Human genetic variation of CYP450 superfamily: analysis of functional diversity in worldwide populations

VDR promotes testosterone synthesis in mouse Leydig cells via regulation of cholesterol side chain cleavage cytochrome P450 (Cyp11a1) expression

BACKGROUND

The vitamin D receptor (VDR) mediates the pleiotropic biological actions that include osteoporosis, immune responses and androgen synthesis.VDR is widely expressed in testis cells such as Leydig cells, Sertoli cells, and sperm. The levels of steroids are critical for sexual development. In the early stage of steroidogenesis, cholesterol is converted to pregnenolone (precursor of most steroid hormones) by cholesterol side-chain lyase (CYP11A1), which eventually synthesizes the male hormone testosterone.

OBJECTIVE

This study aims to reveal how VDR regulates CYP11A1 expression and affects testosterone synthesis in murine Leydig cells.

METHODS

The levels of VDR, CYP11A1 were determined by quantitative real-time polymerase chain reaction (RT-qPCR) or western blot. Targeted relationship between VDR and Cyp11a1 was evaluated by dual-luciferase reporter assay. The levels of testosterone concentrations in cell culture media serum by enzyme-linked immunosorbent assay (ELISA).

RESULTS

Phylogenetic and motif analysis showed that the Cyp11a1 family had sequence loss, which may have special biological functions during evolution. The results of promoter prediction showed that vitamin D response element (VDRE) existed in the upstream promoter region of murine Cyp11a1. Dual-luciferase assay confirmed that VDR could bind candidate VDREs in upstream region of Cyp11a1, and enhance gene expression. Tissue distribution and localizatio analysis showed that Cyp11a1 was mainly expressed in testis, and dominantly existed in murine Leydig cells. Furthermore, over-expression VDR and CYP11A1 significantly increased testosterone synthesis in mice Leydig cells.

CONCLUSIONS

Active vitamin D3 (VD3) and Vdr interference treatment showed that VD3/VDR had a positive regulatory effect on Cyp11a1 expression and testosterone secretion. VDR promotes testosterone synthesis in male mice by up-regulating Cyp11a1 expression, which played an important role for male reproduction.

Functional variant rs10175368 which affects the expression of CYP1B1 plays a protective role against breast cancer in a Chinese Han population

OBJECTIVE

Cytochrome P450 1B1 ( CYP1B1 ) genetic variants are relevant in the pathogenesis of breast cancer. Exploring the relationships between CYP1B1 functional variants and breast cancer could improve our understanding of breast cancer molecular pathophysiology.

METHODS

This is a two-stage hospital-based case-control study of a Chinese Han population. Genotyping was performed to identify candidate gene variants. 3DSNP, ANNOVAR, and RegulomeDB were used to determine functional single nucleotide polymorphisms (SNPs). The relationship between candidate variants and breast cancer risk was evaluated through unconditional logistic regression analysis. The PancanQTL platform was used to perform cis and trans expression quantitative trait loci (eQTL) analysis of positive SNPs. The GSCA platform was then used to compare the gene expression levels of potential target genes between breast cancer tissue and normal tissue adjacent to the cancer.

RESULTS

rs10175368-T acted as a protective factor against breast cancer based on an additive model [odds ratio (OR) = 0.722, 95% confidence interval (CI) = 0.613-0.850; P < 0.001], and was identified as a protective factor in the postmenopausal population (OR = 0.601; 95% CI, 0.474-0.764; P < 0.001). eQTL analysis and analysis of differential expression in carcinoma and paracancerous tissues revealed that the expression level of CYP1B1 - AS1 was associated with rs10175368 and that CYP1B1-AS1 had significantly higher expression levels in breast cancer tissues than in paracancerous tissues.

CONCLUSION

We show, for the first time in a Chinese Han population, that the functional variant rs10175368 plays a protective role against breast cancer, especially in the postmenopausal population.

Occupational risk of organophosphates and other chemical and radiative exposure in the aircraft cabin: A systematic review

Occupational exposure to oil fumes, organophosphates, halogenated flame retardants, and other volatile and semi-volatile contaminants is a concern within the aviation industry. There is no current consensus on the risk attributed to exposure to these chemical classes within the aircraft cabin. Contaminant concentrations rarely exceed conventional air quality guidelines, but concerns have been raised about these guidelines' applicability within the aircraft environment. This systematic review, the largest and most comprehensive completed to date on the subject matter, aims to synthesize the existing research related to chemical and other exposures inside the aircraft cabin to determine the occupational risk that may be attributed said exposure, as well as, determine knowledge gaps in source, pathway, and receptor that may exist. The Science Direct, Scopus, and Web of Science databases were queried with five search terms generating 138 manuscripts that met acceptance criteria and screening. Several potential areas requiring future examination were identified: Potable water on aircraft should be examined as a potential source of pollutant exposure, as should air conditioning expansion turbines. Historical exposure should also be more fully explored, and non-targeted analysis could provide valuable information to comprehend the aircraft cabin exposome. Occupational risk under typical flight scenarios appears to be limited for most healthy individuals. Contaminants of concern were demonstrated to be extant within the cabin, however the concentrations under normal circumstances do not appear to be individually responsible for the symptomologies that are present in impacted individuals. Questions remain regarding those that are more vulnerable or susceptible to exposure. Additionally, establishing the effects of chronic low dose exposure and exposure to contaminant mixtures has not been satisfied. The risk of acute exposure in mitigable fume events is substantial, and technological solutions or the replacement of compounds of concern for safer alternatives should be a priority.

