An impaired glucagon-like peptide-1 response is associated with prediabetes in polycystic ovary syndrome with obesity.

J Int Med Res. 2019 Aug 23;:300060519865351

Authors: Ferjan S, Jensterle M, Oblak T, Zitnik IP, Marc J, Goricar K, Dolzan V, Janez A

PMID: 31438749 [PubMed - as supplied by publisher]

Assessing Asthma Medication Responses in U.S. Minority Children by Whole-Genome Sequencing.

Am J Respir Crit Care Med. 2018 06 15;197(12):1513-1514

Authors: Lorenzo-Salazar JM, Flores C

PMID: 29578752 [PubMed - indexed for MEDLINE]

Locus Coeruleus, Noradrenaline, and Behavior: Network Effect, Network Effects?

Neuron. 2019 Aug 21;103(4):554-556

Authors: Bouret S

Abstract
How does the noradrenergic nucleus locus coeruleus act on target networks to regulate behavior? In this issue of Neuron, Zerbi et al. (2019) combine functional neuroimaging and pharmacogenetics in mice to tackle that question, uncovering a network action underlying stress. And providing insight for cognition?

PMID: 31437450 [PubMed - in process]

Bone metabolism genes variation and response to bisphosphonate treatment in women with postmenopausal osteoporosis.

PLoS One. 2019;14(8):e0221511

Authors: Marozik P, Alekna V, Rudenko E, Tamulaitiene M, Rudenka A, Mastaviciute A, Samokhovec V, Cernovas A, Kobets K, Mosse I

Abstract
INTRODUCTION: Long-term treatment is used in patients with osteoporosis, and bisphosphonates (BPs) are the most commonly prescribed medications. However, in some patients this therapy is not effective, cause different side effects and complications. Unfortunately, at least one year is needed to identify and confirm an ineffectiveness of BPs therapy on bone mineral density (BMD). Among other factors, a response to BPs therapy may also be explained by genetic factors. The aim of this study was to analyze the influence of SOST, PTH, FGF2, FDPS, GGPS1, and LRP5 gene variants on the response to treatment with aminobisphosphonates.
MATERIALS AND METHODS: Women with postmenopausal osteoporosis were included to this study if they used aminobisphosphonates for at least 12 months. Exclusion criteria were: persistence on BPs therapy less than 80%, bone metabolic diseases, diseases deemed to affect bone metabolism, malignant tumours, using of any medications influencing BMD. The study protocol was approved by the local ethics committee. The BMD at the lumbar spine and femoral neck were measured using dual x-ray absorptiometry (GE Lunar) before and at least 12 months after treatment with BPs. According to BMD change, patients were divided in two groups-responders and non-responders to BPs terapy. Polymorphic variants in SOST, PTH, FGF2, FDPS, GGPS1, and LRP5 genes were determined using PCR analysis with TaqMan probes (Thermo Scientific).
RESULTS: In total, 201 women with BPs therapy were included in the study. No statistically significant differences were observed in age, age at menopause, weight, height, BMI and baseline BMD levels between responders (122 subjects) and non-responders (79 subjects). As single markers, the SOST rs1234612 T/T (OR = 2.3; P = 0.02), PTH rs7125774 T/T (OR = 2.8, P = 0.0009), FDPS rs2297480 G/G (OR = 29.3, P = 2.2×10-7), and GGPS1 rs10925503 C/C+C/T (OR = 2.9; P = 0.003) gene variants were over-represented in non-responders group. No significant association between FGF2 rs6854081 and LRP5 rs3736228 gene variants and response to BPs treatment was observed. The carriers of T-T-G-C allelic combination (constructed from rs1234612, rs7125774, rs2297480, and rs10925503) were predisposed to negative response to BPs treatment (OR = 4.9, 95% CI 1.7-14.6, P = 0.005). The C-C-T-C combination was significantly over-represented in responders (OR = 0.1, 95% CI 0.1-0.5, P = 0.006).
CONCLUSIONS: Our findings highlight the importance of identified single gene variants and their allelic combinations for pharmacogenetics of BPs therapy of osteoporosis. Complex screening of these genetic markers could be used as a new strategy for personalized antiresorptive therapy.

PMID: 31437227 [PubMed - in process]

Pharmacogenetics of statins treatment: Efficacy and safety.

