Analysis of 50 SNPs in CYP2D6, CYP2C19, CYP2C9, CYP3A4 and CYP1A2 by MALDI-TOF mass spectrometry in Chinese Han population

Visualized Genotyping from "Sample to Results" Within 25 Minutes by Coupling Recombinase Polymerase Amplification (RPA) With Allele-Specific Invasive Reaction Assisted Gold Nanoparticle Probes Assembling

A simple and rapid genotyping method with less-instrumentation is essential for realizing point-of-care detection of personalized medicine-related gene biomarkers. Herein, we developed a rapid and visualized genotyping method by coupling recombinase polymerase amplification (RPA) with allele-specific invader reaction assisted gold nanoparticle probes assembling. In the method, the DNA targets were firstly amplified by using RPA, which is a rapid isothermal amplification technology. Then an allele-specific invasion reaction was performed to recognize the single nucleotide polymorphisms (SNPs) site in the amplicons, to produce signal molecules that caused discoloration of gold nanoparticle probes. As a result, genotyping was achieved by observing the color change of the reaction by using naked eye without the requirement for any expensive instrument. In order to achieve rapid genotyping detection, the genomic DNA from oral swab lysate samples were used for the RPA templates amplification. In this way, a visualized genotyping from "samples to results" within 25 min was realized. Two clopidogrel related SNPs CYP2C19*2 and CYP2C19*3 of 56 clinical samples were correctly genotyped by using this rapid visualized genotyping assay. In addition, the feasibility for this pathogen genotyping method was also verified by detecting plasmid DNA containing three SARS-COV-2 gene mutation sites, indicating that this method has the potential for clinical sample detection.

MASS SPECTROMETRY-BASED PERSONALIZED DRUG THERAPY

Personalized drug therapy aims to provide tailored treatment for individual patient. Mass spectrometry (MS) is revolutionarily involved in this area because MS is a rapid, customizable, cost-effective, and easy to be used high-throughput method with high sensitivity, specificity, and accuracy. It is driving the formation of a new field, MS-based personalized drug therapy, which currently mainly includes five subfields: therapeutic drug monitoring (TDM), pharmacogenomics (PGx), pharmacomicrobiomics, pharmacoepigenomics, and immunopeptidomics. Gas chromatography-MS (GC-MS) and liquid chromatography-MS (LC-MS) are considered as the gold standard for TDM, which can be used to optimize drug dosage. Matrix-assisted laser desorption ionization-time of flight-MS (MALDI-TOF-MS) significantly improves the capability of detecting biomacromolecule, and largely promotes the application of MS in PGx. It is becoming an indispensable tool for genotyping, which is used to discover and validate genetic biomarkers. In addition, MALDI-TOF-MS also plays important roles in identity of human microbiome whose diversity can explain interindividual differences of drug response. Pharmacoepigenetics is to study the role of epigenetic factors in individualized drug treatment. MS can be used to discover and validate pharmacoepigenetic markers (DNA methylation, histone modification, and noncoding RNA). For the emerging cancer immunotherapy, personalized cancer vaccine has effective immunotherapeutic activity in the clinic. MS-based immunopeptidomics can effectively discover and screen neoantigens. This article systematically reviewed MS-based personalized drug therapy in the above mentioned five subfields. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.

MALDI-TOF-MS-based high throughput genotyping of mutations associated with body measurement traits in cattle

