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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
 
Pharmacogenet Genomics. Author manuscript; available in PMC 2010 November 1.
Published in final edited form as:
PMCID: PMC2875259
NIHMSID: NIHMS201924

Mechanisms of Differential Expression of the CYP2A13 7520C and 7520G Alleles in Human Lung: Allelic Expression Analysis for CYP2A13 Heterogeneous Nuclear RNA, and Evidence for the Involvement of Multiple Cis-Regulatory Single Nucleotide Polymorphisms

Abstract

Objective

To identify the mechanisms underlying the decreased allelic expression of a common CYP2A13 allele (7520C>G) in the human lung; CYP2A13 is expressed selectively in the respiratory tract, and is highly efficient in the metabolic activation of several chemical carcinogens.

Methods

The 7520C/G alleles were compared for mRNA stability in cells and relative heterogenous nuclear RNA (hnRNA) levels in human lungs. Promoter region SNPs were identified and analyzed through in vitro reporter gene assays and gel-shift assays, in order to uncover the causative SNPs responsible for the decreased allelic expression.

Results

1) The 7520C>G SNP does not influence CYP2A13 mRNA stability in CYP2A13-transfected human lung or nasal epithelial cells; 2) levels of the 7520G hnRNA were consistently lower (<10%) than the levels of the 7520C hnRNA in lung samples from nine heterozygous individuals; 3) three SNPs (−1479T>C, −3101T>G, and −7756G>A) in linkage disequilibrium with the 7520C>G variation were found to cause altered interaction with DNA-binding proteins and decreases in promoter activity; 4) the suppressive effects of the −1479T>C, −3101T>G, and −7756G>A SNPs on the CYP2A13 promoter were additive, while the negative effects of the −1479T>C SNP were enhanced by methylation of the −1479C.

Conclusion

The decrease in expression of the 7520G allele was due to cumulative suppressive effects of multiple SNPs, with each by itself having a relatively small effect on CYP2A13 transcription.

Keywords: CYP2A13, Single Nucleotide Polymorphisms, Allelic expression, Transcriptional regulation

Introduction

Cytochrome P450 (CYP or P450) enzymes play an important role in the metabolism of a variety of compounds, including therapeutic agents, environmental toxicants, and chemical carcinogens [1,2]. Variations in P450 expression or activity can contribute substantially to inter-individual differences in therapeutic efficacy or toxicant susceptibility [3]. CYP2A13 is a human P450 enzyme selectively expressed in the respiratory tract [4-6]. CYP2A13 is the most active enzyme in the metabolic activation of a tobacco-specific carcinogen, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), and is also active toward a number of other respiratory-tract toxicants [4, 7-9]. CYP2A13 has been proposed to play a critical role in tobacco-related lung carcinogenesis [4,7]. The CYP2A13 gene is polymorphic; a total of ~20 CYP2A13 haplotypes have been identified to date (http://www.cypalleles.ki.se/cyp2a13.htm). A recent epidemiological study in a Chinese population indicated that an Arg257Cys variation in CYP2A13, leading to decreases in CYP2A13 enzyme activity [10], is associated with a reduced risk of smoking-induced lung adenocarcinoma [11].

Large inter-individual differences in the expression of CYP2A13 mRNA and protein in human lung have also been documented [6, 12]. However, mechanisms that regulate CYP2A13 expression are largely unknown. In a recent study, we found that the transcriptional regulation of CYP2A13 involves C/EBP transcription factors, and that CYP2A13 expression can be influenced by DNA methylation [13]. Furthermore, through an allelic expression analysis of CYP2A13 mRNAs from heterozygous individuals, we identified a low-expressing CYP2A13 allele, marked by a single nucleotide polymorphism (SNP), 7520C>G, in the 3′-untranslated region (3′-UTR); mRNA from the 7520G allele was found to be expressed at 10-fold lower levels than mRNA from the 7520C allele [12]. This remarkable expression difference provides unique opportunities for identification of the mechanisms that are involved in the regulation of CYP2A13 expression, as well as for further study of the potential associations between CYP2A13 expression and risks of smoking-induced lung cancer.