In Vitro Metabolism of Six C-Glycosidic Flavonoids from Passiflora incarnata L

Several medical plants, such as Passiflora incarnata L., contain C-glycosylated flavonoids, which may contribute to their efficacy. Information regarding the bioavailability and metabolism of these compounds is essential, but not sufficiently available. Therefore, the metabolism of the C-glycosylated flavones orientin, isoorientin, schaftoside, isoschaftoside, vitexin, and isovitexin was investigated using the Caco-2 cell line as an in vitro intestinal and epithelial metabolism model. Isovitexin, orientin, and isoorientin showed broad ranges of phase I and II metabolites containing hydroxylated, methoxylated, and sulfated compounds, whereas schaftoside, isoschaftoside, and vitexin underwent poor metabolism. All metabolites were identified via UHPLC-MS or UHPLC-MS/MS using compound libraries containing all conceivable metabolites. Some structures were confirmed via UHPLC-MS experiments with reference compounds after a cleavage reaction using glucuronidase and sulfatase. Of particular interest is the observed cleavage of the C–C bonds between sugar and aglycone residues in isovitexin, orientin, and isoorientin, resulting in unexpected glucuronidated or sulfated luteolin and apigenin derivatives. These findings indicate that C-glycosidic flavones can be highly metabolized in the intestine. In particular, flavonoids with ortho-dihydroxy groups showed sulfated metabolites. The identified glucuronidated or sulfated aglycones demonstrate that enzymes expressed by Caco-2 cells are able to potentially cleave C–C bonds in vitro.

Han Chinese specific cytochrome P450 polymorphisms and their impact on the metabolism of anti-hypertensive drugs with adrenoreceptor blocking properties

Introduction: Cytochrome P450 (CYP) is a monooxygenase superfamily mediating the elimination of anti-hypertensive drugs. Polymorphisms of CYP would lead to differential drug efficacy. Building relationships between genotype and phenotype will benefit individual medical treatment of hypertension.Areas covered: The review systematically summarizes the polymorphisms of four CYPs (CYP2C9, CYP2C19, CYP2D6, and CYP3A4) concentrated distributed in the Han Chinese population. Moreover, the activity of variants on metabolizing anti-hypertensive drugs are reviewed, especially drugs with adrenoceptor blocking properties, as well as their clinical relevancies.Expert opinion: The polymorphisms of CYP can cause stratification in drug exposure of antihypertensive drugs. Although the clinical relevance has been built partially, the translational medicine still lacks reliable data support. Furthermore, the studies have demonstrated that even the same CYP variant will exhibit different catalytic capability for different drugs, which is another obstacle to hinder its application. With the deepening of multiomics research and structural biology, nucleotide polymorphisms can be combined with transcriptome, proteome, metabolome and molecular structure analyses to study the susceptibility to hypertension and drug efficacy. A complete data chain would be further estabolished by combining studies of pharmacokinetics-pharmacodynamics, which can effectively promote the precise application of anti-hypertensive drugs.

Racial Disparity in Drug Disposition in the Digestive Tract

The major determinants of drug or, al bioavailability are absorption and metabolism in the digestive tract. Genetic variations can cause significant differences in transporter and enzyme protein expression and function. The racial distribution of selected efflux transporter (i.e., Pgp, BCRP, MRP2) and metabolism enzyme (i.e., UGT1A1, UGT1A8) single nucleotide polymorphisms (SNPs) that are highly expressed in the digestive tract are reviewed in this paper with emphasis on the allele frequency and the impact on drug absorption, metabolism, and in vivo drug exposure. Additionally, preclinical and clinical models used to study the impact of transporter/enzyme SNPs on protein expression and function are also reviewed. The results showed that allele frequency of the major drug efflux transporters and the major intestinal metabolic enzymes are highly different in different races, leading to different drug disposition and exposure. The conclusion is that genetic polymorphism is frequently observed in different races and the related protein expression and drug absorption/metabolism function and drug in vivo exposure can be significantly affected, resulting in variations in drug response. Basic research on race-dependent drug absorption/metabolism is expected, and FDA regulations of drug dosing adjustment based on racial disparity are suggested.

Probing prodrug metabolism and reciprocal toxicity with an integrated and humanized multi-tissue organ-on-a-chip platform

Current drug development techniques are expensive and inefficient, partially due to the use of preclinical models that do not accurately recapitulate in vivo drug efficacy and cytotoxicity. To address this challenge, we report on an integrated, in vitro multi-organoid system that enables parallel assessment of drug efficiency and toxicity on multiple 3D tissue organoids. Built in a low-cost, adhesive film-based microfluidic device, these miniaturized structures require less than 200 µL fluid volume and are amenable to both matrix-based 3D cell culture and spheroid aggregate integration, each supported with an in situ photocrosslinkable hyaluronic acid hydrogel. Here, we demonstrate this technology first with a three-organoid device consisting of liver, cardiac, and lung constructs. We show that these multiple tissue types can be kept in common circulation with high viability for 21 days and validate the platform by investigating liver metabolism of the prodrug capecitabine into 5-fluorouracil (5-FU) and observing downstream toxicity in lung and cardiac organoids. Then we expand the integrated system to accommodate six humanized constructs, including liver, cardiac, lung, endothelium, brain, and testes organoids. Following a 14-day incubation in common media, we demonstrate multi-tissue interactions by metabolizing the alkylating prodrug ifosfamide in the liver organoid to produce chloroacetaldehyde and induce downstream neurotoxicity. Our results establish an expandable, multi-organoid body-on-a-chip system that can be fabricated easily and used for the accurate characterization of drug interactions in vitro. STATEMENT OF SIGNIFICANCE: The use of 3-dimensional (3D) in vitro models in drug development has advanced over the past decade. However, with several exceptions, the majority of research studies using 3D in vitro models, such as organoids, employ single tissue types, in isolated environments with no "communication" between different tissues. This is a significant limiting factor because in the human body there is significant signaling between different cells, tissues, and organs. Here we employ a low-cost, adhesive film-based microfluidic device approach, paired with a versatile extracellular matrix-derived hyaluronic acid hydrogel to support integrated systems of 3 and 6 3D organoid and cell constructs. Moreover, we demonstrate an integrated response to drugs, in which downstream toxicity is dependent on the presence of liver organoids.

