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The Department of Biopharmaceutical Sciences, University of California, San Francisco, California
(Received June 7, 2007; Accepted October 15, 2007)
| Abstract |
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The level of ABCB1 mRNA expression is an important determinant of P-gp expression levels. Interindividual differences in ABCB1 mRNA expression levels observed in the liver (Schuetz et al., 1995
), small intestine (Moriya et al., 2002
; Nakamura et al., 2002
; Lindell et al., 2003
), and kidney (Uwai et al., 2004
) may contribute to the variable drug response of P-gp substrates. Genetic variation in ABCB1 is one possible mechanism influencing ABCB1 mRNA levels. Several studies have investigated the effects of coding region ABCB1 polymorphisms, such as 2677G>T and 3435C>T, on mRNA expression. The 3435C>T synonymous variant is the most commonly studied with respect to mRNA levels. It was initially linked with increased mRNA expression (Moriya et al., 2002
); however, data from subsequent studies are not in agreement (Siegmund et al., 2002
; Uwai et al., 2004
; Owen et al., 2005
; Haenisch et al., 2007
). An in vitro study measured different mRNA stabilities between the C and T alleles of 3435 (Wang et al., 2005
), so it is possible that this variant causes changes at the cellular level that may extend to clinical phenotypes.
Mechanisms that alter mRNA levels can change P-gp expression and potentially P-gp transport activity. Steady-state ABCB1 mRNA levels reflect the balance between gene transcription (i.e., synthesis) and mRNA stability (i.e., decay). Recent evidence has demonstrated that the 3'-UTR of mRNA is an important regulatory site controlling interactions with mRNA degradation machinery (Hollams et al., 2002
; Tourriere et al., 2002
; Mangus et al., 2003
; Wilkie et al., 2003
). 3'-UTR RNA-binding proteins that recognize specific mRNA sequence elements and secondary structure dictate the fate of mRNA transcripts. Polymorphisms in the 3'-UTR of ABCB1 could disrupt RNA-protein interactions, resulting in altered mRNA stability.
The current studies were designed to test whether polymorphisms in the 3'-UTR of ABCB1 affected mRNA stability. ABCB1 3'-UTR polymorphisms were identified in an ethnically diverse panel of DNA samples. Stable cell lines expressing ABCB1 reference and the three most common 3'-UTR variants were established in order to measure the rate of ABCB1 mRNA decay after cessation of transcription. The estimated mRNA half-life served as a measure of ABCB1 mRNA stability.
| Materials and Methods |
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Cell Culture. Growth media for HEK293 Flp-In cells contained Dulbecco's modified Eagle's with high glucose (4.5 g/l) supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, and either 100 µg/ml Zeocin (parental cells) or 75 µg/ml hygromycin (ABCB1 stable cells). Human lymphoblast cell lines (GM12814, GM12815, GM17102, GM12892, GM18506, and GM18562) were obtained from the Coriell Cell Repository and maintained in suspension with RPMI 1640 medium supplemented with 15% fetal bovine serum and 1% penicillin/streptomycin. All cell lines were passaged every 2 to 4 days in T25 (lymphoblasts) or T75 (HEK293) flasks and maintained in 5% CO2 at 37°C.
Identification of ABCB1 3'-UTR Variants. Genomic DNA from 247 human samples from the Coriell Institute was used to identify 3'-UTR polymorphisms in ABCB1. Direct sequencing of the 3'-UTR was performed with forward and reverse primers (5'-GGTGTTTCAGAATGGCAGAGTC-3' and 5'-CTGCTTAACCATTCCCACAAAA-3', respectively) using previously reported methods (Kroetz et al., 2003
; Leabman et al., 2003
).