J Clin Pharm Ther. 2019 Aug 22;:

Authors: Guan ZW, Wu KR, Li R, Yin Y, Li XL, Zhang SF, Li Y

Abstract
WHAT IS KNOWN AND OBJECTIVE: Statins are widely used worldwide in the prevention and treatment of coronary atherosclerotic heart disease and ischaemic stroke. However, in clinical application, statins have shown great individual differences in terms of the efficacy and safety, some of which are related to genetic factors. The purpose of this article was to summarize the recent advances about the correlation between gene polymorphisms and the efficacy/safety of statins.
METHODS: We searched the databases including PharmGKB and PubMed (published before June 2019) using the keywords such as 'statin', 'gene polymorphism' and 'SNP' and obtained more than 100 articles. In this review, we described the clinical studies of genetic variants associated with both the efficacy and adverse reactions of statins. We also clarified the importance of taking pharmacogenetic variation into account to improve the clinical application of statins.
RESULTS AND DISCUSSION: The available data were collected and analysed to present the polymorphisms of candidate genes encoding the most promising proteins including SLCO1B1 (encoding uptake transporters); ABCB1, ABCC2, ABCG2 (encoding effluent transporter); APOE, APOA5 (encoding apolipoprotein); genes encoding cytochrome P450 enzyme system; KIF6, HMGCR, LDLR, LPA, PCSK9, COQ2, CETP, etc These genes were proved to be related to the pharmacodynamics and pharmacokinetics of statins, thus affecting the efficacy and safety.
WHAT IS NEW AND CONCLUSION: In this paper, the correlation between gene polymorphisms and the efficacy/safety of statins was summarized. The authors reached a consensus that the variants of the genes encoding uptake and effluent transporters have the most effect on the efficacy/safety of statins. It pointed out that it is desirable to do genetic testing of these transporter genes to reduce the incidence of myopathy or to achieve better outcomes before patients use statins, especially in the regions with high frequency of risk allele.

PMID: 31436349 [PubMed - as supplied by publisher]

Global genetic diversity of human apolipoproteins and effects on cardiovascular disease risk.

J Lipid Res. 2018 10;59(10):1987-2000

Authors: Zhou Y, Mägi R, Milani L, Lauschke VM

Abstract
Abnormal plasma apolipoprotein levels are consistently implicated in CVD risk. Although 30% to 60% of their interindividual variability is genetic, common genetic variants explain only 10% to 20% of these differences. Rare genetic variants may be major sources of the missing heritability, yet quantitative evaluations of their contribution to phenotypic variability are lacking. Here, we analyzed whole-genome and whole-exome sequencing data from 138,632 individuals across seven major human populations to present a systematic overview of genetic apolipoprotein variability. We provide population-specific frequencies of 38 clinically important apolipoprotein alleles and identify further 6,875 genetic variants, 33% of which are novel and 98.7% of which are rare with minor allele frequencies <1%. We predicted the functional impact of rare variants and found that their relative importance differed drastically between genes and among ethnicities. Importantly, we validated the clinical relevance of multiple variants with predicted effects by leveraging association data from the CARDIoGRAM (Coronary Artery Disease Genomewide Replication and Meta-analysis) and Global Lipids Genetics consortia. Overall, we provide a consolidated overview of population-specific apolipoprotein genetics as a valuable data resource for scientists and clinicians, estimate the importance of rare genetic variants for the missing heritability of apolipoprotein-associated disease traits, and pinpoint multiple novel apolipoprotein variants with putative population-specific impacts on serum lipid levels.

PMID: 30076208 [PubMed - indexed for MEDLINE]

Antiulcer activity of methanol-chloroform extract of Channa striatus fillet.