Defining screening panel of functional variants of CYP1A1, CYP2C9, CYP2C19, CYP2D6, and CYP3A4 genes in Serbian population

Plethora of drugs and toxic substances is metabolized by cytochrome P450 enzymes (CYP450). These enzymes are coded by highly variable genes abundant with single nucleotide variants (SNVs) and small insertions/deletions (indels) that affect the functionality of the enzymes, increasing or decreasing their activity. CYP genes genotyping, followed by haplotype inference, provides substrate specific metabolic phenotype prediction. This is crucial in pharmacogenetics and applicable in molecular autopsy. However, high number of alleles in CYP450 superfamily and interethnic variability in frequency distribution require precise gene panel customization. To estimate informativeness of SNVs and alleles in CYP gene families 1, 2, and 3, associated with metabolic alterations, 500 unrelated individuals from 5 regions of Serbia were genotyped using TaqMan assays to determine frequencies of CYP2C9 *2 and *3, CYP2C19 *2 and *17 alleles, four variants in CYP2D6 (rs3892097, rs1065852, rs28371725, rs28371706) gene, and CYP3A4*1B allele. In addition, CYP1A1 rs4646903 and rs1048943 (m1 and m2) variants were genotyped by RFLP. Our results showed that frequencies of tested variants in Serbian population corresponded to general European population and somewhat differed from neighboring populations. SNV rs1065852, the main contributor to non-functional CYP2D6 *4, significantly departed from Hardy-Weinberg equilibrium. With the exception of rs28371706 in CYP2D6 and rs2740574 in CYP3A4, which were very rare in our sample, all other tested variants in CYP2 family are informative and appropriate for pharmacogenetic testing, molecular autopsy, and medico-legal genetic analyses.

Diversity In Precision Medicine And Pharmacogenetics: Methodological And Conceptual Considerations For Broadening Participation

Genome-wide association studies (GWAS) have revealed important links between genetic markers across the human genome and phenotypic traits, including risk factors for disease. Studies have shown that GWAS continue to be overwhelmingly conducted on people of primarily European descent, despite the fact that the vast majority of human genomic variation is present in non-European populations such as those in Africa. To enhance our understanding of diversity in the pharmacogenomics and precision medicine literature, this review provides a window into the representation of biogeographical populations that have been studied for pharmacogenetic traits, such as enzyme metabolism and adverse drug response. Using the Medical Subject Headings (MeSH) ontology search terms in PubMed, studies were identified that are either population-based, or include a description of the study population on the basis of biological or environmental diversity. The results of this scoping review indicate that the majority of relevant papers (>95% of studies tagged in PubMed with MeSH terms “precision medicine” or “pharmacogenetics”, N=23,701) are not annotated with the “population group” MeSH term, suggesting that the majority of studies in this literature are not population-based, or the authors chose not to describe the study population. Among those studies related to pharmacogenetics or precision medicine that are specific to human population groups (N=1006) and were included in the analysis after filtering and screening on eligibility criteria (N=192), the majority of single-population studies included individuals of African, Asian, and European origins, or genetic ancestry. Combining studies of single and multiple populations, 33% involve participants of Asian origin or ancestry; 30% European; 24% African; 10% Hispanic or Latino; and < 3% American Indian or Alaska Native. These data provide a baseline for future comparison, indicating which biogeographic groups have informed the pharmacogenomic knowledgebase specific to diverse human populations. Challenges and potential solutions to improve diversity in the field and in genetics research more broadly are discussed.

Effects of CYP1A enzyme specific inhibitor on pharmacokinetics of para-acetaminophen in Bactrian camel

The effects of CYP1A enzyme on the pharmacokinetics of p-acetaminophen were studied in Bactrian camel. Twelve Bactrian camels were divided into 2 groups, then given a single dose of p-acetaminophen only or with the enzyme inhibitor lomefloxacin. Blood samples were collected after different intervals, and p-acetaminophen concentration was determined by high-performance liquid chromatography. Pharmacokinetic parameters were analyzed by Phoenix WinNonLin v.7.0. The results show that lomefloxacin can significantly inhibit Bactrian camel CYP1A enzyme, as evidenced by the prolonged elimination half-life, increased maximum plasma concentration and area under the curve values and the shortened time to peak concentration for p-acetaminophenol in the substrate with inhibitor group. The results lay a foundation for revealing the particular characteristics of the CYP1A enzyme in Bactrian camels.

Aerotoxic syndrome, discussion of possible diagnostic criteria

Introduction: The term aerotoxic syndrome (ATS) was proposed 20 years ago to describe a constellation of symptoms reported by pilots and cabin crew following exposure to hydraulic fluids, engine oil, and pyrolysis products during flight. Hydraulic fluids and engine oil contain a large number of potentially toxic chemicals, including various organophosphate compounds (OPCs). However, ATS is not yet recognised as a valid diagnosis in aviation or general medicine, because the incidence and aetiology continues to be debated.Discussion: Early studies report findings from symptom surveys or cognitive assessments of small samples of self-selected aircrew, but objective measures of exposure were lacking. Over the last decade, researchers have used more sophisticated techniques to measure exposure, such as on board monitoring studies and biomarkers of exposure (e.g., reduced levels of serum butyrylcholinesterases [BChE]) and more sophisticated techniques to detect nervous system injuries such as fMRI and autoantibody testing. Consideration has also been given to inter-individual differences in the ability to metabolise certain chemical compounds as a result of genetic polymorphisms and exclusion of other potential causes of ill health.Conclusions: We discuss factors which suggest a diagnosis of probable ATS; recommend an assessment protocol which incorporates the aforementioned techniques; and propose diagnostic criteria for probable ATS, based on our previously reported findings in aircrew and the results of recent studies.