In the present study, we have performed a series of experiments to identify the mechanisms responsible for the low expression of the 7520G allele. Given the location of the 7520C>G in the 3′-UTR, we first tested the hypothesis that the 7520C>G change renders the CYP2A13 mRNA unstable. We then tested the alternative hypothesis that the allelic expression difference was due to a decrease in transcriptional activity of the 7520G allele. We developed a protocol for quantitative allelic expression analysis of heterogeneous nuclear RNA (hnRNA), the primary transcript; the underlying rationale is that abundance of hnRNA is an indicator of transcriptional activity of a given promoter in vivo [14]. Through allelic expression analysis of hnRNA, we confirmed that the 7520G allele had much reduced transcriptional activity in human lung, compared to the transcriptional activity of the 7520C allele. Subsequent studies were designed to identify additional SNPs, located in the 5′-flanking region of the CYP2A13 gene, that are in linkage disequilibrium (LD) with the 7520C>G SNP, and that could be potentially responsible for the expression differences between the 7520C/G alleles. The 5′-flanking region SNPs were characterized using several experimental approaches, including computational analysis for potential transcription factor binding sites, gel-shift assays with methylated or un-methylated DNA probes, and reporter gene assays with single or composite SNP sites. Our results indicate that the decrease in expression of the 7520G allele was due at least partly to cumulative, suppressive effects of multiple SNPs, including −1479T>C, −3101T>G, and −7756G>A, with each by itself having a relatively small effect on CYP2A13 transcription.

Methods

Plasmid construction

Detailed methods for the preparation of various expression vectors and reporter gene constructs are described in Supplemental Materials. The pCMV_2A13_UTRwt and pCMV_2A13_UTRmut expression plasmids contained the full-length CYP2A13*1 cDNA, with either 7520C or 7520G, respectively, in the 3′-UTR, preceded by a CMV promoter. The p2A13_−1479T plasmid, containing a 2-kb CYP2A13*1 promoter fragment in a pGL3_Basic (Promega, Madison, WI) luciferase reporter vector, was originally named p2A13_2k [13]; the p2A13_−1479C plasmid contains a C at −1479, instead of a T. The p2A13_−1479C and p2A13_−1479T constructs were methylated in vitro with CpG methylase M. SssI (New England Biolabs, Ipswich, MA), in the presence of 16 μmol/L S-adenosylmethionine (New England Biolabs). The reaction was carried out at 37°C for 6 h. Complete methylation was confirmed by digestion with methylation-sensitive BstU I (New England Biolabs). The p2A13_−3101T, p2A13_−3101G, p2A13_−7756G, p2A13_−7756A, p2A13_−7756G/−3101T, p2A13_−7756A/−3101G, p2A13_−7756G/−3101T/−1479T, and p2A13_−7756A/−3101G/−1479C constructs each contained a 245-bp (−6 to −250) CYP2A13*1 promoter fragment in the pGL3_Basic vector, with additional one, two, or three SNP-containing DNA fragments inserted further upstream of the 245-bp CYP2A13 promoter. All promoter constructs were confirmed by DNA sequencing.

Preparation of DNA and RNA from human lung samples, and first-strand DNA synthesis

DNA and RNA were isolated from resected normal lung biopsy or autopsy tissues (adult tissues were provided by the National Cancer Institute Cooperative Human Tissue Network; fetal tissues were provided by the University of Washington Birth Defects Research Laboratory, Seattle, WA). Individuals selected for analysis were previously genotyped as heterozygotes for the 7520C>G variation [12]. DNA samples used for haplotype analysis, cis-variation identification, and methylation status analysis were isolated from normal lung tissues with the DNeasy tissue kit (Qiagen). Total RNA used for allelic expression analysis was isolated from the same individuals with use of an RNeasy kit (Qiagen). Prior to RT, total RNA samples were first treated with RNase-free DNase I (Invitrogen) for 15 min at room temperature, in order to eliminate potential genomic DNA contamination. The RNA samples were then reverse-transcribed into first-strand DNA with 2 μg of total RNA in a total volume of 20 μl RT reaction, using the SuperScript III first-strand synthesis system and either a random primer or an oligo dT primer (Invitrogen). Reverse transcriptase was omitted in negative control reactions.