ABCB1 Plasmids. Full-length ABCB1 cDNA was subcloned into pcDNA5/FRT and used as a template to create 3'-UTR variant plasmids. The +193A>G variant was already present and was changed back to the reference nucleotide. Mutagenesis primers were designed for +89A>T (forward 5'-AACACTTACAGAATTTTGAAGAGGTATCTGT and reverse 5'-ACAGATACCCTCTTCAAAATTCTGTAAGTGTT) and +146G>A (forward 5'-GTCTTCAGAGACTTCATAATTAAAGGAACAG and reverse 5'-CTGTTCCTTTAATTATGAAGTCTCTGAAGAC) and reversion of +193A>G (forward 5'-AAGTGGAGAGAAATCATAGTTTAAACTGCAT and reverse 5'-ATGCAGTTTAAACTATGATTTCTCTCCACTT). The QuikChange Site-Directed Mutagenesis Kit (Stratagene, La Jolla, CA) with Pfu turbo polymerase was used according to the manufacturer's protocol to introduce the desired variants. Direct sequencing verified the base changes.
ABCB1 Flp293 Stable Cell Lines. HEK293 Flp-In cells were seeded at 5 x 105 cells/well in 6-well plates in medium without antibiotics. One day later, cells were transfected with 3.6 µg of p0G44, 0.4 µg of ABCB1/pcDNA5/FRT, and 6 µl of Lipofectamine 2000 in a total well volume of 2 ml. Fresh medium was added
5 h after transfection. The following day, cells were split into six new wells and, 2 to 3 h later, medium containing 75 µg/ml hygromycin was added. Drug selection lasted 10 to 14 days, and fresh hygromycin medium was added every 2 to 3 days. Surviving cell colonies were propagated and screened for surface P-gp expression by flow cytometry. P-gp positive clones were further screened for ABCB1 mRNA expression using TaqMan quantitative real-time PCR.
ABCB1 mRNA Half-Life in Flp293 Stable Cell Lines and Lymphoblast Cell Lines. ABCB1 reference, +89A>T, +146G>A, and +193A>G Flp293 cell lines were seeded in 12-well plates at 6 x 105 cells/well and allowed to grow for 24 h. For each cell line, triplicate wells were seeded for each time point. Medium containing 7.5 µg/ml actinomycin D was added to the wells, and cells were harvested over a 24-h period. Total RNA was isolated from each sample using TRIzol and quantitated using UV spectrophotometry (NanoDrop Technologies, Wilmington, DE). Equal amounts of total RNA were reverse transcribed using Moloney murine leukemia virus reverse transcriptase (Promega, Madison, WI) according to the manufacturer's instructions. TaqMan primers (forward 5'-TGATCATTGAAAAAACCCCTTTG and reverse 5'-TCCAGGCTCAGTCCCTGAAG) and probe [5'-(6-FAM)-ACGGAAGGCCTAATGCCGAACACATT-(BHQ1)] for ABCB1 were designed using Primer Express (Applied Biosystems, Foster City, CA) and were purchased from Integrated DNA Technologies (Coralville, IA). The 25-µl reaction volume contained 10x TaqMan Buffer (UCSF Genome Core, San Francisco, CA), 5.5 mM MgCl2, 200 µM deoxynucleoside-5'-triphosphates (Promega, Madison, WI), 0.625 U AmpliTaq Gold (Applied Biosystems), 1 µl of cDNA, 500 nM forward and reverse primers, 200 nM probe, and PCR-grade H2O. Reactions were run on an ABI Prism 7700 and cycling conditions were as follows: 12 min at 95°C followed by 45 cycles of 15 s at 95°C and 1 min at 60°C. The threshold limit was set so that it intersected all samples during the log-linear phase of amplification, and the corresponding CT values for each set of triplicates were normalized to the average t = 0 value using the equation for percentage of mRNA remaining: [2(CT, t = 0 - CT, t = x)] * 100, where x equals time after t = 0 in hours. The decay slope (k) for percentage of mRNA versus time was determined using logarithmic data fitting (Excel; Microsoft, Redmond, WA). The half-life was calculated from the equation t1/2 = ln 2/k. All experiments were carried out in triplicate.
For each lymphoblastoid cell line, cells were seeded in three wells of a six-well plate at 5 x 105 cells/well in 4 ml of medium. After 24 h, actinomycin D was added to each well at a final concentration of 7.5 µg/ml and 0.5-ml aliquots were removed at each time point (0, 2, 4, 8, 12, and 24 h). Cell aliquots were pelleted, and TRIzol was added to isolate total RNA. ABCB1 mRNA expression and ABCB1 mRNA half-life were determined as described above except that double the amount of RNA was reverse-transcribed, and double the volume of cDNA was used in each TaqMan reaction. The experiment was performed twice.