Exploration of genes in relation to body measurement traits through large-scaled mutation identification is highly conductive for the genomics-assisted breeding of superior productivity cattle. In this investigation, 31 objective mutations were genotyped synchronously in 384 yellow cattle of 8 breeds through the application of optimized MALDI-TOF-MS and multiplex PCR techniques. High genotyping rate was obtained as well as greatly decreased cost which was below one thirtieth of the routine analysis. Results from genotyping revealed 23 mutations as valid mutations in the studied cattle population with gene heterozygosity and effective allele number varying from 0.0052 to 0.4998 and 1.0052 to 1.9991, respectively. Among the 23 effective mutations, 12 was classified as moderate polymorphism (0.25 < PIC < 0.5) while the other 11 belonged to low polymorphism (PIC < 0.25), 7 mutations did not obey the HW equilibrium (p < 0.05) and linkage mainly appeared between mutations of UCP2 and PTHR1 genes. Furthermore, 8 body measurement traits in the 384 cattle were recorded to validate their association with tag mutations, and significant correlations were found in 12 mutations of 9 genes including PTHR1, CDK6, IHH, HHIP, GHRL, COL1A1, INS, GDF5 and UCP2, of which, PTHR1 was proved to be the most potential contributor to bone modeling in cattle. Results highlight the potential application value of 12 novel mutations in enhancing cattle production traits as well as the high genotyping rate achieved by MALDI-TOF-MS coupled with multiplex PCR technique.

Interethnic variation of CYP2C19 alleles, 'predicted' phenotypes and 'measured' metabolic phenotypes across world populations

The present study evaluates the worldwide frequency distribution of CYP2C19 alleles and CYP2C19 metabolic phenotypes ('predicted' from genotypes and 'measured' with a probe drug) among healthy volunteers from different ethnic groups and geographic regions, as well as the relationship between the 'predicted' and 'measured' CYP2C19 metabolic phenotypes. A total of 52 181 healthy volunteers were studied within 138 selected original research papers. CYP2C19*17 was 42- and 24-fold more frequent in Mediterranean-South Europeans and Middle Easterns than in East Asians (P<0.001, in both cases). Contrarily, CYP2C19*2 and CYP2C19*3 alleles were more frequent in East Asians (30.26% and 6.89%, respectively), and even a twofold higher frequency of these alleles was found in Native populations from Oceania (61.30% and 14.42%, respectively; P<0.001, in all cases), which may be a consequence of genetic drift process in the Pacific Islands. Regarding CYP2C19 metabolic phenotype, poor metabolizers (PMs) were more frequent among Asians than in Europeans, contrarily to the phenomenon reported for CYP2D6. A correlation has been found between the frequencies of CYP2C19 poor metabolism 'predicted' from CYP2C19 genotypes (gPMs) and the poor metabolic phenotype 'measured' with a probe drug (mPMs) when subjects are either classified by ethnicity (r=0.94, P<0.001) or geographic region (r=0.99, P=0.002). Nevertheless, further research is needed in African and Asian populations, which are under-represented, and additional CYP2C19 variants and the 'measured' phenotype should be studied.

CD24 polymorphisms cannot predict pathologic complete response to anthracycline- and taxane-based neoadjuvant chemotherapy in breast cancer

INTRODUCTION

To evaluate the correlations between CD24 polymorphisms and clinicopathologic variables of patients with breast cancer.

PATIENTS AND METHODS

Single-nucleotide polymorphisms (SNPs) of CD24 were genotyped by the Sequenom MassArray iPLEX Gold System in 170 patients with breast cancer, and a total of 120 patients with histologically confirmed T2-4N0-2 M0 breast cancer were recruited to therapy with docetaxel, doxorubicin, and cyclophosphamide (TAC) as neoadjuvant chemotherapy. Data were analyzed by the chi-square test and logistic regression analysis.

RESULTS

There were no significant correlations between CD24 polymorphisms and any of the clinicopathologic variables, and no significant associations were found between either of the polymorphisms and CD24 protein expression. The clinical response rate and the pathologic complete response (pCR) rate were 68.8% and 27.1% in patients with the CD24 rs3838646 CA/CA genotype, and 87.5% and 20.8% in CD24 CA/Del and Del/Del genotype. There were no statistically significant differences between the CA/CA group and the Del allele group. The clinical response rate was 85.4% in patients with the CD24 rs52812045 C/C genotype and 63.9% in patients with the CD24 C/T and T/T genotype. There was a statistically significant difference between the C/C group and the T allele group (odds ratio = 0.28; 95% confidence interval, 0.11-0.73, P = .01). The pCR rate was 29.2% in patients with the CD24 rs52812045 C/C genotype and 23.6% in patients with the CD24 C/T and T/T genotype. There were no statistically significant differences between the C/C group and the T allele group. In a multivariate analysis, there was no correlation between CD24 rs3838646 or rs52812045 genotype and pCR.