Pak J Pharm Sci. 2018 Jan;31(1):143-151

Authors: Azemi AK, Abd Rahim MH, Mamat SS, Mat Jais AM, Zakaria ZA

Abstract
Channa striatus (Haruan) is Malaysian freshwater fish that is traditionally used to treat ailments related to wound and also ulcers. The aimed of the present study was to determine the mechanisms of anti-ulcer activity of chloroform: methanol extract of C. striatus fillet (CMCS) in rats. The antiulcer profile of CMCS, given orally in the doses of 50, 250 and 500mg/kg, was assessed using the ethanol- and indomethacin-induced gastric ulcer models. The mechanisms of antiulcer of CMCS were determined as follows; i) the antisecretory activity of CMCS was measured using the pyloric ligation rat model, and; ii) the role of nitric oxide (NO) and sulfhydryl compounds in the modulation of CMCS antiulcer activity were determined by pre-treating the rats with L-NAME or NEM, respectively, followed by the pre-treatment of rats with CMCS before subjecting the animals to the ethanol-induced gastric ulcer model. From the results obtained, CMCS exerted significant (P<0.05) antiulcer activity in both models of gastric ulcer wherein the macroscopic and microscopic analysis of the stomach supported the antiulcer claim. With regard to its antisecretory effect, CMCS did not change the volume and pH, but reduce the total acidity only at the lower doses of the gastric juice. Moreover, CMCS demonstrated antiulcer activity was reversed by NEM, but not affected by L-NAME. In conclusion, CMCS shows antiulcer activity that is modulated via its cytoprotective, but not antisecretory effect, and in the presence of sulfhysryl compounds, but not NO.

PMID: 29348096 [PubMed - indexed for MEDLINE]

The ImPreSS Trial: Implementation of Point-of-Care Pharmacogenomic Decision Support in Perioperative Care.

Clin Pharmacol Ther. 2019 Aug 21;:

Authors: Truong TM, Apfelbaum J, Shahul S, Anitescu M, Danahey K, Knoebel RW, Liebovitz D, Karrison T, van Wijk XMR, Yeo KJ, Meltzer D, Ratain MJ, O'Donnell PH

PMID: 31433489 [PubMed - as supplied by publisher]

A Rapid Phenotypic Whole-Cell Screening Approach for the Identification of Small-Molecule Inhibitors That Counter β-Lactamase Resistance in Pseudomonas aeruginosa.

SLAS Discov. 2018 01;23(1):55-64

Authors: Collia D, Bannister TD, Tan H, Jin S, Langaee T, Shumate J, Scampavia L, Spicer TP

Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that is prevalent in hospitals and continues to develop resistance to multiple classes of antibiotics. Historically, β-lactam antibiotics have been the first line of therapeutic defense. However, the emergence of multidrug-resistant (MDR) strains of P. aeruginosa, such as AmpC β-lactamase overproducing mutants, limits the effectiveness of current antibiotics. Among AmpC hyperproducing clinical isolates, inactivation of AmpG, which is essential for the expression of AmpC, increases bacterial sensitivity to β-lactam antibiotics. We hypothesize that inhibition of AmpG activity will enhance the efficacy of β-lactams against P. aeruginosa. Here, using a highly drug-resistant AmpC-inducible laboratory strain PAO1, we describe an ultra-high-throughput whole-cell turbidity assay designed to identify small-molecule inhibitors of the AmpG. We screened 645,000 compounds to identify compounds with the ability to inhibit bacterial growth in the presence of cefoxitin, an AmpC inducer, and identified 2663 inhibitors that were also tested in the absence of cefoxitin to determine AmpG specificity. The Z' and signal-to-background ratio were robust at 0.87 ± 0.05 and 2.2 ± 0.2, respectively. Through a series of secondary and tertiary studies, including a novel luciferase-based counterscreen, we ultimately identified eight potential AmpG-specific inhibitors.

PMID: 28850797 [PubMed - indexed for MEDLINE]

Genome-wide association study of cerebral small vessel disease reveals established and novel loci.

Brain. 2019 Aug 20;:

Authors: Chung J, Marini S, Pera J, Norrving B, Jimenez-Conde J, Roquer J, Fernandez-Cadenas I, Tirschwell DL, Selim M, Brown DL, Silliman SL, Worrall BB, Meschia JF, Demel S, Greenberg SM, Slowik A, Lindgren A, Schmidt R, Traylor M, Sargurupremraj M, Tiedt S, Malik R, Debette S, Dichgans M, Langefeld CD, Woo D, Rosand J, Anderson CD