Three patients with probable aerotoxic syndrome

Introduction: "Aerotoxic syndrome" is a debated entity. Regulatory authorities consider long-term health effects to be an unlikely consequence of exposure to contaminated air because several air quality monitoring studies report low concentrations of toxic chemicals in cabin air. We describe two pilots and one flight attendant, who developed ill health during their flying career which improved after cessation of flying.Case details: The most frequently reported symptoms were headache, balance problems, fatigue, gastro-intestinal complaints and cognitive impairment. One of these patients had reduced levels of butyrylcholinesterase after a flight suggesting exposure to organophosphate compounds had occurred. All three were found to have elevated neuronal and glial auto-antibodies, biomarkers of central nervous system injury, and all three had genetic polymorphisms of paraoxonase (PON-1) and two of cytochrome P450, leading to a reduced ability to metabolize organophosphate compound (OPs).Discussion: A similar constellation of symptoms has been described in other studies of aircrew, although objective evidence of exposure is lacking in most of these studies. Reduced levels of butyrylcholinesterases in one of our cases is suggestive of causation and elevated neuronal and glial autoantibodies provide objective evidence of damage to the central nervous system. We consider further research is warranted.

Deciphering DMET genetic data: comprehensive assessment of Northwestern Han, Tibetan, Uyghur populations and their comparison to eleven 1000 genome populations

We investigated the allele frequencies of drug absorption, distribution, metabolism and elimination (ADME)-related drug-metabolizing enzymes and transporters (DMET) genes in the Northwestern Han, Tibetan and Uyghur populations and compared the related genes in these three populations with those in eleven 1000 Genome populations. We examined 1936 single nucleotide polymorphisms of 225 DMET genes involved in ADME processes and found 732, 679 and 804 sites were polymorphic in Han, Tibetan and Uyghur. Tibetan differed from Han in only four sites (p < .05), whereas Uyghur differed from Han and Tibetan in 24 and 21 sites, respectively (p < .05). The distributions of 1058 genotyping data of 245 individuals from Han, Tibetan and Uyghur were compared with 1207 other individuals from the eleven 1000 Genomes populations. The top four populations in Han that exhibited the smallest pairwise Fst values were CHB, Tibetan, CHD and JPT; those in Tibetan were Han, CHB, Uyghur and CHD; and those in Uyghur were Han, Tibetan, GIH and CEU. MEGA results revealed that CHB, CHD, JPT, Han, Tibetan and Uyghur were grouped in cluster 1. GIH, MEX, CEU and TSI were grouped in cluster 2. MKK, ASW, LWK and YRI were grouped in cluster 3.

Percentage of faecal excretion of meloxicam in the Cape vultures (Gyps corprotheres)

Asian Gyps vulture species are gradually recovering from the devastating effect of diclofenac being present in contaminated carcasses. This drug was responsible for the death of over 10 million vultures in India, Nepal and Pakistan. To prevent the extinction of vultures, meloxicam was introduced after the ban of veterinary diclofenac. Meloxicam's safety in vultures was attributed to its short elimination half-life in contrast with diclofenac. The reason for the rapid elimination of meloxicam is yet to be explained. The aim of this study was to evaluate the role of biotransformation in the elimination of meloxicam. Six Cape griffon vultures (Gyps coprotheres) were treated with 2 mg/kg meloxicam intramuscularly for faecal and plasma quantification of meloxicam concentration over time. In the plasma meloxicam was characterised by a half-life, mean residence time, clearance and volume of distribution at steady state of 0.37 ± 0.10 h, 0.90 ± 0.12 h, 0.02 ± 0.00 l/h kg and 0.02 ± 0.00 l/kg respectively (presented as geometric mean). Over the 24 h monitoring period, the total non-metabolised meloxicam in the faeces was 1.35 ± 0.71% of the total concentration in the plasma. Based on the short meloxicam elimination half-life and low cumulative concentration of total faecal meloxicam over a period in excess of 10 half-lives, this study indicates that Cape griffon vultures are efficient metaboliser of meloxicam, which is suggestive of different set of cytochrome enzymes being involved in the metabolism to that for diclofenac in this species. Identification of orthologous human CYP2C9 and CYP3A4 enzyme families in vultures will be an important further step in explaining the differences in the metabolic pathway(s) of meloxicam and diclofenac for the species.

Application of pharmacogenetics in clinical practice: problems and solutions

This paper discusses difficulties of pharmacogenomic data integration into clinical practice. It emphasizes the need for developing simple and easy to use bioinformatics tools to help prescribers to rapidly access and use genetic data in clinical decision-making at the point of encounter.

Pharmacogenomics in Psychiatric Practice

Pharmacogenomic testing in psychiatry is becoming an established clinical procedure. Several vendors provide clinical interpretation of combinatorial pharmacogenomic testing of gene variants that have documented predictive implications regarding either pharmacologic response or adverse effects in depression and other psychiatric conditions. Such gene profiles have demonstrated improvements in outcome in depression, and reduction of cost of care of patients with inadequate clinical response. Additionally, several new gene variants are being studied to predict specific response in individuals. Many of these genes have demonstrated a role in the pathophysiology of depression or specific depressive symptoms. This article reviews the current state-of-the-art application of psychiatric pharmacogenomics.