Allelic expression analysis of hnRNA

The allelic expression analysis of CYP2A13 (7520C/G) hnRNAs was carried out using the general strategy described previously for allelic expression analysis of CYP2A13 (7520C/G) mRNAs [12], but with PCR primers that are specific for hnRNA. The first PCR was performed to amply a 511-bp fragment (from intron 8 to 3′-UTR) of CYP2A13 primary transcript, using primers 2A13HnI8F1 (5′-gaggatcggagtctcctctg-3′) and 2A13R-RT2 (5′-tcacagctctgaaggacatc-3′). Reaction mixtures, in a total volume of 25 μl, contained 2 μl of RT product, 2.5 mM MgCl2, 0.32 μM of each primer, 0.2 mM dNTP, 2.5 μl 10×PCR buffer and 2.5 U HotstarTaq polymerase (Qiagen). After a preincubation at 95°C for 15 min, the reaction was carried out for 55 cycles, with each cycle consisting of a denaturation at 95°C for 30 s, annealing at 64°C for 45 s, and extension at 72°C for 45 s, followed by a final extension at 72°C for 10 min. The second PCR was carried out using 2A13HnI8F2 (5′-tccctagagagtgcagccg-3′) and 2A13R-RT1 (5′-tgttccctctaaccacctct-3′) to amplify a 398-bp fragment. PCR was performed on the LightCycler using allele-specific hybridization probes designed and synthesized by TIB MolBiol (Adelphia, NJ), as described previously [12]. The reaction mixtures, in a total volume of 10 μl, contained 2 μl of 10-fold diluted 1st PCR product, 2.0 mM MgCl2, 0.3 μM each primer, 0.3 μM Sensor [C] or Sensor [G] probe, 0.3 μM Anchor probe, and 1 μl LightCycler FastStart hybridization probe reagent mix (Roche Applied Science). The second PCR and melting curve analysis were performed essentially as previously described, except that PCR reactions were carried out for 60 cycles (each cycle consisting of denaturation at 95°C for 10 s, annealing at 66°C for 10 s, and extension at 72°C for 15 s) [12]. Purified CYP2A13 (7520C/G) fragments, at various molar ratios (10:1; 5:1; 3:1; 1:1; 1:3; as well as 7520C only and 7520G only), were used as PCR templates for generation of standard curves. For each sample, PCR was run in quadruplicate and included negative control reactions, in which the reverse transcriptase was omitted during the RT step; the controls enabled us to detect potential contamination by genomic DNA.

Haplotype analysis for known CYP2A13 SNPs, methylation analysis of CYP2A13 promoter, and identification of additional SNPs in CYP2A13 5′-intergenic region

Molecular cloning and DNA sequencing were performed to identify CYP2A13 haplotypes and known SNPs (between −2 kb and 3′-UTR) that are physically linked with the 7520G variation. Additional SNPs in CYP2A13 5′-intergenic region were identified by PCR-based sequencing analysis of genomic fragments from 7520C/G heterozygotes. Details of these studies are described in the Supplemental Materials. Procedures for methylation analysis of the CYP2A13 promoter at the −1479 SNP site are also described in the Supplemental Materials.

Reporter gene assays in H441 cells

NCI-H441 human lung cancer cells (ATCC) were cultured at 37°C under 5% CO2 in RPMI1640 medium (Invitrogen) supplemented with 10% fetal bovine serum. Cells (2 × 105) were seeded into 12-well plates 24 h before transfection. For transfection, cells were washed two times with serum-free MEM and incubated with Opti-MEM (Invitrogen), prior to the addition of a luciferase reporter construct or the pGL3-Basic vector control (0.5 or 0.8 μg), and an internal control reporter plasmid (pRL-TK or pRL-SV40; 0.1 μg), premixed with serum-free MEM containing Lipofectamine 2000 (Invitrogen) or Fugene 6 reagent (Roche Applied Sciences). After 6 h, the culture medium was replaced with RPMI1640 medium containing 10% fetal bovine serum. Luciferase activities were determined 24 h after transfection, using the Luciferase Reporter Assay System (Promega).