Abstract
Intracerebral haemorrhage and small vessel ischaemic stroke (SVS) are the most acute manifestations of cerebral small vessel disease, with no established preventive approaches beyond hypertension management. Combined genome-wide association study (GWAS) of these two correlated diseases may improve statistical power to detect novel genetic factors for cerebral small vessel disease, elucidating underlying disease mechanisms that may form the basis for future treatments. Because intracerebral haemorrhage location is an adequate surrogate for distinct histopathological variants of cerebral small vessel disease (lobar for cerebral amyloid angiopathy and non-lobar for arteriolosclerosis), we performed GWAS of intracerebral haemorrhage by location in 1813 subjects (755 lobar and 1005 non-lobar) and 1711 stroke-free control subjects. Intracerebral haemorrhage GWAS results by location were meta-analysed with GWAS results for SVS from MEGASTROKE, using 'Multi-Trait Analysis of GWAS' (MTAG) to integrate summary data across traits and generate combined effect estimates. After combining intracerebral haemorrhage and SVS datasets, our sample size included 241 024 participants (6255 intracerebral haemorrhage or SVS cases and 233 058 control subjects). Genome-wide significant associations were observed for non-lobar intracerebral haemorrhage enhanced by SVS with rs2758605 [MTAG P-value (P) = 2.6 × 10-8] at 1q22; rs72932727 (P = 1.7 × 10-8) at 2q33; and rs9515201 (P = 5.3 × 10-10) at 13q34. In the GTEx gene expression library, rs2758605 (1q22), rs72932727 (2q33) and rs9515201 (13q34) are significant cis-eQTLs for PMF1 (P = 1 × 10-4 in tibial nerve), NBEAL1, FAM117B and CARF (P < 2.1 × 10-7 in arteries) and COL4A2 and COL4A1 (P < 0.01 in brain putamen), respectively. Leveraging S-PrediXcan for gene-based association testing with the predicted expression models in tissues related with nerve, artery, and non-lobar brain, we found that experiment-wide significant (P < 8.5 × 10-7) associations at three genes at 2q33 including NBEAL1, FAM117B and WDR12 and genome-wide significant associations at two genes including ICA1L at 2q33 and ZCCHC14 at 16q24. Brain cell-type specific expression profiling libraries reveal that SEMA4A, SLC25A44 and PMF1 at 1q22 and COL4A1 and COL4A2 at 13q34 were mainly expressed in endothelial cells, while the genes at 2q33 (FAM117B, CARF and NBEAL1) were expressed in various cell types including astrocytes, oligodendrocytes and neurons. Our cross-phenotype genetic study of intracerebral haemorrhage and SVS demonstrates novel genome-wide associations for non-lobar intracerebral haemorrhage at 2q33 and 13q34. Our replication of the 1q22 locus previous seen in traditional GWAS of intracerebral haemorrhage, as well as the rediscovery of 13q34, which had previously been reported in candidate gene studies with other cerebral small vessel disease-related traits strengthens the credibility of applying this novel genome-wide approach across intracerebral haemorrhage and SVS.

PMID: 31430377 [PubMed - as supplied by publisher]

Risk-benefit balance assessment of SSRI antidepressant use during pregnancy and lactation based on best available evidence - an update.

Expert Opin Drug Saf. 2019 Aug 20;:

Authors: Fischer Fumeaux CJ, Morisod Harari M, Weisskopf E, Eap CB, Epiney M, Vial Y, Csajka C, Bickle Graz M, Panchaud A

Abstract
Introduction: Depression affects 300 million individuals worldwide. While selective serotonin reuptake inhibitors (SSRI) are one of the first-line pharmacological treatments of major depression in the general population, there is still uncertainty regarding their potential benefits and risks during pregnancy. Areas covered: Outcomes requisite for a proper risk/benefit assessment of SSRI in pregnancy and lactation were considered: (a) potential risks associated with untreated depression, (b) effectiveness of different treatment options of depression, (c) potential risks associated with SSRI. Expert opinion: Despite the growing amount of literature on SSRI use during pregnancy, no new trials assessing the benefits of SSRIs on maternal depression were found. In the light of new data regarding the potential risks, depressed SSRI-treated pregnant women and their children seem at increased risk for several complications (mostly of small absolute risk). The interpretation of these findings remains quite similar to our previous review as the available methodogy doesn't allow to disentangle the potential effect of SSRIs from those of the disease itself or/and of its unmeasured associated risk factors. Thus, in pregnant or lactating women who require a pharmacological treatment, SSRIs can still be considered as appropriate when effective as the abundant data support their relative safety.

PMID: 31430189 [PubMed - as supplied by publisher]

Using Pharmacogenomic Testing in Primary Care: Protocol for a Pilot Randomized Controlled Study.

