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Experimental Therapeutics, Preclinical Pharmacology |
Departments of Surgical Oncology [F. M., H. Z., M-C. H.], Molecular and Cellular Oncology [W-P. L., M-C. H.], and Pathology [A. S.], The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, and Department of Biological Chemistry, University of California at Davis Cancer Center, Sacramento, California 95817 [H-J. K.]
| ABSTRACT |
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| Introduction |
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Trastuzumab, a monoclonal antibody against HER2/neu, is now in clinical use both as a single agent and in combination with chemotherapeutic agents. TK inhibitors targeting HER2/neu and EGFR are also being tested in clinical trials. Understanding the TK expression patterns in breast cancer is essential for selecting particular TK inhibitors for clinical use and for identifying new therapeutic targets.
We hypothesized that breast cancers have significant variability in their TK expression profiles, and that there may also be novel TKs that are differentially expressed in breast cancer and affect cancer biology. We used a differential display assay based on the conserved sequences in TKs to study their expression profiles in normal breast and breast cancer cell lines.
| Materials and Methods |
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TK Display Assay.
Total RNA was isolated from cell lines and breast tissue with the TRIZOL reagent (Life Technologies, Inc., Carlsbad, CA), and the TKDA was carried out by a modification of the method described by Robinson and colleagues (8
, 9)
. Total RNA was reverse transcribed after annealing with the antisense degenerate primer Primer 3, 5'-CACAGGTTACCRHAIGMCCAIACRTC-3', using the Superscript preamplification system (Life Technologies, Inc.) RT-PCR was performed using degenerate primers; the sense primers were Primer 1, 5'-CAGGTCACCAARRTIDCNGAYTTYGG-3', and Primer 2, 5'-CCAGGTCACCAARRTTDCNGAYTTYGG-3', and the antisense primer was Primer 3. The mixed bases were defined as follows: N = A + C + T + G, D = A + T + G, H = A + T + C, R = A + G, Y = C + T, M = A + C, and I = deoxyinosine. Alignment of the amino acid sequences corresponding to the primers and the TK consensus sequences are presented in Fig. 1A
. RT-PCR was performed with DNA polymerase (FB-600060; Fisher Scientific, Pittsburgh, PA) in the presence of 25 mM MgCl2. Amplification was carried out at an annealing temperature of 44°C for 5 cycles and then at 55°C for 25 cycles. Amplified products were analyzed by gel electrophoresis on an 8% polyacrylamide gel (Fig. 1B)
. The primer sets yielded RT-PCR products that were consistently 154170 bp because of the relatively constant spacing of the conserved motifs from which the primers were derived. A DNA was stained with 1 µg/ml ethidium bromide. The 154170-bp RT-PCR products were excised from the polyacrylamide gel, eluted, precipitated, and dissolved in TE buffer (10 mM Tris, 1 mM EDTA, pH 8.0). RT-PCR was repeated using a sense primer radiolabeled on the 5' end with [
-32P]ATP (Amersham Life Science, Buckinghamshire, United Kingdom) and T4 polynucleotide kinase (New England Biolabs, Beverly, MA) before PCR. The 154170-bp RT-PCR products were again excised from the gel and eluted. Equal amounts of radioactive DNA (105 cpm) were digested with a panel of restriction enzymes: AciI, AluI, CfoI, DdeI, HaeI1I, HinfI, MnlI, MspI, Sau3aI, Sau96I, ScrfI, Tru9I, and RsaI. Digestion products and uncut control DNA were resolved on a 6% acrylamide DNA sequencing gel and autoradiographed (Fig. 1B)
. A sequencing reaction was used as a size marker. The uncut kinases remained as tightly clustered 154170-bp nucleotide bands (Fig. 2)
. Up to 10 kinases were cleaved with a given restriction enzyme, and different kinases were represented by bands of different sizes displayed in a DNA sequencing gel (Fig. 2)
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RT-PCR for Specific Kinases.
RT-PCR was performed at an annealing temperature of 55°C using primers 5'-GGTGGCTGTGAAGACGATGA-3' and 5'-CTCAGATACTCCATGCCACT-5' for Axl, 5'-TTGCTGCGCCAGAGCCGC-3' and 5'-GATGATGGCCTGCTCCAG-3' for Syk, and 5'-AGTCATCGTGGAGGATGATG-3' and 5'-AGGTTGACAGGTTCCAACTG-3' for PDGFR
. Amplification of GAPDH was performed as a control using primers 5'-AAGGTGAAGGTCGGAG-TCAAC-3' and 5'-CATGAGTCCTTCCACGATACC-3'. PCR products were analyzed by 1.5% agarose gel electrophoresis.