Gel Shift Assays

Nuclear extracts from H441 cells were prepared using a CelLytic NuCLEAR Extraction Kit (Sigma, Saint Louis, MO). The resulting nuclear pellet was resuspended in 20 mM HEPES, pH 7.9, 1.5 mM MgCl2, 0.42 M NaCl, 0.2 mM EDTA, 25% glycerol, 1.0 mM DTT and a protease inhibitor cocktail (Sigma Cat.# P 8340). The nuclear extracts were stored in small aliquots at −80 °C before use. Nuclear extracts from fresh human lung tissues were prepared as described previously [13]. Oligonucleotide probes, including those with a methylated C at the −1479T>C SNP site, were synthesized by Integrated DNA Technologies. Complementary oligonucleotides were annealed, and the resulting double-stranded oligonucleotide probes were end-labeled with γ-32P-ATP (Amersham Biosciences Corp., Piscataway, NJ). Gel shift assays were carried out by incubation of 4 or 5 μg of a nuclear extract with the γ-32P-labeled DNA probes (~100,000 cpm) in a 25-μl incubation mixture containing 50 mM Tris–HCl, 10 mM MgCl2, 1 mM DTT, 1 mM EDTA, 12% glycerol, and 1.0 μg of poly(dI–dT) (Amersham Pharmacia Biotech). Unlabeled, double-stranded oligonucleotides were added, before the addition of a labeled probe, at 5-to 50-fold molar excess, as potential competitors. After incubation at room temperature for 30 min, the samples were loaded on 5% non-denaturing polyacrylamide gels that had been pre-run at 150 V for 1 h in Tris-glycine buffer. After electrophoresis at 180 V for 1 h, the gels were dried, and radioactive signals were visualized by exposure to an X-ray film (Kodak X-AR; Sigma) at −80°C for 24-36 h.

Results

The 7520C>G variation does not change the stability of CYP2A13 mRNA

The 7520C>G variation, which was previously found to be strongly associated with a low allelic expression in human lung [12], is located in the last exon of the CYP2A13 gene, and in the 3′-UTR of the CYP2A13 mRNA. To determine the cause of the low allelic expression of the CYP2A13 7520G alleles, we first tested the hypothesis that the low-expressing, 7520G-containing CYP2A13 mRNA has lower stability than does the high-expressing, 7520C-containing CYP2A13 mRNA. The rates of mRNA degradation were determined, following the addition of an RNA polymerase inhibitor, actinomycin D, in cells transiently transfected with an expression vector for CYP2A13. The results of this study (see Supplemental Materials) suggested that the 7520C>G change does not alter the stability of CYP2A13 mRNA in human lung or nasal mucosa.

Decreased allelic expression of the CYP2A13 7520G allele occurred at the transcriptional level

To test the hypothesis that the decreased allelic expression of the CYP2A13 7520G allele is due to a lowered rate of transcription, we determined the relative abundances of the primary transcripts (hnRNA) for the 7520C and 7520G alleles. The strategy for allelic-expression analysis of CYP2A13 hnRNA is outlined in Figure 1A. Because of the low abundance of hnRNAs, nested-PCR was carried out, to increase detection sensitivity. The allelic hnRNA expression analysis was performed for RNA samples isolated from normal lung tissues of nine 7520C/G subjects (Table 1); the tissue samples were previously found to exhibit substantially decreased expression of the 7520G allele at the mRNA level [12]. As shown in Table 1, the ratios of the relative hnRNA levels of the two alleles (7520C:7520G), as estimated from the peak-height ratios of the two respective PCR products, were greater than 10 for all nine lung samples tested using either the 7520C or the 7520G hybridization probe; this result indicated essentially monoallelic expression of the 7520C allele. An example of the melting curves of hnRNA-PCR products generated from the 7520C/G samples is shown in Figure 1 (B and C). In control experiments, PCR products derived either from genomic DNA of 7520C/G heterozygous lung samples (Fig. 1B) or from a 1:1 mixture of standard 7520C and 7520G templates (Fig. 1B and 1C), were also analyzed; these control samples each yielded two peaks representing the two alleles, in contrast to the single peak detected in the hnRNA-PCR products. In negative control experiments (not shown), in which the reverse transcriptase was omitted, no product was detected, indicating negligible levels of genomic DNA contamination in the reverse-transcribed cDNA preparation. Plots of the ratios of the maximum 7520G and 7520C peak heights on the melting curve versus the ratios of standard 7520G and 7520C template concentrations were linear (not shown), with R2 values being greater than 0.997 for all analyses. Taken together, these data demonstrated that the decreased expression of the 7520G allele is manifested at the transcriptional, rather than the post-transcriptional, level.