Statistical Analysis. Half-life values from three experiments for ABCB1 reference, +89A>T, +146G>A, and + 193A>G Flp293 cell lines were averaged, and the standard deviation was calculated. Student's t test was used to determine whether the mean half-lives for the variants were different from reference with an
value of 0.05.
| Results |
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Genetic Analysis of the ABCB1 3'-UTR. Little research has been done on the 3'-UTR of ABCB1, so predictive measures were used to ascertain the potential impact of ABCB1 +89A>T, +146G>A, and +193A>G on mRNA stability. Sequence alignments with other mammalian species using ClustalW (version 1.83) were used to compare the 3'-UTR of human ABCB1 with corresponding sequences from mouse, rat, and rhesus monkey. The sequences ranged in length from 350 to 401 base pairs, and 175 base positions were 100% identical compared with the human sequence (Fig. 1). Using the human sequence as a reference, the sequence similarity of these four species is 46%, and it increases to 90% if only human and rhesus monkey are compared. There are six 3'-UTR variant sites that are 100% identical in the three other species: +21, +89, +146, +193, +252, and + 355. The other three variant sites are only conserved in rhesus monkey. The multiple species alignment also revealed contiguous sections of 100% conservation that could indicate functional importance, so the ABCB1 3'-UTR sequence was analyzed against a database of known 5'- and 3'-UTR sequence elements (Pesole and Liuni, 1999
). An internal ribosome entry site (IRES) element, which enables translation initiation independent of the 5' cap, was found between +282 and +380; however, IRES elements generally are located in the 5'-UTR (Pesole et al., 1999
). No other potential RNA binding sites were identified using UTRscan (http://www.ba.itb.cnr.it/UTR).
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80-fold, and P-gp surface expression quantitated by flow cytometry showed a
25-fold increase compared with the host Flp293 cells. Additionally, the steady-state mRNA levels before actinomycin D exposure (t = 0) for the ABCB1 3'-UTR variants differed by no more than 15% of reference (n = 3; data not shown). The mRNA stability of transcripts is commonly determined by measuring mRNA half-life. ABCB1 Flp293 reference, +89A>T, +146G>A, and +193A>G stable cell lines were exposed to actinomycin D to stop whole-genome transcription. The ABCB1 mRNA levels over a 24-h period were normalized to the t = 0 point to convert the data into percentage of mRNA remaining for each cell line. A plot of percentage of mRNA versus time shows the rate of ABCB1 mRNA decay for each cell line (Fig. 2) and provides a measurement of mRNA half-life. The average half-lives from three experiments for +89A>T, +146G>A, and +193A>G were 8.3 ± 1.4, 9.6 ± 0.8, and 10.3 ± 1.2 h, respectively, and were not significantly different from reference (9.4 ± 1.3 h). As a negative control, the ABCB1 reference cell line was not exposed to actinomycin D to verify constant ABCB1 mRNA expression during the 24-h period.
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| Discussion |
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The numerous efforts to associate ABCB1 coding region SNPs with clinical phenotypes have not produced conclusive results. It is possible that unidentified SNPs in linkage disequilibrium with the commonly studied SNPs may be causative. To our knowledge, the +89A>T, +146G>A, and +193A>G variants have not been investigated and were chosen for study based on a high allele frequency in at least one ethnic group and a significant degree of evolutionary conservation at these sites. It is important for ABCB1 pharmacogenetic research to examine noncoding polymorphisms, especially in relation to their probable mechanistic effects in vitro.
Regulatory proteins bind to specific elements in the 3'-UTR and interact with RNA degradation machinery by promoting or repressing degradation (Tourriere et al., 2002
). A common sequence motif containing adenine-uracil (AU) repeats is thought to confer rapid degradation, and one study hypothesized the AU-rich regions of the c-myc and ABCB1 3'-UTRs could destabilize β-globin mRNA. In HepG2 cells, c-myc, ABCB1, and β-globin mRNA have half-lives of 30 min, 8 h, and >24 h, respectively (Prokipcak et al., 1999
). Chimeras containing the β-globin coding region with either the ABCB1 3'-UTR or the c-myc 3'-UTR showed that β-globin half-life was only decreased by c-myc (Prokipcak et al., 1999
). It should be noted that our measured half-life for reference ABCB1 in HEK293 cells (
9.4 h) is very similar to that seen in HepG2 cells.