Distinctiveness of the Roma population within CYP2B6 worldwide variation

AIM

To determine variation of CYP2B6 gene within the genetically specific Croatian Roma (Gypsy) population originating from India and to examine it in the worldwide perspective.

MATERIALS & METHODS

Seven SNP loci (rs12721655, rs2279343, rs28399499, rs34097093, rs3745274, rs7260329 and rs8192709) were genotyped in 439 subjects using Kompetitive Allele Specific PCR (KASP) method.

RESULTS

The Croatian Roma took an outlying position in CYP2B6 variation from the worldwide perspective mainly due to their exceptionally high minor allele frequency (MAF) for rs8192709 (12.8%), and lower for rs2279343 (21.1%) compared with south Asian populations.

CONCLUSION

This study provides the first data of several CYP2B6 polymorphisms in Roma population and indicates the need for systematic investigation of the most important pharmacogenes' variants in this large, transnationally isolated population worldwide.

Evidence of Polygenic Adaptation in the Systems Genetics of Anthropometric Traits

Many signals of natural selection have been identified in the human genome. However, except for some single-locus mechanisms, most molecular processes generating these adaptation signals are still unknown. We developed an approach that integrates datasets related to genome-wide association studies (GWAS) with information about systems biology and genetic signatures of natural selection to identify evidence of polygenic adaptation. Specifically, we focused on five anthropometric measurements: body mass index (BMI), height, waist-to-hip ratio adjusted for BMI (WHR), and waist circumference adjusted for BMI (WC), and sex differences for WHR and WC. We performed an enrichment analysis for signals of natural selection in protein interaction networks associated with anthropometric traits in European populations. The adaptation signals-enriched gene networks associated highlighted epistatic interactions in the context of polygenic selection for the investigated traits. These polygenic mechanisms indicated intriguing selective mechanisms related to the anthropometric traits: adult locomotory behavior for BMI, infection resistance for height, interplay between lipid transport and immune systems for WHR, and female-specific polygenic adaptation for WHR and WC. In conclusion, we observed evidence of polygenic adaptation in the context of systems genetics of anthropometric traits that indicates polygenic mechanisms related to the natural selection in European populations.

Effects of CYP3A5 genetic polymorphism and smoking on the prognosis of non-small-cell lung cancer

Objective

We aimed to explore the impacts of the rs776746 polymorphism in the CYP3A5 gene and smoking on the prognosis of non-small-cell lung cancer (NSCLC).

Materials and methods

Our study enrolled 104 early NSCLC patients undergoing surgery and 107 advanced NSCLC patients undergoing chemotherapy, hospitalized between December 2009 and December 2012 at the First Affiliated Hospital of Liaoning Medical University. All subjects with complete follow-up data were pathologically diagnosed. The rs776746 polymorphism and different genotypes (*1/*1, *1/*3, and *3/*3) were identified by polymerase chain-reaction restriction fragment-length polymorphism.

Results

Clinical response to chemotherapy in NSCLC patients with *1/*1 + *1/*3 genotypes were significantly worse than in those with the *3/*3 genotype (17.78% vs 56.45%, P<0.001), and after Bonferroni adjustment, the differences still showed significance (P_c<0.01). The mortality risk of NSCLC patients undergoing chemotherapy with the *3/*3 genotype was 0.617 times those with *1/*1 + *1/*3 genotypes (relative risk [RR] 0.617, 95% confidence interval [CI] 0.402–0.948; P=0.028), while the mortality risk of smoking patients was 1.743 times greater than that of nonsmoker patients (RR 1.743, 95% CI 1.133–2.679; P=0.042). Furthermore, a 3.087-fold mortality risk was found in NSCLC patients undergoing surgery with the *3/*3 genotype compared with those with *1/*1 + *1/*3 genotypes (RR 3.087, 95% CI 1.197–7.961; P=0.020). In NSCLC patients undergoing surgery, the mortality risk of smokers was 1.896 times greater than nonsmokers (RR 1.896, 95% CI 1.040–3.455; P=0.037).

Conclusion

Our study demonstrated that the CYP3A5 rs776746 polymorphism and smoking may influence the prognosis of NSCLC patients undergoing chemotherapy and surgery.

Dissecting ancestry genomic background in substance dependence genome-wide association studies

AIMS

To understand the role of ancestral genomic background in substance dependence (SD) genome-wide association studies (GWAS), we analyzed population diversity at genetic loci associated with SD traits and evaluated its effect on GWAS outcomes.

MATERIALS & METHODS

We investigated 24 genes with variants associated with SD by GWAS; and 82 loci with putative subordinate roles with respect to SD-associated genes.

RESULTS

We observed high ancestry-related frequency differences in common functional alleles in GWAS relevant genes and their interactive partners. Common functional alleles with high frequency differences demonstrated significant effects on the GWAS outcomes.

CONCLUSION

Population differences in SD GWAS outcomes seem not to be influenced by general variation across the genome, but by ancestry-related local haplotype structures at SD-associated loci.

International warfarin genotype-guided dosing algorithms in the Turkish population and their preventive effects on major and life-threatening hemorrhagic events

AIM

To determine the accuracy of international warfarin pharmacogenetic algorithms developed on large multiethnic cohorts (comprising more than 1000 subjects) to predict therapeutic warfarin doses in Turkish patients.

MATERIALS & METHODS

We investigated two Turkish warfarin-treated cohorts: patients with no history of hemorrhagic or thromboembolic event and patients with major and life-threatening hemorrhagic events.

RESULTS

International pharmacogenetic algorithms showed good performances in predicting the therapeutic dose of patients with no history of bleedings, but they did not significantly detect the incorrect warfarin dose of patients with major and life-threatening hemorrhagic events.

