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Profiling SLCO and SLC22 Genes in the NCI-60 Cancer Cell Lines to Identify Drug Uptake Transporters

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Profiling SLCO and SLC22 Genes in the NCI-60 Cancer Cell Lines to Identify Drug Uptake Transporters 3081 Profiling SLCO and SLC22 genes in the NCI-60 cancer cell lines to identify drug uptake transporters Mitsunori Okabe,1 Gergely Szaka´cs,1,3 predicted by the statistical correlations, expression of Mark A. Reimers,2,4 Toshihiro Suzuki,1,5 SLC22A4 resulted in increased cellular uptake and Matthew D. Hall,1 Takaaki Abe,6 heightened sensitivity to mitoxantrone and doxorubicin. John N. Weinstein,2 and Michael M. Gottesman1 Our results indicate that the gene expression database can be used to identify SLCO and SLC22 family members Laboratories of 1Cell Biology and 2Molecular Pharmacology, that confer sensitivity to cancer cells. [Mol Cancer Ther Center for Cancer Research, National Cancer Institute, NIH, 2008;7(9):3081–91] Bethesda, Maryland; 3Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary; 4Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia; 5Department of Analytical Introduction Biochemistry, Meiji Pharmaceutical University, Tokyo, Japan; One of the major mechanisms of adaptive cellular and 6Division of Nephrology, Endocrinology, and Vascular Medicine, Department of Medicine, Tohoku University Graduate anticancer drug resistance [multidrug resistance (MDR)] School of Medicine, Sendai, Japan is diminished cellular accumulation conferred by a combi- nation of decreased transporter-mediated drug uptake and increased energy-dependent effluxof drugs (1). This occurs Abstract in concert with a variety of metabolic changes in cells that Molecular and pharmacologic profiling of the NCI-60 cell affect the ability of cytotoxic drugs to kill cells, including panel offers the possibility of identifying pathways alterations in the cell cycle, increased repair of DNA involved in drug resistance or sensitivity. Of these, damage, reduced apoptosis, and altered metabolism of decreased uptake of anticancer drugs mediated by efflux drugs. Of these mechanisms, the one most commonly transporters represents one of the best studied mecha- encountered in the laboratory is the increased effluxof a nisms. Previous studies have also shown that uptake broad range of cytotoxic drugs mediated by ATP binding transporters can influence cytotoxicity by altering the cassette (ABC) transporters (2). P-glycoprotein, encoded by cellular uptake of anticancer drugs. Using quantitative ABCB1 (also known as MDR1), stands out among ABC real-time PCR, we measured the mRNA expression of two transporters by conferring the strongest resistance to a wide solute carrier (SLC) families, the organic cation/zwitterion variety of drugs and has been shown to be implicated in transporters (SLC22 family) and the organic anion trans- clinical drug resistance (3). In addition to P-glycoprotein, porters (SLCO family), totaling 23genes in normal tissues 11 of 48 known human ABC transporters have been shown and the NCI-60 cell panel. By correlating the mRNA to play some role in the drug resistance of cancer cells expression pattern of the SLCO and SLC22 family member in vivo and/or in vitro (4). gene products with the growth-inhibitory profiles of 1,429 Recently, we have used a bioinformatic approach to anticancer drugs and drug candidate compounds tested identify ABC transporter substrates. We profiled mRNA on the NCI-60 cell lines, we identified SLC proteins that expression of all 48 ABC transporters in 60 diverse cancer are likely to play a dominant role in drug sensitivity. To cell lines (the NCI-60) used by the National Cancer Institute substantiate some of the SLC-drug pairs for which the to screen for anticancer activity of >100,000 compounds SLC member was predicted to be sensitizing, follow-up submitted for testing. In our previous study, by correlating experiments were performed using engineered and char- the expression profiles with the growth-inhibitory profiles acterized cell lines overexpressing SLC22A4 (OCTN1). As of a subset of 1,429 compounds (incorporating antican- cer drugs and drug candidates) tested against the cells, we successfully identified several cytotoxic substrates recognized by different ABC transporters (5). Received 3/7/08; revised 6/9/08; accepted 6/30/08. As mentioned above, resistance can also result from Grant support: Intramural Research Program of the NIH, National Cancer reduced transporter-mediated drug uptake, and the net Institute, and Japan Society for the Promotion of Science. G. Szaka´cs is a accumulation of an anticancer drug in a cell is probably Bolyai fellow and a special fellow of the Leukemia and Lymphoma Society. influenced by the concurrent actions of uptake and efflux