived cell lines from MSU-1.1 cells malignantly transformed by various methods clearly exhibited downregulation of ST7 mRNA and protein, we conclude that at least in mesenchymal-derived tumor cell lines, the downregulation of ST7 is frequently associated with neoplastic transformation.
Our data also suggest that the regulation of ST7 expression occurs at both the transcriptional and post-transcriptional levels. In most cases, the steady state protein level of ST7 correlates well with its mRNA level. However, in three malignant cell lines tested in this study, i.e., HT1080, VIP:FT and RD, which were derived from sarcomas taken from patients, the steady state mRNA level of ST7 was comparable to that seen in normal human fibroblasts, whereas the ST7 protein was barely detectable. This may reflect failure of translation initiation or a defect in the stability of the protein product.
According to the apparent molecular weight of the protein on SDS – PAGE gel, the cDNA we have isolated can account for the entire coding region of the novel protein. Of the two forms of the ST7 mRNA that we isolated, the shorter lacks 57 nucleotides at the 5′ end and encodes a protein of 840 amino acids that lacks residues 27 – 45 found at the amino terminal end of the longer ST7 protein (indicated by double underline in Figure 3b). This omission does not affect the open reading frame. The two isoforms presumably result from alternative splicing. The significance of the 5′ end heterogeneity awaits more detailed functional analyses.
The amino-terminal half of the predicted ST7 protein product contains five imperfect 40-amino acid repeats. This set of repeats is homologous to the cystein-rich, ligand-binding domain in the human LDL receptor. Many cell surface and secreted proteins contain repeated cysteine-rich motifs that are each 40 – 50 amino acids in length and contain six cysteine residues linked in three disulfide bridges (Doolittle et al., 1984; Apella et al., 1988; Daly et al., 1995). The common functional characteristic of these repeats is their ability to mediate protein-protein interactions. Therefore, it is possible that this conserved sequence in ST7 is involved in ligand binding. However, it cannot be ruled out that this cystein-rich repeat sequence codes for a structural motif common to a number of extracytoplasmic protein domains. Since the ST7 protein shares no other significant homology with any known protein, we can only speculate as to its function. One possibility is that the ST7 protein is a component of a signal transduction pathway that negatively regulates cell growth. The predicted membrane-spanning structure of the ST7 protein suggests that it acts as a cellular receptor or co-receptor, functioning as a ligand-regulated suppressor of a signaling unit like the recently cloned tumor suppressor gene patched, which encodes a receptor for Sonic hedgehog (Stone et al., 1996). Another possibility is that ST7 protein participates in cellular adhesion in a fashion similar to the candidate tumor suppressor gene DCC (for deleted in colorectal cancer) (Cho and Fearon, 1995; Fearon, 1996), or ST7 protein undergoes proteolysis on the cell surface, releasing a locally acting chemical signal. Any of these mechanisms could play a role in tumorigenesis.
It is interesting to note that the ST7 gene is mapped to chromosome region 8q22.1-23.1. 8q22 is a common site of chromosome fragility (Furuya et al., 1989). The translocation t(8 : 21) (q22;q22) is a typical chromosomal abnormality associated with acute myeloid leukemia (Rabbitts, 1994). Deletions or loss of heterozygosity (LOH) of 8q22 has also been reported in human colon adenocarcinomas (Shabtai et al., 1988) and breast carcinomas (Miyazaki et al., 1997). Since the ST7 gene is located in a locus of high polymorphism in cancer biopsies, it would be interesting to determine whether defects in ST7 are involved in the etiology of cancer. The cloning of the ST7 cDNA and the availability of the ST7-specific antibody should facilitate further experiments designed to better understand the function of the novel gene and its role in tumorigenesis.