Fig. 1
Allelic expression analysis for CYP2A13 hnRNA. A. Strategy for allelic expression analysis of CYP2A13 hnRNA. DNase-treated total RNA was reverse-transcribed (RT), and the resulting first-strand cDNA fragments that contain the CYP2A13 7520C/G variation ...
Table 1
Relative levels of CYP2A13 −7520C and CYP2A13 −7520G primary transcripts in human lung tissuesa

Functional Analysis of the −1479T>C variation

Haplotype analysis for SNPs previously identified within the CYP2A13 gene and the proximal 2-kb promoter region of 16 7520C/G heterozygotes [12] indicated that the 7520C>G variation is physically linked to −1479T>C and −1240A>G in the CYP2A13*1H, *1N, *1P, and *8B alleles (see Supplemental Materials). Database analysis (TFsearch: http://www.cbrc.jp/research/db/TFSEARCH.html) for potential transcription factor binding sites in CYP2A13 5′-flanking region indicated that −1479T>C, but not −1240A>G, lies within the sequence that composes putative binding sites for several regulatory proteins, including the POU factor Brn-2 [15], at 81.2% identity, the cut-like homeodomain protein [16], at 79% identity, and the transcriptional repressor CDP [17], at 76.5% identity. Therefore, −1479T>C was selected for subsequent functional analysis.

To determine whether the −1479T>C change alters the binding of putative transcription factors, we performed gel-shift assays using nuclear extracts prepared from human lung. A broad, but faint, shift band, suggesting the occurrence of multiple protein binding complexes, was detected with the −1479T probe, whereas a single, strong, shift band, with a size approximating that of the band detected by the −1479T probe, was detected with the −1479C probe (Fig. 2A). Binding specificity was confirmed by competition with excess unlabeled probe.

Fig. 2
Functional analysis of the −1479T>C variation. A. Gel shift assays. Nuclear extracts (5 μg) from human lung were incubated with 32P-labeled −1479T, −1479C, or methylated −1479C (−1479MeC) oligonucleotide ...

The −1479T>C change creates a new CpG site, a potential target for DNA methylation. To determine whether methylation of the allele-specific CpG site at −1479 alters the binding of transcription factors, we also performed gel-shift assays using labeled, methylated −1479C probe and corresponding unlabeled, methylated competitor (Fig. 2B). Similar to the un-methylated probe, the methylated probe formed specific DNA-protein complexes with human lung nuclear extract; however, the complexes formed appeared as faint duplex bands, in contrast to the single predominant band formed with the unmethylated −1479C probe (Fig. 2A). These results suggested that methylation of −1479C interferes with interactions of the site with nuclear proteins in human lung.

To confirm the anticipated negative effects of the −1479T>C variation on promoter activity, we performed reporter gene assays in H441 cells, a human lung adenocarcinoma epithelial cell line, using promoter constructs containing either −1479T or −1479C (Fig. 2C). Furthermore, to determine whether the methylation status of the allele-specific CpG site at −1479 affects CYP2A13 promoter activity, we also conducted reporter gene assays using a methylated CYP2A13 promoter construct containing either a T or a C at −1479 (Fig. 2C). We found the two constructs to be completely methylated in vitro, at all C-nucleotides, as confirmed by restriction analysis with a methylation-sensitive endonuclease BstU I, which cut the un-methylated constructs at multiple sites, but did not cut the methylated constructs (data not shown). As shown in Figure 2D, the −1479T>C variation led to a small (15%), but statistically significant (p<0.05), decrease in promoter activity in H441 cells, in the absence of promoter methylation. General C-methylation of the promoter constructs led to substantial deceases in promoter activity, regardless of whether the nucleotide at −1479 was a T or a C. However, the −1479T>C change was accompanied by a 32% decrease in promoter activity when the promoter was methylated; this extent of decrease was 2-fold higher than that seen with unmethylated promoter constructs.

To determine whether the allele-specific CpG site at −1479 is methylated in human lung, we first performed methylation-sensitive sequencing for DNA samples from four −1479T/C individuals. The bisulfite-induced change of un-methylated C to T was complete under the assay conditions used, as indicated by the total conversion of −1481C, −1472C, and −1471C to T (Fig. 3, panels A and B). However, −1479C persisted after bisulfite treatment (Fig. 3, panel B). We conclude that the −1479C was at least partially methylated in human lung.

Fig. 3
Methylation analysis of the 7520G allele-specific CpG site at −1479. The sequence was determined for a 7520C/G lung sample (P5 in Table 1). Genomic DNA was either untreated (A), or pretreated with bisulfite to convert un-methylated C to T (B), ...