CONCLUSION

CD24 rs3838646 and rs52812045 polymorphism could not predict the pathologic complete response to anthracycline- and taxane-based neoadjuvant chemotherapy in breast cancer. Additional larger studies are required to confirm this finding.

p73 G4C14-to-A4T14 polymorphisms are positively correlated with triple-negative breast cancer in southwestern China

p73 gene shares structural and functional similarities to p53 and plays an important role in modulating cell cycle arrest and apoptosis. A common non-coding polymorphism of p73 G4C14-to-A4T14 (rs2273953 and rs1801173) at exon 2 may affect gene expression, thus, it may lead to functional significance. The correlation of this polymorphism with clinicopathologic variables of patients with breast cancer has not been investigated. In this study, single-nucleotide polymorphisms (SNPs) of p73 G4C14-to-A4T14 were genotyped by Sequenom MassArray-iPLEX GOLD System in 170 patients with breast cancer. Data were analyzed via t test, chi-square test, and logistic regression analysis. There was no significant correlation between p73 G4C14-to-A4T14 polymorphisms and the patient characteristics, such as clinical TNM stage, menopausal status, axillary lymph node metastasis, pathological type, estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2). No significant relationship was observed between the p73 G4C14-to-A4T14 polymorphism and p73 protein expression in cancer tissues. The frequency of GC/GC genotype in patients with triple-negative breast cancer (TNBC) was 78.9 %, that of patients with others was 57.6 %, and the difference had statistical significance (χ ( 2 ) = 5.74, P = 0.02). p73 G4C14-to-A4T14 polymorphisms were negatively correlated with chemosensitivity for anthracycline-based chemotherapy in breast cancer (P > 0.05). p73 G4C14-to-A4T14 polymorphisms are positively correlated with TNBC, and p73 gene may play a critical role in a novel therapeutic strategy to TNBC. Additional larger studies are required to test these hypotheses.

Unexpectedly high blood concentration of bisoprolol after an incorrect prescription: A case report

An elderly person died of uncontrolled bradycardia in a hospital. The doctor had prescribed 1.35 mg of bisoprolol fumarate orally, but a nurse mistakenly gave the patient 10 mg of the drug 9 hours prior to her death. Bisoprolol was detected in her blood by liquid chromatography-mass spectrometry at a concentration of 176 ng/mL. Even if the patient had chronic heart failure, this concentration is double the expected value. This patient was found to have a mutation within cytochrome P2D6, with thymidine substituted for cytosine at position 100 and cytosine for guanine at position 4180, causing proline to serine and threonine to serine amino acid substitutions. This mutation in the intermediate metabolizer allele reportedly reduces enzyme activity by half. However, in addition to the type of cytochrome P450 allelic variant, the amount of enzyme product influences metabolism of this drug. In this case, the high blood concentration of bisoprolol was only partly attributable to an error in prescription; its concentration was inexplicably high.

CYP3A4 and CYP2C19 genetic polymorphisms and zolpidem metabolism in the Chinese Han population: a pilot study