Western Blot Analysis.
Whole-cell extracts were lysed using buffer A [20 mM Tris (pH 7.5), 10% glycerol, 1% Triton X-100, 0.15 mM NaCl, 1 mM ß-mercaptoethanol, 1 mM Na3VO4, 1 mM aprotinin, and 1 mM phenylmethylsulfonyl fluoride]. Samples were then centrifuged, and the supernatants were heated to 100°C for 5 min and separated by 8% SDS-PAGE. After transferring to nitrocellulose and blocking with 5% milk, the membranes were incubated with antibodies against Axl (Santa Cruz Biotechnology, Santa Cruz, CA). As a loading control, the membranes were stripped and incubated with an antibody against actin (Boehringer Mannheim, Indianapolis, IN). Immunocomplexes were detected with an ECL chemiluminescence system (Amersham Corp., Arlington Heights, IL).
Northern Blot Analysis.
Total RNA was extracted from cell lines using TRIZOL reagent as described previously. Ten µg of total RNA from each cell line were resolved on a formaldehyde gel and transferred onto nylon membranes (GeneScreen; New England Nuclear Life Science Products, Boston, MA). A 303-bp Axl fragment was randomly labeled with [
-32P]dCTP using the random primer DNA labeling system (Life Technologies, Inc.). The membranes were then stripped and rehybridized with a GAPDH probe as a loading control. Signals were detected with autoradiography.
| Results |
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TKDA products corresponding to receptor TKs Axl, cell adhesion kinase (Cak or trkE), FGFR4, MET, and RET and nonreceptor TKs Arg, BRK, JAK1, Rak, and YES were identified (Fig. 3A)
. Their identities were confirmed by at least two separate restriction enzyme digestions. Furthermore, the expression patterns of Arg, Axl, BRK, Cak, HEK8, JAK1, MET, Rak, and YES were confirmed by subcloning and sequencing of RT-PCR products.
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The TK profiles were compared using cDNAs generated from RT-PCR of cell lines using antisense degenerate Primer 1, an oligo dT primer, or random hexamers. The TK profiles were reproducible regardless of the method used to produce the cDNA. However, optimal results were obtained using the antisense degenerate primer, possibly because that method was the least vulnerable to RNA degradation.
We additionally studied the TK profiles of five normal breast specimens and seven invasive carcinomas (six ductal and one lobular) with TKDA. Overall, the TK profile of the breast tissues was remarkably similar to that of the breast cell lines. All TKs detected in breast cell lines were detected in breast tissue. An additional TK, Tie, was detected only in the tissue; this kinase may be endothelial in origin.
RT-PCR Analysis of Specific Kinases.
TKDA revealed differential expression of Axl in breast cancer cell lines; therefore, we further evaluated Axl expression at the RNA and protein level. RT-PCR using Axl-specific primers detected Axl mRNA in normal MCF10A and MCF12A breast cell lines and in breast cancer cell lines BT549 and MDA-MB-231 (Fig. 4A)
. However, Northern blot analysis demonstrated that the mean expression level of Axl was higher in BT549 cells and 12-fold higher in MDA-MB-231 cells than in normal breast cells MCF10A and MCF12A (Fig. 4B)
. Overexpression of Axl in BT549 and MDA-MB-231 cells was confirmed by Western blot analysis with polyclonal anti-Axl antibodies (Fig. 4C)
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, one of the therapeutic targets of signal transduction inhibitor 571. Syk expression was detected in normal MCF12A but not MCF10A breast cells. Syk mRNA was also not detected in four of six breast cancer cell lines tested (Fig. 5A)
mRNA was not detected in normal breast or breast cancer cell lines, but it was detected in rhabdomyosarcoma cell line A204 (Fig. 5B)
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| Discussion |
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Several TKs are known to be expressed in human malignancies, and some are thought to be involved in the development of specific malignancies, including Bcr-Abl in chronic myelogenous leukemia and the RET receptor TK in medullary thyroid carcinoma. Overall, TK activity in invasive breast cancer has been shown to be greater than that in normal breast tissue (10 , 11) . Moreover, several TKs that have been reported to be expressed in breast cancer are proposed to play a role in breast cancer biology. For example, EGFR and HER2/neu are overexpressed in 3550% and 2030% of invasive breast cancers, respectively, and predict a poor prognosis (1 , 12 , 13) . BRK, a TK cloned from a metastatic breast tumor (3) , has been reported to be overexpressed in two thirds of breast tumors (14) , the c-Met receptor has been found to be expressed at high levels in poorly differentiated breast cancer cells (5) , and c-Src has also been reported to be overexpressed in breast cancer (4) . In addition, McLeskey et al. (5) showed that several breast cancer cell lines express high levels of FGFR; 10% of primary breast tumor samples have been found to have amplification of the FGFR4 gene (15) , and 9% amplification of FGFR1 (16) . In contrast, c-kit has been found to be expressed significantly less in breast cancer than in normal breast tissue (7 , 17) . Furthermore, Syk has been reported to be lost in invasive breast cancer and is proposed to be a potential tumor suppressor in human breast carcinomas (6) . Thus, several TKs are expressed in breast cancer, potentially exerting some opposing effects on cell growth and proliferation.
