Functional Evaluation of Genetic and Environmental Regulators of P450 mRNA Levels

Variations in the activities of Cytochrome P450s are one of the major factors responsible for inter-individual differences in drug clearance rates, which may cause serious toxicity or inefficacy of therapeutic drugs. Various mRNA level is one of the key factors for different activity of the major P450 genes. Although both genetic and environmental regulators of P450 gene expression have been widely investigated, few studies have evaluated the functional importance of cis- and trans-regulatory factors and environmental factors in the modulation of inter-individual expression variations of the P450 genes. In this study, we measured the mRNA levels of seven major P450 genes (CYP1A1, CYP1A2, CYP2C9, CYP2C19, CYP2D6, CYP3A4 and CYP3A5) in 96 liver biopsy samples from Chinese population. Both trans-acting (mRNA levels and non-synonymous SNPs of putative regulator genes) and cis-acting (gene copy number and functional SNPs) factors were investigated to identify the determinants of the expression variations of these seven P450 genes. We found that expression variations of most P450 genes, regulator genes and housekeeping genes were positively correlated at the mRNA level. After partial correlation analysis using ACTB and GAPDH expression to eliminate the effect of global regulators, a UPGMA (Unweighted Pair Group Method with Arithmetic Mean) tree was constructed to reveal the effects of specific regulation networks potentially masked by global regulators. Combined with the functional analysis of regulators, our results suggested that expression variation at the mRNA level was mediated by several factors in a gene-specific manner. Cis-acting genetic variants might play key roles in the expression variation of CYP2D6 and CYP3A5, environmental inducers might play key roles in CYP1A1 and CYP1A2 variation and global regulators might play key roles in CYP2C9 variation. In addition, the functions of regulators that play less important roles in controlling expression variation for each P450 gene were determined

Polymorphisms in the ADRB2 gene and Graves disease: a case-control study and a meta-analysis of available evidence

<p>Abstract</p> <p>Background</p> <p>The beta-2-Adrenergic receptor (<it>ADRB2</it>) gene on chromosome 5q33.1 is an important immunoregulatory factor. We and others have previously implicated chromosomal region 5q31-33 for contribution to the genetic susceptibility to Graves disease (GD) in East-Asian populations. Two recent studies showed associations between the single nucleotide polymorphism (SNP) rs1042714 in the <it>ADRB2 </it>gene and GD. In this study, we aimed to fully investigate whether the <it>ADRB2 </it>gene conferred susceptibility to GD in Chinese population, and to perform a meta-analysis of association between <it>ADRB2 </it>and GD.</p> <p>Methods</p> <p>Approximately 1 kb upstream the transcription start site and the entire coding regions of the <it>ADRB2 </it>gene were resequenced in 48 Han Chinese individuals to determine the linkage disequilibrium (LD) patterns. Tag SNPs were selected and genotyped in a case-control collection of 1,118 South Han Chinese subjects, which included 428 GD patients and 690 control subjects. A meta-analysis was performed with the data obtained in the present samples and those available from prior studies.</p> <p>Results</p> <p>Fifteen SNPs in the <it>ADRB2 </it>gene were identified by resequencing and one SNP was novel. Ten tag SNPs were investigated further to assess association of <it>ADRB2 </it>in the case-control collection. Neither individual tag SNP nor haplotypes showed association with GD in Han Chinese population (P > 0.05). Our meta-analysis of the <it>ADRB2 </it>SNP rs1042714 measured heterogeneity between the ethnic groups (I²= 53.1%) and no association to GD was observed in the overall three studies with a random effects model (OR = 1.13, 95% CI, 0.95 to 1.36; P = 0.18). However, significant association was found from the combined data of Caucasian population with a fixed effects model (OR = 1.18, 95% CI, 1.06 to 1.32; P = 0.002; I²= 5.9%).</p> <p>Conclusion</p> <p>Our study indicated that the <it>ADRB2 </it>gene did not exert a substantial influence on GD susceptibility in Han Chinese population, but contributed to a detectable GD risk in Caucasian population. This inconsistency resulted largely from between-ethnicity heterogeneity.</p

Gene-Wide Characterization of Common Quantitative Trait Loci for <em>ABCB1</em> mRNA Expression in Normal Liver Tissues in the Chinese Population

<div><p>In order to comprehensively screen genetic variants leading to differential expression of the important human <em>ABCB1</em> gene in the primary drug-metabolizing organ, <em>ABCB1</em> mRNA expression levels were measured in 73 normal liver tissue samples from Chinese subjects. A set of Tag SNPs. were genotyped. In addition, imputation was performed within a 500 kb region around the <em>ABCB1</em> gene using the reference panels of 1,000 Genome project and HapMap III. Bayesian regression was used to assess the strength of associations by compute Bayes Factors for imputed SNPs. Through imputation and linkage disequilibrium analysis, the imputed loci rs28373093, rs1002205, rs1029421, rs2285647, and rs10235835, may represent independent and strong association signals. rs28373093, a polymorphism 1.5 kb upstream from the <em>ABCB1</em> transcription start site, has the strongest association. 2677 G>A/T and 3435C>T confer a clear gene-dosage effect on <em>ABCB1</em> mRNA expression. The systematic characterization of gene-wide common quantitative trait loci associated with <em>ABCB1</em> mRNA expression in normal liver tissues would provide the candidate markers to ABCB1-relevant clinical phenotypes in Chinese population.</p> </div

Allele specific <i>ABCB1</i> mRNA expression in normal liver samples and the phases of Tag SNPs with significant associations.

<p>In the upper panel, allelic expression ratios of samples heterozygous for at least one marker SNP are presented by bar plots. Each allelic expression ratio was independently measured in triplicate using SNaPshot. In the lower panel, each pair of columns represents the two phases of associated Tag SNPs in each sample heterozygous for marker SNP. Alleles associated with higher gene expression are denoted in pink, and alleles associated with reduced expression in cyan.</p

LD plot of SNPs with top-ranked BFs in CHB of 1000 Genome Phase I.

<p>The colors indicate the strength of pairwise LD according to <i>r</i>² metrics. The SNPs marked with asterisks represent independent strong associations. Tag SNPs are shadowed in pink.</p

Multi-SNP results of Bayesian analyses.

<p>(A) BF values of pairwise loci combinations in Multi-SNP analyses. The colors are corresponding to BFs. (B) BF values and posterior probabilities for different multi-SNP combinations. Means of BFs corresponding to different SNP combinations are charted in line, and means of posterior probabilities in bars.</p

Allelic expression ratios resulted from collaborative effects of different alleles of multiple functional SNPs.

<p>Allele M1 and M2 of the marker SNP indicating AEI correspond to the alleles of single <i>cis</i>-acting SNP or the haplotypes consisting of multiple <i>cis</i>-acting SNPs which are in the same phase with M1 and M2. Positive-effect alleles associated with high gene expression are denoted in pink, and negative-effect alleles associated with low expression are denoted in cyan. In the left panel, allelic expression ratios clearly indicate the effect of single <i>cis</i>-acting SNP. In the right panel, allelic expression ratios are blurred by multiple <i>cis</i>-acting effects.</p