Zolpidem (ZPD) is an imidazopyridine hypnotic and little is known about the pharmacogenetics of ZPD. Our objective was to evaluate inter-individual genetic variation in conjunction with metabolic ratios of ZPD found in a toxicological analysis. Healthy individuals (n=300) were genotyped for CYP2D6, CYP2C19, CYP2C9, CYP3A4 and CYP1A2 by allele-specific primer extension followed by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS). Twenty-four Chinese volunteers were chosen and divided into the following four groups (n=6/group): group 1: CYP3A4*18 (wild-type, W), CYP2C19*2 (W); group 2: CYP3A4*18 (mutant, M), CYP2C19*2 (W); group 3: CYP3A4*18 (W), CYP2C19*2 (M); and group 4: CYP3A4*18 (M), CYP2C19*2 (M). ZPD and its major metabolites zolpidem 6-carboxylic acid (ZCA) and zolpidem phenyl-4-carboxylic acid (ZPCA) were determined after oral administration of ZPD (10mg), using an UPLC-MS/MS method. Positive correlations between CYP3A4 and CYP2C19 alleles and ZPD metabolism were found. The results of this study show that CYP3A4*18 increases CYP3A4 activity while CYP2C19*2 reduces CYP2C19 activity; the latter mutation is associated with the poor metabolism of ZPD in the Chinese Han population. The results also suggest that genetic factors play a major role in the metabolism of individual drugs with implications for both forensic science and clinical pharmacogenetics.

Paraoxonase-1 is not a major determinant of stent thrombosis in a Taiwanese population

Background

Clopidogrel is a prodrug that undergoes in vivo bioactivation to show its antiplatelet effects. Recent studies have shown that cytochrome P450 (CYP), ATP-binding cassette transporters (ABCB1), and paraoxonase-1 (PON1) play crucial roles in clopidogrel bioactivation. Here, we aim to determine the effects of genetic polymorphisms of CYP (CYP 2C19*2, CYP 2C19*3, and CYP 2C19*17), ABCB1 (ABCB1 3435C>T, ABCB1 129T>C, and ABCB1 2677G>T/A), and PON1 (PON1 Q192R, PON1 L55M, and PON1 108C>T) on the development of stent thrombosis (ST) in patients receiving clopidogrel after percutaneous coronary intervention (PCI).

Methods and Results

We evaluated the incidence of ST (0.64%) in 4964 patients who were recruited in the CAPTAIN registry (Cardiovascular Atherosclerosis and Percutaneous TrAnsluminal INterventions). The presence of genetic polymorphisms was assessed in 20 subjects who developed ST after aspirin and clopidogrel therapy and in 40 age- and sex-matched control subjects who did not develop ST, which was documented after 9 months of angiographic follow-up. ST was acute in 5 subjects, subacute in 7, late in 7, and very late in 1. The presence of CYP 2C19*2 allele was significantly associated with ST (adjusted odds ratio [ORadj]: 4.20, 95% confidence interval [CI], 1.263–9.544; P = 0.031). However, genetic variations in PON1 and ABCB1 showed no significant association with ST.

Conclusion

We conclude that in a Taiwanese population, PON1 Q192R genotype is not associated with ST development after PCI. However, the presence of CYP 2C19*2 allele is a risk factor for ST development after PCI.

Association of p73 G4C14-A4T14 polymorphisms with genetic susceptibilities to breast cancer: a case-control study

The aim of this study was to evaluate the association of p73 G4C14-A4T14 polymorphisms with susceptibility to breast cancer in Chongqing women of Han Nationality in China. In a case-control study, single-nucleotide polymorphisms of p73 G4C14-A4T14 at exon 2 were genotyped by Sequenom MassArray(®) iPLEX GOLD System in 170 patients with breast cancer and 178 healthy controls. Data were analyzed via t test, Chi-square test, and logistic regression analysis. The distribution of p73 genotypes and allelotypes had no significant difference between patients with breast cancer and healthy controls (χ(2) = 2.750, P = 0.253; χ(2) = 2.195, P = 0.138). More risk of developing triple negative breast cancer (TNBC) was found in the individuals who carried with GC/GC genotype than individuals carried with GC/AT and AT/AT genotypes (OR = 2.99; 95 % CI, 1.30-6.89; P = 0.010). p73 G4C14-A4T14 polymorphisms are closely associated with the increased risk for TNBC in Chongqing women of Han Nationality in China; GC/GC genotype is susceptible genotype for TNBC in Chongqing women of Han Nationality in China. The patients with breast cancer who carried with GC/GC genotype may have bad prognosis. Additional larger studies are required to confirm these findings.