The mRNA stability of ABCB1 is a regulated process dependent on multiple factors, such as stress and cell type. The human leukemia cell line K562 is a disease-state model for studying mechanisms controlling P-gp overexpression due to drug exposure. ABCB1 mRNA half-life in K562 cells is 1 h, but short-term incubation with drugs, such as vinblastine and doxorubicin, increased the half-life to 10 h with no changes in transcriptional activity (Yague et al., 2003
). Studies in rats have revealed that carcinogenesis in the liver can modulate the mRNA stability of Pgp1–3 (human P-gp orthologs) by dramatically increasing their normally short half-life (2 versus 12 h) (Lee et al., 1998
). Subsequent studies determined that the increased mRNA stability in rat liver tumors was associated with a decrease in P-gp mRNA fragments, indicating there was less mRNA degradation (Lee et al., 2005
). Even in healthy organs free of stress, rat P-gp mRNA has tissue-specific half-lives that range from 2 to 12 h (Lee and Ling, 2003
).
There are no literature reports discussing possible regulatory sites in the 3'-UTR of ABCB1. Our sequence analysis indicates that there may be functionally important segments based on high conservation with other mammalian species; however, the UTRscan database did not find any probable elements. The 3'-UTR field is rapidly growing and has yet to reach the same knowledge base as promoter research, which has identified thousands of transcription factors and DNA binding elements (Matys et al., 2003
). In contrast, UTRscan currently searches for 31 known degenerative elements, so it is possible there are many more yet to be identified.
The stability of mRNA may be altered by 3'-UTR polymorphisms if recognition of specific mRNA sequence and secondary structure by regulatory proteins is disrupted (Shen et al., 1999
; Hollams et al., 2002
; Tourriere et al., 2002
). A polymorphism in the 3'-UTR of human tumor necrosis factor-
changes binding affinity for a multiprotein complex that contains the HuR regulatory protein (Di Marco et al., 2001
). HuR binds AU-rich elements in the 3'-UTR of certain genes (Peng et al., 1998
) and has been shown to stabilize mRNA containing tumor necrosis factor-
3'-UTR sequence motifs (Dean et al., 2001
). There is one report that the 3435C>T synonymous variant decreases mRNA stability (Wang et al., 2005
), but to our knowledge no pharmacogenetic research of this type has been conducted for ABCB1 3'-UTR variants. Thus, our mRNA half-life data represent novel findings as to the effects the +89A>T, +146G>A, and +193A>G polymorphisms have on ABCB1 mRNA stability and demonstrate the utility of using stable cell lines made with Flp-In technology for these measurements. Similarly, studies in lymphoblastoid cell lines carrying 3'-UTR variants suggest that decay of endogenous ABCB1 mRNA is not affected by these specific polymorphisms. Future mRNA stability experiments should investigate other ABCB1 3'-UTR variants and/or haplotypes. Furthermore, the 5'-UTR may play a role in mRNA stability based on the closed-loop hypothesis (Wilkie et al., 2003
). The possible interactions between both UTRs in the cytosol suggest 5'-UTR polymorphisms could modify regulatory protein interactions that propagate to the 3'-UTR and affect mRNA stability.
| Acknowledgments |
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| Footnotes |
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Article, publication date, and citation information can be found at http://dmd.aspetjournals.org.
ABBREVIATIONS: P-gp, P-glycoprotein; UTR, untranslated region; ABC, ATP binding cassette; Flp293, HEK293 Flp-In; SNP, single-nucleotide polymorphism; PCR, polymerase chain reaction; IRES, internal ribosome entry site; AU, adenine-uracil.
Address correspondence to: Deanna L. Kroetz, UCSF Box 2911, 1550 4th St. RH584E, San Francisco, CA 94158-2911. E-mail: deanna.kroetz{at}ucsf.edu
| References |
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mRNA impairs binding of the post-transcriptional regulatory protein HuR to TNF
mRNA. Nucleic Acids Res 29: 863-871.This article has been cited by other articles:
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