Materials and methods
Cells and cell culture
The infinite life span human fibroblast cell strain MSU-1.1 and its derivative cell lines were routinely cultured in Eagle's minimum essential medium modified by addition of L-aspartic acid (0.2 mM), L-serine (0.2 mM) and pyruvate (1 mM) and supplemented with 10% SCS (Hyclone Laboratory, Logan, UT, USA), penicillin (100 units/ml), streptomycin (100 μg/ml) and hydrocortisone (1 μg/ml) (complete medium) at 37°C in a humidified incubator containing 5% CO2 in air.
Differential mRNA display
Non-tumorigenic infinite life span human fibroblast cell strain MSU-1.1 and one of its tumorigenic derivative cell lines, designated 6A/SB1, were used as sources of RNA for this study. Differential mRNA display and TA cloning were carried out essentially as described (Qing et al., 1997).
Northern blot analysis
Total RNA from cells in exponential growth was extracted using RNAzolB (Tel-Test, Friendswood, TX, USA) according to manufacturer's instructions. For Northern blot analysis, RNA (15 μg) from each cell line was electrophoresed on 1.2% agarose/2.2 M formaldehyde gels, and then was transferred to hybond-N membrane and immobilized by UV crosslinking (UV Stratalinker 2400, Stratagene, La Jolla, CA, USA). The cDNA probe was radiolabeled using a random primed labeling method (Feinberg and Vogelstein, 1983). The blots were hybridized as previously described (Qing et al., 1997). For analysis of ST7 expression in various normal human tissues, the Multiple Tissue Northern Blot was purchased from Clontech (Clontech, Palo Alto, CA, USA). Variation in RNA loading per lane was evaluated by probing with the GAPDH cDNA or β-actin as the control.
Cloning of human ST7 cDNA
The directional human fibroblast cDNA library (a generous gift from Dr Legerski, The University of Texas, MD Anderson Cancer Center (Houston, TX, USA) referred to as Library 9) was used to obtain the full-length cDNA corresponding to the ST7 gene. We screened the library by the High Fidelity Expand PCR method (Boehringer Mannheim) with a vector-specific primer (5′-CCGGAAGCTTCTAGAGATCCCTCGA) and an ST7 gene-specific primer based on the partial ST7 sequence obtained from differential display (5′-GCTCCAACTTGTATACAATCTCCC). Plasmid DNA derived from 10×106 independent clones was used as the template. The 50 μl PCR mixture contained 1.75 mM MgCl2, 0.2 mM dNTP, 15 pmol of each primer, 100 ng of library plasmid DNA and 2.5 units of the mixture Taq and Pwo DNA polymerase. The PCR cycling consisted of initial denaturation at 94°C for 2 m, followed by 10 cycles of 94°C for 30 s, 63°C for 30 s, and 68°C for 3 m, followed by another 20 cycles with the same parameters, except that the elongation time was extended for 15 s for each new cycle, followed by final elongation at 68°C for 10 m. The PCR product was separated by electrophoresis in 1% agarose gel, and the major bands were purified using Qiaquick Gel Extraction kit (Qiagen, Chatsworth, CA, USA). The purified DNA (about 2.6 kbp, noted as clone A) was used as probe for Northern analysis and cloned into the pCRII vector using the TA cloning method (Invitrogen, San Diego, CA, USA).
To obtain an additional 5′ sequence of this gene, we screened a human skeletal muscle cDNA library (a generous gift from Dr Ki-Han Kim, Purdue University, West Lafayette, IN, USA) by PCR using one primer from the 5′ end of clone A, designated JM131 (5′-GGGTTGAAAAGCAGCAGGAGTTGGAGG) and another vector-specific primer from the region of the cloning site of λgt11 (5′-GATTGGTGGCGACGACTCCTGGAGC). The fragment generated was subcloned and designated clone B.
Clone C, which contains the first translation initiation codon, was isolated by the 5′ rapid amplification of cDNA ends (5′-RACE) method using a human heart Marathon-ready cDNA (Clontech) with the ST7 gene-specific primer JM131. The PCR products were subcloned into the pCRII vector as above and sequenced.