Taken together, these findings indicate that the allele-specific CpG site at −1479, which is at least partially methylated in human lung, contributes to the decreased allelic expression of the CYP2A13 gene. Nevertheless, it was clear that the observed extent of decrease in promoter activity could not totally account for the more than 10-fold difference in allelic expression of the 7520C/G alleles in human lung. Furthermore, the −1479T>C change was also a part of the *1O allele (see Supplemental Materials, Table S2); the individual harboring the *1O allele had a *1O/*1N genotype, and the 7520G-containing *1N allele had lower expression than did the *1O allele. Therefore, the −1479T>C change alone appears insufficient to decrease the allelic expression to the extent observed for 7520G-containing alleles. Consequently, we considered, in our further studies, the possibility that additional cis-regulatory polymorphisms, located in the regions farther upstream of the 2-kb 5′-flanking region of the CYP2A13 gene, contribute to the decreased expression of the 7520G allele.

Identification of additional polymorphisms linked to the 7520G allele

To identify additional polymorphisms in the CYP2A13 5′-flanking region, we sequenced the region from −1676 to −25723 bp, for three 7520C/G individuals (P2, P5, and A10 in Table 1) and, as a control, one 7520C/C individual. A total of 10 common SNPs were identified for the three heterozygotes (Table 2); none of the 10 SNPs was found in the 7520C/C individual. Database analysis for potential transcription factor binding sites, with a threshold consensus score of 70, revealed that each of the 10 common SNPs could lead to allele-differential binding for one or more transcription factors, some of which are lung-enriched transcription factors (Table 2).

Table 2
Common SNPs identified in CYP2A13 7520C/G individuals a

The 10 SNPs are all found in the DB-SNP database (http://www.ncbi.nlm.nih.gov/projects/SNP/), and two of them (−3101T>G and −7756G>A) are also represented on the HapMap (http://www.hapmap.org/cgi-perl/gbrowse/hapmap_B36/). The −3101T>G and −7756G>A SNPs are in linkage disequilibrium (LD) (with a LOD score of 12.2; HapMap). Physical linkage between these SNPs and the 7520C/G variation has not been examined; the 7520C>G variation is not yet represented on the current version of HapMap. However, the common occurrence of the 10 SNPs among the three 7520C/G individuals, and the SNPs’ absence in the 7520C/C individual, suggested that these polymorphisms are likely in LD with the 7520C>G variation. Further genotypic analysis of nine additional 7520C/G individuals and three additional 7520C/C individuals for the −3101T>G and −7756G>A SNP sites, sites for which allele frequencies had been found previously to vary from 0% to 29% in differing populations (HapMap), confirmed significant association among −3101T>G, −7756G>A, and 7520C>G SNPs (P<0.001; Fisher’s Exact test). Taken together, these data suggested that the −3101T>G and −7756G>A SNPs, and most likely also the other eight common SNPs, are linked with the 7520C>G SNP.

Allele-differential binding of nuclear proteins to −3101T/G and −7756G/A in gel-shift assays

To determine whether the common SNPs identified in the 5′-flanking region alter the binding of transcription factors, we performed gel-shift assays for the 10 SNPs using nuclear extracts prepared from H441 cells, which are known to support CYP2A13 expression after a combined treatment with AzaC and TSA [13]. Probes containing −3101T>G, −7756G>A (Fig 4), −4729 C>T, or −6495C>T (data not shown) revealed allelic differential binding by nuclear proteins, whereas probes containing the other SNPs either did not form any protein-binding complex under the conditions used, or else did not show differential binding by nuclear proteins (data not shown). The −3101T probe formed three binding complexes, whereas the −3101G probe generated binding complexes that were barely detectable (Fig. 4A), indicating greatly diminished binding affinity. The three complexes formed by the −3101T probe were all competed by the addition of a 50-fold excess amount of unlabeled probe (data not shown), which confirmed that the three complexes detected were all specific. Both −7756A and −7756G probes gave rise to a single gel-shift band; although the band intensity was lower for the −7756A probe than for the −7756G probe (Fig 4B), the allele-related differential binding was not as remarkable as was observed for the −3101T/G probes. In order to rule out the possibility that the difference in the band intensities is due to variations in labeling efficiency, rather than differences in intrinsic binding affinity, we performed reciprocal competition assays. We found that, no matter which labeled probe was used, the −7756G competitor was always more effective than was the −7756A competitor (Fig. 4B). The DNA probes for the −7756 SNP included sequences that resemble a cAMP-response element binding (CREB) sequence. However, an oligonucleotide containing the CREB consensus sequence was not able to compete for nuclear protein binding to the −7756 probes, a result indicating that other, unidentified transcription factors must be involved (data not shown).