In the present study, we found that the receptor TK Axl was overexpressed at the mRNA and protein level in some breast cancer cell lines. Axl was initially identified as a protein encoded by a transforming gene from primary human myeloid leukemia cells (18) . Growth arrest-specific gene 6, which is the ligand for Axl (19) , mediates mitogenic activity in Axl-overexpressing cells (20) . Overexpression of Axl has been reported in thyroid cancer (21) and hepatocellular cancer (22) . The expression of Axl has also been found to be higher in a metastatic prostate cell line than in a less aggressive prostate carcinoma cell line or in normal prostate cells (23) . Axl has also been reported to be expressed 10-fold more in colon cancer metastases than in other normal and malignant tissues (24) . Our study suggests that Axl is overexpressed in a subgroup of breast cancers. We have reported recently that adenovirus type 5 E1A down-regulates the expression of Axl at a transcriptional level, and that down-regulation of Axl is involved in E1A-mediated growth suppression and E1A-induced apoptosis (25) . Further study is needed to determine whether Axl will be useful as a therapeutic target in a subgroup of breast tumors.
Craven et al. (24) and Cance et al. (26) have previously attempted to systematically identify TKs expressed in breast cancer cell line 600PEI and in a primary tumor library by performing RT-PCR with a different set of degenerate primers and constructing and sequencing these kinase-specific cDNA libraries. The advantages of TKDA are that it allows for simultaneous profiling of up to 4050 TKs (8) , as well as provide a potential for novel gene discovery. It may be less sensitive to RNA degradation than are other RNA-based assays, because the primers chosen for TKDA are close to the 3' end of the RNA and flank a short RNA sequence (120 bp without primers). The disadvantages of TKDA are that it, similar to other PCR-based assays, has a contamination potential, and there is also a potential for nonspecific priming with degenerate primers, as we observed when they amplified with 18S rRNA and mitochondrial cytochrome c oxidase subunit II; however, >90% of clones obtained with degenerate primers are protein kinases (8) . There is also a potential for misidentification of TKs with the assay, because identification is dependent on restriction digest pattern; thus, attention must be paid to ensure that all digestions actually work, and consideration must be given to performing confirmatory double digests if needed. Another limitation of the assay is that it is not quantitative: it is more useful for determining the presence or absence of TK expression than for determining relative expression levels. TKDA is fairly labor intensive and requires large amounts of RNA to produce reproducible results. Therefore, it is unlikely to be used routinely in clinical practice; however, it is a valuable research tool. Overall, the kinase profiles found were fairly reproducible in cell lines. However, the expression of four protein kinases (RET, Axl, GCK, and one potential novel kinase) were found to be more variable. The expression of these kinases may be sensitive to culture conditions, such as cell confluence, pH, and relative serum starvation, or may represent a variation in assay conditions.
In summary, we used a TKDA to profile the TK expression pattern in breast cancer. Several TKs were found to be differentially expressed in commonly used breast cancer cell lines. This heterogeneity should be taken into consideration when studying breast cancer biology. Tailoring TK inhibitors to the expression profile of each tumor may enhance their therapeutic efficacy.
| ACKNOWLEDGMENTS |
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| FOOTNOTES |
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1 Supported by NIH Grants 5T32CA09599-11 and 1K08-CA91895-01 (to F. M.) and NIH Grants R0-1 CA58880 and P50 CA83639 (to M-C. H.). ![]()
2 To whom requests for reprints should be addressed, at Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Box 108, Houston, TX 77030. Phone: (713) 792-3668; Fax: (713) 794-0209; E-mail: mhung{at}mdacc.org ![]()
3 The abbreviations used are: TK, tyrosine kinase; TKDA, TK display assay; EGFR, epidermal growth factor receptor; FGFR fibroblast growth factor receptor; RT-PCR, reverse transcription-PCR; PDGFR, platelet-derived growth factor receptor; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; JAK, Janus kinase. ![]()
Received 9/19/01; revised 11/19/01; accepted 11/19/01.
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