CONCLUSION

Although genetic information can predict the therapeutic warfarin dose, the accuracy of the international pharmacogenetic algorithms is not sufficient to be used for warfarin screening in Turkish patients.

Organs-on-chips at the frontiers of drug discovery

Improving the effectiveness of preclinical predictions of human drug responses is critical to reducing costly failures in clinical trials. Recent advances in cell biology, microfabrication and microfluidics have enabled the development of microengineered models of the functional units of human organs - known as organs-on-chips - that could provide the basis for preclinical assays with greater predictive power. Here, we examine the new opportunities for the application of organ-on-chip technologies in a range of areas in preclinical drug discovery, such as target identification and validation, target-based screening, and phenotypic screening. We also discuss emerging drug discovery opportunities enabled by organs-on-chips, as well as important challenges in realizing the full potential of this technology.

Characterization of human cytochrome P450s involved in the bioactivation of tri-ortho-cresyl phosphate (ToCP)

Tri-ortho-cresyl phosphate (ToCP) is a multipurpose organophosphorus compound that is neurotoxic and suspected to be involved in aerotoxic syndrome in humans. It has been reported that not ToCP itself but a metabolite of ToCP, namely, 2-(ortho-cresyl)-4H-1,2,3-benzodioxaphosphoran-2-one (CBDP), may be responsible for this effect as it can irreversibly bind to human butyrylcholinesterase (BuChE) and human acetylcholinesterase (AChE). The bioactivation of ToCP into CBDP involves Cytochrome P450s (P450s). However, the individual human P450s responsible for this bioactivation have not been identified yet. In the present study, we aimed to investigate the metabolism of ToCP by different P450s and to determine the inhibitory effect of the in vitro generated ToCP-metabolites on human BuChE and AChE. Human liver microsomes, rat liver microsomes, and recombinant human P450s were used for that purpose. The recombinant P450s 2B6, 2C18, 2D6, 3A4 and 3A5 showed highest activity of ToCP-bioactivation to BuChE-inhibitory metabolites. Inhibition experiments using pooled human liver microsomes indicated that P450 3A4 and 3A5 were mainly involved in human hepatic bioactivation of ToCP. In addition, these experiments indicated a minor role for P450 1A2. Formation of CBDP by in-house expressed recombinant human P450s 1A2 and 3A4 was proven by both LC-MS and GC-MS analysis. When ToCP was incubated with P450 1A2 and 3A4 in the presence of human BuChE, CBDP-BuChE-adducts were detected by LC-MS/MS which were not present in the corresponding control incubations. These results confirmed the role of human P450s 1A2 and 3A4 in ToCP metabolism and demonstrated that CBDP is the metabolite responsible for the BuChE inactivation. Interindividual differences at the level of P450 1A2 and 3A4 might play an important role in the susceptibility of humans in developing neurotoxic effects, such as aerotoxic syndrome, after exposure to ToCP.

Genetic diversity of disease-associated loci in Turkish population

Many consortia and international projects have investigated the human genetic variation of a large number of ethno-geographic groups. However, populations with peculiar genetic features, such as the Turkish population, are still absent in publically available datasets. To explore the genetic predisposition to health-related traits of the Turkish population, we analyzed 34 genes associated with different health-related traits (for example, lipid metabolism, cardio-vascular diseases, hormone metabolism, cellular detoxification, aging and energy metabolism). We observed relevant differences between the Turkish population and populations with non-European ancestries (that is, Africa and East Asia) in some of the investigated genes (that is, AGT, APOE, CYP1B1, GNB3, IL10, IL6, LIPC and PON1). As most complex traits are highly polygenic, we developed polygenic scores associated with different health-related traits to explore the genetic diversity of the Turkish population with respect to other human groups. This approach showed significant differences between the Turkish population and populations with non-European ancestries, as well as between Turkish and Northern European individuals. This last finding is in agreement with the genetic structure of European and Middle East populations, and may also agree with epidemiological evidences about the health disparities of Turkish communities in Northern European countries.

The Affymetrix DMET Plus platform reveals unique distribution of ADME-related variants in ethnic Arabs

Background. The Affymetrix Drug Metabolizing Enzymes and Transporters (DMET) Plus Premier Pack has been designed to genotype 1936 gene variants thought to be essential for screening patients in personalized drug therapy. These variants include the cytochrome P450s (CYP450s), the key metabolizing enzymes, many other enzymes involved in phase I and phase II pharmacokinetic reactions, and signaling mediators associated with variability in clinical response to numerous drugs not only among individuals, but also between ethnic populations. Materials and Methods. We genotyped 600 Saudi individuals for 1936 variants on the DMET platform to evaluate their clinical potential in personalized medicine in ethnic Arabs. Results. Approximately 49% each of the 437 CYP450 variants, 56% of the 581 transporters, 56% of 419 transferases, 48% of the 104 dehydrogenases, and 58% of the remaining 390 variants were detected. Several variants, such as rs3740071, rs6193, rs258751, rs6199, rs11568421, and rs8187797, exhibited significantly either higher or lower minor allele frequencies (MAFs) than those in other ethnic groups. Discussion. The present study revealed some unique distribution trends for several variants in Arabs, which displayed partly inverse allelic prevalence compared to other ethnic populations. The results point therefore to the need to verify and ascertain the prevalence of a variant as a prerequisite for engaging it in clinical routine screening in personalized medicine in any given population.