Fig. 4
Gel-shift assays using DNA probes containing −3101T>G (A) or −7756G>A (B) variations. Nuclear extracts (4 μg) from H441 cells were incubated with 32P-labeled oligonucleotide probes. Unlabeled probes were added at ...

Additive effects of −1479T>C, −3101T>G, and −7756G>A variants on CYP2A13 promoter activity

We used transient transfection and reporter gene assays to investigate the individual effects of the −3101T>G and −7756G>A variations, as well as combined effects of the −1479T>C, −3101T>G, and −7756G>A variations, on CYP2A13 promoter activity in H441 cells. A DNA fragment containing one, two, or all three of the SNP sites was inserted upstream of a 245-bp CYP2A13 promoter-luciferase vector [13], and the luciferase activity was then compared among cells transfected with differing CYP2A13 promoter constructs. As shown in Figure 5, the construct containing −3101G or −7756A had, respectively, 19% or 25% lower promoter activities than did the construct containing −3101T or −7756G, whereas the construct containing the −3101G/−7756A double mutation had ~45% lower promoter activity than did the construct containing −3101T/−7756G. Furthermore, the construct containing the −1479C/−3101G/−7756A triple mutation had 56% lower activities than did the construct containing −1479T/−3101T/−7756G. Together with the aforementioned demonstration of allelic differential protein binding, these data suggested not only that the three SNPs are located in or near the sequence comprising a transcriptional factor binding site, but also that the sequence changes hinder the function of the relevant transcription factors. Moreover, the resultant negative effects of the three SNPs on CYP2A13 promoter activity are additive.

Fig. 5Fig. 5
Reporter gene assays for CYP2A13 promoter constructs containing −1479T>C, −3101T>G, and −7756G>A variations. A. Structure of the CYP2A13 promoter constructs. The constructs, prepared in the pGL3_Basic vector, ...

Discussion

Allelic variation in gene expression appears to be common in the human genome [18,19]. For P450 genes, allelic differential expression has been reported for CYP3A4 [20] and CYP3A5 [21], in addition to CYP2A13 [12, 22]. Knowledge of SNPs uniquely associated with a high- or low-expressing allele (i.e., marker SNPs) could provide a means by which to predict, based on genotyping analysis, the relative total expression levels of the gene in a study population. Furthermore, information on the identity of the SNPs that are responsible for the differing expression levels between two given alleles (i.e., causative SNPs) would shed light on the molecular mechanisms underlying the variable gene expression.

Previously, we had developed a PCR-based allelic expression assay, through which we discovered that the 7520C>G variation is associated with decreased (>10-fold) CYP2A13 allelic expression [12]. In the present studies, we have further extended the assay to allelic expression analysis of the CYP2A13 hnRNA, an approach that allowed us to conclude that the decreased expression of the 7520G allele is occurring at the level of transcription. Our real-time PCR-based method for quantitative allelic mRNA or hnRNA expression analysis combines melting-curve analysis with the use of allele-specific hybridization probes [12]. Several other methods have been developed for allelic mRNA expression analysis [e.g., 23,24]. A semi-quantitative method for allelic hnRNA expression analysis was described recently for determination of relative expression levels of two CYP3A4 alleles in human liver [20]. Notably, allelic hnRNA expression analysis is technically challenging, given the much lower abundance of hnRNA than that of mRNA; however, it can substantially enhance the capability to perform allelic expression analysis, in that it makes it possible to determine relative expression levels for most, if not all, SNPs located either in the exons or in the introns. Additional discussions on allelic expression analysis are included in Supplemental Materials.