DNA sequencing and sequence analysis
Both strands of the cDNA inserts in the pCRII vector were sequenced manually by the dideoxy chain termination method with the SP6 and T7 primers using a Fidelity DNA Sequencing kit (Oncor, Gaithersburg, MD, USA). For long cDNA inserts, synthetic oligonucleotides were used as primers to complete the sequence. Resolution was improved in some regions by replacing dGTP with deaza-dITP in the nucleotide mixture. The cDNA sequence and deduced protein sequences were analysed by FASTA and BLAST programs with the DNA and protein databases at the National Center for Biotechnology Information (NCBI). Secondary structure predictions and the properties of the putative protein were calculated using the GCG program (Genetic Computer Group, Madison, WI, USA).
Production of anti-ST7 antibody
The peptide corresponding to the C-terminus of the ST7 protein (CLEVTLKNETSDDEA in the single-letter amino acid code; corresponding to amino acids 841 to 855 of ST7) was synthesized by the Macrostructural Facility of the Department of Biochemistry, Michigan State University. The synthetic peptide was coupled to keyhole limpet hemocyanin (KLH) with the chemical crosslinker glutaraldehyde. To obtain anti-ST7 antibody, 200 μg of KLH-conjugated peptide was emulsified with an equal volume of TiterMax (Cytrx, Norcross, GA, USA) in a total volume of 1 ml, and 0.1 ml was injected subcutaneously into each of four sites on each of two female New Zealand White rabbits. The rabbits were administered booster shots after four weeks. They were bled on days 42 and 56 and serum was prepared according to standard protocol (Sambrook et al., 1989) and this serum was designated B250.
Western blotting analysis
Cell lysates were prepared with RIPA buffer composed of 50 mM Tris-HCl, pH 7.2, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.5% deoxycholic acid, 2 mM phenylmethylsulfonyl fluoride, 1 mM EDTA and 0.15 units/ml aprotinin as described (Qing et al., 1997). Aliquots of cell lysates containing 25 μg of protein were mixed with the sample buffer (0.05 M Tris-HCl, pH 6.9, 9% glycerol, 2.3% SDS, 0.1% bromophenol blue and 5% β-Mercaptoethanol), separated on a SDS/polyacrylamide gel (10%), and electroblotted onto an Immobilon-P membrane (Millipore, Bedford, MA, USA). The blots were incubated for 2 h at room temperature in Tris-buffered saline (20 mM Tris-HCl, pH 7.6, 137 mM NaCl) containing 0.1% (v/v) Tween 20 and 5% (w/v) non-fat dry milk (blocking solution), and then incubated for 2 h at room temperature with B250, the rabbit anti-ST7 antibody, diluted 1 : 500 in the same solution. The blots were washed several times and then incubated with horseradish peroxidase-conjugated goat-anti-rabbit IgG (Sigma, St Louis, MO, USA) that had been diluted 1 : 5000 with blocking solution. Enhanced Chemiluminescence (Amersham, Arlington Heights, IL, USA) was used according to the manufacturer's recommendations to detect the signal.
Chromosomal localization of ST7 gene
The 2.6 kb ST7 cDNA was used as a probe to screen a human P1 genomic DNA library (Genome System). Three clones were isolated. One of these, 17792, was labeled as a probe for fluorescent in situ hybridization.
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We thank Dr Legerski at the University of Texas, MD Anderson Cancer Center, Houston and Dr Ki-Han Kim at Purdue University, West Lafayette for kindly providing us the cDNA libraries. The expert assistance on computer work from Dr David Dewitt at Michigan State University is gratefully acknowledged. This research was supported by DHHS grants CA60907 from the National Cancer Institute and AG11026 from the National Institute on Aging.
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Qing, J., Wei, D., Maher, V. et al. Cloning and characterization of a novel gene encoding a putative transmembrane protein with altered expression in some human transformed and tumor-derived cell lines. Oncogene 18, 335–342 (1999) doi:10.1038/sj.onc.1202290
- differential display
- cell transformation
- gene expression
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