Genotyping of CYP2C19 polymorphisms and its clinical validation in the ethnic Arab population

OBJECTIVES

The drug-metabolizing enzymes and transporters (DMET) Plus microarray and x-Tag assays have recently been developed for genotyping individuals in personalized medicine. Furthermore, the cytochrome 450-2C19 (CYP2C19) is a key metabolic enzyme encoded by a polymorphic gene commonly associated with diminished metabolism and variable clinical responses to several drugs in an ethnicity-dependent fashion. Therefore, validation of these clinical procedures as well as knowledge of the ethnic-specific incidences of these gene variants is prerequisite for determining their clinical relevance in any given population.

METHODS

We determined the distribution of familiar CYP2C19 variants by the DMET Plus chip in 600 candidates and replicated the findings by the Affymetrix Axiom Genome-Wide Asian Structure Identification Array in 5413 individuals, all Saudis of ethic Arab origin. We then tested the robustness of employing the Luminex xMAP system clinically by comparing the results of genotyping 500 Saudi individuals visiting the Blood Bank of our institution with the findings of the two platforms.

KEY FINDINGS

The DMET Plus genotyping revealed that eight of the CYP2C19 variants showed some changes. Thereby, the CYP2C19*17 exhibited the highest minor allele frequency (MAF) of 0.256, followed by the CYP2C19_801 (frequency = 0.055). Six other variants, including the CYP2C19*3, showed MAF in the range of 0.001-0.002. We replicated the frequencies of the CYP2C19*17 and CYP2C19*3, and additionally established that of the CYP2C19*2 (0.099) using the Axiom platform. The xTag genotyping also indicated that 0.834 of the 500 Saudi individuals were extensive metabolizers (*1/*1), 0.158 carried the *1/*2 genotype, 0.01% carried *2/*2 (poor metabolizers) and one each (0.2%) harboured the *1/*8, *2/*3 (intermediate metabolizers) and *8/*8 (poor metabolizers) genotypes.

CONCLUSIONS

The results showed reproducible genotyping of the CYP2C19 variants in the Saudi Arab population using two Affymetrix platforms and phenotyping using the Luminex xTag assay. The prevalence of two clinically relevant genotypes (CYP2C19*2 and CYP2C19*3) were similar to other ethnic groups, while that of the CYP2C19*17 was comparably higher.

Tricresyl phosphate and the aerotoxic syndrome of flight crew members--current gaps in knowledge

Tricresyl phosphate (TCP), and in particular its tri-ortho substituted isomer (o,o,o-TCP), has been frequently used in aircraft engine oil. Bleed air, provided to the flight deck and cabin can contain traces of TCP. TCP can cause neurotoxic effects in humans. Regularly, airline pilots complain about loss of memory, headaches, dizziness, tunnel vision and other neurotoxic effects. The concentrations of TCP reported in flight deck air (max. ca. 50-100 ng m(-3) total TCP) do not exceed provisional toxicity thresholds. These thresholds, however, contain a very high uncertainty and need further underpinning. The many non-detects and relatively low TCP concentrations reported suggest that TCP on its own is not likely to be responsible for the reported health problems of pilots. Specific conditions in air planes and other toxic compounds present in bleed air, whether or not in combination with TCP, may be responsible for the reported neurotoxic syndromes. Sensitivity of individuals seems to be an important factor as well. The clinical signs observed with a selected group of pilots are serious enough to call for further elucidation of this issue.

In silico analysis of TTR gene (coding and non-coding regions, and interactive network) and its implications in transthyretin-related amyloidosis

INTRODUCTION

Transthyretin (TTR)-related amyloidosis is a life-threatening disease. Currently, several questions about the pathogenic mechanisms of TTR-related amyloidosis remain unanswered.

METHODS

We have investigated various TTR-related issues using different in silico approaches.

RESULTS

Using an amino acid similarity-based analysis, we have indicated the most relevant TTR secondary structures in determining mutation impact. Our amyloidogenic propensity analysis of TTR missense substitutions has highlighted a similar pattern for wild-type and mutated TTR amino β acid sequences. However, some mutations present differences with respect to the general distribution. We have identified non-coding variants in cis-regulatory elements of the TTR gene, and our analysis on V122I-related haplotypes has indicated differences in non-coding regulatory variants, suggesting differences among V122I carriers. The analysis of methylation status indicated CpG sites that may affect TTR expression. Finally, our interactive network analysis revealed functional partners of TTR that may play a modifier role in the pathogenesis of TTR-related amyloidosis.

DISCUSSION AND CONCLUSION

Our data provided new insights into the pathogenesis of TTR-related amyloidosis that, if they were to be confirmed through experimental investigations, could significantly improve our understanding of the disease.

Pharmacogenetic insights into migraine treatment in children

Pediatric migraine is a disabling condition that can affect the everyday activities and emotional states of children. Due to the multifactorial character of the pathology and the variety of the disease's phenotypes, establishment of an effective treatment is often challenging. Pharmacological treatment is often administered off-label and includes very different drugs, from analgesics to antidepressants. Since interindividual variability in therapy response commonly causes inefficacy and an exacerbation of symptoms, pharmacogenetics may help to decrease the prescription rate of useless or unsafe drugs. If there are many drugs used in migraine, then there are even more candidate or established pharmacogenetic markers that are implicated in clinical profiles. This article presents the current situation regarding the pharmacogenetics of drugs used in pediatric migraine.

Human pharmacogenomic variation of antihypertensive drugs: from population genetics to personalized medicine

Aim: To investigate the human pharmacogenetic variation related to antihypertensive drugs, providing a survey of functional interpopulation differences in hypertension pharmacogenes. Materials & methods: The study was divided into two stages. In the first stage, we analyzed 1249 variants located in 57 hypertension pharmacogenes. This first-stage analysis confirmed that geographic origin strongly affects hypertension pharmacogenomic variation and that 31 pharmacogenes are geographically differentiated. In the second stage, we focused our attention on the ethnic-differentiated pharmacogenes, investigating 55,521 genetic variants. In silico analyses were performed to predict the effect of genetic variation. Results: Our analyses indicated functional interpopulation differences, suggesting insight into the mechanisms of antihypertensive drug response. Moreover, our data suggested that rare variants mainly determine the functionality of genes related to antihypertensive drugs. Conclusion: Our study provided important knowledge about the genetics of the antihypertensive drug response, suggesting that next-generation sequencing technologies may develop reliable pharmacogenetic tests for antihypertensive drugs.