Our finding, that the 7520C>G change, which occurs in the 3′-UTR, does not lead to altered mRNA stability, suggests that the 7520C>G SNP is a marker for, rather than a cause of, the decreased expression of the 7520G allele. This notion is consistent with the finding of allelic hnRNA expression analysis, namely, that the decreased expression of the 7520G allele occurred at the level of transcription. Subsequent search for causative SNPs in the 5′-flanking region led to the identification of −1479T>C, −3101T>G, and −7756G>A, all of which are associated with altered DNA-protein binding in gel-shift assays and decreased CYP2A13 promoter activity in reporter gene assays. It is noteworthy that, although the extents of decreases in promoter activities in reporter constructs containing a single SNP were all relatively low, an additive effect was seen among −1479T>C, −3101T>G and −7756G>A, while the effect of the −1479T>C change was enhanced by methylation of the −1479C. Thus, the evidence supporting the designation of −1479T>C, −3101T>G, and −7756G>A as causative SNPs for the low expression of the 7520G allele is compelling, even though we cannot exclude the possibility that additional causative SNPs occur further upstream or elsewhere in the surrounding genomic regions.

Based on our present findings, we propose that the CYP2A13 promoter in the 7520G allele is suppressed by the cumulative effects of several causative SNPs located in proximal, as well as distal, 5′-flanking regions of the gene. It seems reasonable to assume that occurrence of only a single causative SNP is insufficient to induce a substantial decrease in CYP2A13 expression, an assumption supported by the fact that the −1479T>C change is also a part of the *1O allele; the latter, which does not contain the 7520C>G change, has higher expression than does the 7520G-containing *1N allele. It remains to be determined whether this model of transcriptional modulation by multiple cis-regulatory SNPs is operative in other CYP2A13 alleles or other CYP genes. Unquestionably, for a mechanism involving the interplay of multiple SNPs, causality will be much harder to establish than in a situation in which only a single SNP is operative. Furthermore, the protein factors that interact with the identified causative SNPs have yet to be identified. In that context, it will be interesting to determine whether proteins binding at these three causative SNPs interact with the C/EBP factors that were recently found to activate regulatory elements at the proximal region of the CYP2A13 promoter [13].

Our recent study [13], also demonstrated that DNA methylation is involved in the silencing of the CYP2A13 gene in H441 cells, a result indicating that DNA methylation may play a role in transcriptional regulation of the CYP2A13 gene. DNA methylation has been found to be associated with differential allelic expression in other studies [20,25], although, for methylation at a given site, it is not always obvious whether the methylation actually contributes to the differential allelic expression, or else whether the methylation is merely a consequence of decreased promoter activity. Here, we have discovered not only that the allele-specific CpG site at −1479 upstream of the CYP2A13 gene, known to be associated with the low-expressing 7520G allele, is at least partially methylated in human lung tissues, but also that in vitro methylation at this site leads to altered nuclear protein binding in gel-shift assays, and a reduction in relative promoter activity in reporter gene assays. Therefore, methylation at the allele-specific −1479C likely contributed to the decreased expression of the 7520G allele.

In conclusion, we have successfully adapted our original allelic gene expression analysis method to the analysis of relative hnRNA levels. Through the application of this new approach, as well as through studies on mRNA stability, we have found that the CYP2A13 7520C>G variation is likely a marker, but not a causative SNP, for low CYP2A13 expression. We have further identified three causative SNPs at the 5′-flanking region of the low-expressing CYP2A13 7520G allele; our results indicate that the substantially decreased expression of the 7520G allele is caused by probably additive effects of these genetic variations, as well as allele-specific methylation at the −1479C. The discovery of these causative SNPs could eventually lead to the identification of additional transcription factors involved in the regulation of CYP2A13 expression, and the knowledge of the marker and causative SNPs for this common, low-expressing CYP2A13 allele will facilitate future epidemiological studies designed to associate genetic variations that affect CYP2A13 expression or function and lung cancer risks. In this context, there is a remarkable interindividual difference in the susceptibility to smoking-induced lung cancer, as exemplified by the fact that only one in nine smokers develops lung cancer [26]. CYP2A13 expression levels in human lung biopsy samples also vary, by >100 fold [6,12]. Thus, for a determination of whether CYP2A13 plays an important role in procarcinogen activation and smoking-induced carcinogenesis in the human lung, efforts to identify the “expression phenotypes” for other common CYP2A13 alleles are warranted.

Supplementary Material

Acknowledgments

We gratefully acknowledge the use of the services of the Molecular Genetics Core Facility of the Wadsworth Center. We thank Dr. Adriana Verschoor for reading the manuscript.

This work was supported in part by U.S. Public Health Service grant CA092596 from the National Institutes of Health.

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