The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked transporters. The solute carrier (SLC) gene series encodes a advertisement in accordance with 18 U.S.C. Section 1734 solely to large family of passive transporters, ion-coupled trans- indicate this fact. porters, and exchangers that rely on a concentration Requests for reprints: Michael M. Gottesman, Laboratory of Cell Biology, gradient across the membrane or cotransport/counter- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892. Phone: 301-496-1530; Fax: 301-402-0450; E-mail: transport to facilitate substrate transport. In the physio- [email protected] logic setting, SLC transporters are responsible for the Copyright C 2008 American Association for Cancer Research. absorption and excretion of a wide variety of endogenous doi:10.1158/1535-7163.MCT-08-0539 and exogenous compounds. The human organic anion Mol Cancer Ther 2008;7(9). September 2008 Downloaded from mct.aacrjournals.org on September 25, 2021. © 2008 American Association for Cancer Research. 3082 Identifying Uptake Transporters for Anticancer Drugs transporting peptide (OATP or SLC21) family is composed (described below). Stock solutions were aliquoted and of 11 members that transport endogenous organic anions stored at -80jC. [ethyl 1-14C]TEA bromide (55.0 mCi/mmol) (e.g., bile salts and bilirubin) and xenobiotics. The organic and [3H(G)]mitoxantrone (1.5 Ci/mmol) were from cation (and carnitine) transporter (OCT, SLC22) family has American Radiolabeled Chemicals, and (14) doxorubicin members that are able to transport organic cations/zwit- hydrochloride (55.0 mCi/mmol) was from Amersham. All terions and anions (6–8). Within the SLC22 family, there are other chemicals and reagents were of analytical grade. sixmain cation transporters; SLC22A1 (OCT1), SLC22A2 Preparation of Total RNA (OCT2), SLC22A3 (OCT3), SLC22A4 (OCTN1), SLC22A5 Total RNA from human normal tissues was obtained from (OCTN2), and SLC2A16 (OCT6), three of which are known Clontech. Total RNA from the 60 cancer cell lines was to transport the zwitterion carnitine (SLC22A4, SLC22A5, prepared and provided by DTP.7 For consistency in RNA and SLC22A16; ref. 8). quality, DTP has adopted standard operating procedures Studies have proven that uptake transporters can indeed that include the use of matched serum batches and confer sensitivity to anticancer drugs (9–14). For example, harvesting the cells at a particular confluence (17). Never- methotrexate has been shown to be a substrate for organic theless, the quality (purity and integrity) of the RNA anion-transporting polypeptide 1B3 (SLCO1B3, OATP1B3; samples was assessed using an Agilent 2100 Bioanalyzer. ref. 9). (Note: In this report, we refer to individual proteins The RNA was quantitated using a spectrophotometer of the SLCO and SLC22 family by using series numbers (Ultrospec 3100 pro; Amersham). for SLC genes and also the general protein nomenclature. Real-time Quantitative ReverseTranscription-PCR See http://www.genenames.org/.) Similarly, studies have Expression levels of the SLCO and SLC22 family shown that the organic cation transporters SLC22A1 genes were measured by real-time quantitative reverse (OCT1), SLC22A2 (OCT2), and SLC22A3 (OCT3) mediate transcription-PCR (RT-PCR) using ABI PRISM 7900HT cell sensitivity to platinum drugs such as cisplatin, car- (Applied Biosystems). For information on specific oligonu- boplatin, and oxaliplatin (12–15). cleotide primers and TaqMan probes for each of the SLC Huang et al. have exploited the NCI-60 database to members, see Supplementary Tables S4 and S5. Synthesis of correlate oligonucleotide array data with the potencies of cDNA from total RNA samples was carried out using 119 standard anticancer drugs and showed that SLC29A1 TaqMan Reverse Transcription Reagents (Applied Biosys- plays a role in the cellular uptake of the nucleoside tems) with 1 Ag total RNA/50 AL reaction volume. The analogues azacytidine and inosine-glycodialdehyde (16). cDNA (0.5 AL reverse transcription sample) was amplified In this study, we have measured the mRNA expression of using TaqMan Universal PCR Master MixReagents two SLC families in normal human tissues and the NCI-60 (Applied Biosystems) in a total volume of 10 AL. The PCR cell line panel. Because reproducible, quantitative correla- mixture was preincubated at 50jC for 2 min, incubated at tions between the expression and the sensitivity were 95jC for 10 min, and amplified by 40 cycles at 95jC for 15 s required, we chose to measure transcript expression by and 60jC for 1 min. No-template (water) reaction mixtures quantitative real-time PCR to gain a perspective on the were prepared as negative controls. potential role of SLCO and SLC22 transporters in drug Data Processing response. We show that positively correlated drug-gene During the PCR amplification,
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