Original submitted 19 September 2013; Revision submitted 14 November 2013

Functional variation of the transthyretin gene among human populations and its correlation with amyloidosis phenotypes

INTRODUCTION

Heterogeneity in the genotype-phenotype correlation of transthyretin (TTR)-related amyloidosis has been reported, suggesting that other factors may interact with disease-causing mutations. Additional genetic variants in the TTR gene and its surrounding regions may influence disease phenotype. To explore this hypothesis, we analyzed the TTR variation among human populations to identify functional inter-ethnic differences that could influence the TTR-related amyloidosis.

METHODS

Using the 1000 Genomes Project database, we analyzed a 20 kb region in 1092 apparently healthy individuals who belonged to 14 human populations. In silico analyses were performed to determine the functional impact of genetic variants.

RESULTS

These analyses showed that significant ethnic differences are present in the TTR gene, and some differences may affect TTR gene function. Specifically, the non-coding variants potentially associated with regulatory function showed a significant diversity between African and non-African individuals.

DISCUSSION AND CONCLUSIONS

Our results highlighted that cis-regulatory variants may contribute to the cardiac TTR-related amyloidosis observed in patients carrier of Val122Ile mutation, the most common in population with African origin. Indeed, non-coding variants differentiated in Africans are, in some cases, located in binding sites of transcription factors involved in cardiac development and function (i.e. E2F3_2, REST, and TEAD).

Functional diversity of the glutathione peroxidase gene family among human populations: implications for genetic predisposition to disease and drug response

Aim: To analyze the human genetic variation of glutathione peroxidases (GPX), estimating the functional differences among human populations and suggesting interethnic differences in predisposition to disease and drug response. Materials & methods: Using 1000 Genomes Project data, we analyzed 723 GPX variants in 1092 individuals belonging to 14 populations. Combining functional prediction analyses of coding and noncoding variants, we developed a method to estimate haplotype functionality. Results: GPX rare variants have a higher functional impact than common variants. The frequency among Asian patients of haplotypes associated with normal functionality is significantly higher for GPX1 and lower for GPX3 than for non-Asian patients; no adaptation signals in GPX1 and GPX3 were found in Asian patients. Conclusion: GPX1 and GPX3 differences may be associated with alterations in antioxidant capacity and redox regulation, which suggests diverse susceptibility to complex disease and diverse response to relevant drugs in Asians compared with individuals with other ethnic origins.

Original submitted 7 February 2013; Revision submitted 16 May 2013

Allele frequency distribution of CYP2C9 2 and CYP2C9 3 polymorphisms in six Mexican populations

Allele frequency differences of functional CYP2C9 polymorphisms are responsible for some of the variation in drug response observed in human populations. The most relevant CYP2C9 functional variants are CYP2C9*2 (rs1799853) and CYP2C9 3 (rs1057910). These polymorphisms show variation in allele frequencies among different population groups. The present study aimed to analyze these polymorphisms in 947 Mexican-Mestizo from Mexico City and 483 individuals from five indigenous Mexican populations: Nahua, Teenek, Tarahumara, Purepecha and Huichol. The CYP2C9*2 allele frequencies in the Mestizo, Nahua and Teenek populations were 0.051, 0.007 and 0.005, respectively. As for CYP2C9 3, the allelic frequencies in the Mestizo, Nahua and Teenek populations were 0.04, 0.005 and 0.005, respectively. The CYP2C9 2 and CYP2C9 3 alleles were not observed in the Tarahumara, Purepecha and Huichol populations. These findings are in agreement with previous studies reporting very low allele frequencies for these polymorphisms in American Indigenous populations.

Glutathione S-transferase polymorphisms, asthma susceptibility and confounding variables: a meta-analysis

Oxidative stress is one of the main risk factors for asthma development. Glutathione S-transferases play an important role in antioxidant defences and may influence asthma susceptibility. In particular, GSTM1 and GSTT1 positive/null genotypes and the GSTP1 Ile105 Val polymorphism have been analyzed in a number of genetic association studies, with conflicting outcomes. Two previous meta-analyses have attempted to clarify the associations between GST genes and asthma, but these studies have also showed contrasting results. Our aim was to perform a meta-analysis that included independent genetic association studies on GSTM1, GSTP1, and GSTT1, evaluating also the effect of potential confounding variables (i.e. ethnicity, population age, and urbanization). Systematic review and meta-analysis of the effects of GST genes on asthma were conducted. The meta-analyses were performed using a fixed or, where appropriate, random effects model. The meta-analysis of the GSTM1 (n = 35), GSTT1 (n = 31) and GSTP1 (n = 28) studies suggests that no significant associations with asthma susceptibility were observed for GSTM1 and GSTP1 gene polymorphisms, whereas a significant outcome was detected for the GSTT1 positive/null genotype (pooled OR = 1.33, 95 %CI = 1.10-1.60). However, high between-study heterogeneity was identified in all the general analyses (p heterogenetity < 0.05). The stratification analysis seems to explain the heterogeneity only in few cases. This picture is probably due to the interactive process of genetics and environment that characterizes disease pathogenesis. Further studies on interactions of GST genes with the potential oxidative stress sources and with other antioxidant genes are needed to explain the role of GST enzymes in asthma.