JMIR Res Protoc. 2019 Aug 19;8(8):e13848

Authors: Manzor Mitrzyk B, Kadri R, Farris KB, Ellingrod VL, Klinkman MS, Ruffin Iv MT, Plegue MA, Buis LR

Abstract
BACKGROUND: Antidepressants are used by primary care providers to treat a variety of conditions, including (but not limited to) depression and anxiety. A trial-and-error approach is typically used to identify effective therapy, as treatment efficacy and safety can vary based on the response, which is affected by certain gene types. Pharmacokinetic pharmacogenomic (PGx) testing provides phenotypic classification of individuals as poor, intermediate, extensive, and ultrarapid CYP450 metabolizers, providing information for optimal drug selection.
OBJECTIVE: The objective of this pilot study is to examine the feasibility, acceptability, and preliminary effectiveness of PGx testing when used after starting a new antidepressant medication.
METHODS: We are conducting a pilot study with physicians from 6 Department of Family Medicine clinics at the University of Michigan who are willing to use PGx test results to manage antidepressant medication use. From enrolled physicians, patients were recruited to participate in a 6-month randomized, wait-list controlled trial in which patient participants newly prescribed an antidepressant had PGx testing and were randomized equally to have the results released to their primary care physician as soon as results were available or after 3 months. Patients were excluded if they had been taking the antidepressant for more than 4 weeks or if they had undergone PGx testing in the past. Physician participants completed a baseline survey to assess demographics, as well as knowledge, feasibility, and acceptability of PGx testing for this population. At the conclusion of the study, physician participants will complete a survey to assess knowledge, satisfaction, feasibility, acceptability, perceived effectiveness, and barriers to widespread adoption of PGx testing. Patient participants will complete a baseline, 3-month, and 6-month assessment, and control patient participants will have an additional 9-month assessment. Data collected will include the reason for antidepressant use, self-reported medication adherence, side effects, patient health questionnaire 8-item depression scale, generalized anxiety disorder 7-item scale, 12-Item Short-Form Health Survey, work status or changes, and physician and emergency department visits. PGx knowledge and perceptions (including acceptability and feasibility) as well as demographic information will also be obtained.
RESULTS: We recruited 23 physician participants between November 2017 and January 2019, and 52 patient participants between January 2018 and April 2019. Currently, all physician and patient participants have been recruited, and we expect data collection to conclude in January 2020.
CONCLUSIONS: This study will examine the preliminary effectiveness of PGx testing after treatment initiation and determine the feasibility and acceptability of PGx testing for use in primary care. Through this study, we expect to demonstrate the benefit of PGx testing and lay the foundation for translating this approach into use within primary care.
TRIAL REGISTRATION: ClinicalTrials.gov NCT03270891; https://clinicaltrials.gov/ct2/show/NCT03270891.
INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR1-10.2196/13848.

PMID: 31429417 [PubMed]

Identification of Potential Crucial Genes and Key Pathways in Breast Cancer Using Bioinformatic Analysis.

Front Genet. 2019;10:695

Authors: Deng JL, Xu YH, Wang G

Abstract
Background: The molecular mechanism of tumorigenesis remains to be fully understood in breast cancer. It is urgently required to identify genes that are associated with breast cancer development and prognosis and to elucidate the underlying molecular mechanisms. In the present study, we aimed to identify potential pathogenic and prognostic differentially expressed genes (DEGs) in breast adenocarcinoma through bioinformatic analysis of public datasets. Methods: Four datasets (GSE21422, GSE29431, GSE42568, and GSE61304) from Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA) dataset were used for the bioinformatic analysis. DEGs were identified using LIMMA Package of R. The GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses were conducted through FunRich. The protein-protein interaction (PPI) network of the DEGs was established through STRING (Search Tool for the Retrieval of Interacting Genes database) website, visualized by Cytoscape and further analyzed by Molecular Complex Detection (MCODE). UALCAN and Kaplan-Meier (KM) plotter were employed to analyze the expression levels and prognostic values of hub genes. The expression levels of the hub genes were also validated in clinical samples from breast cancer patients. In addition, the gene-drug interaction network was constructed using Comparative Toxicogenomics Database (CTD). Results: In total, 203 up-regulated and 118 down-regulated DEGs were identified. Mitotic cell cycle and epithelial-to-mesenchymal transition pathway were the major enriched pathways for the up-regulated and down-regulated genes, respectively. The PPI network was constructed with 314 nodes and 1,810 interactions, and two significant modules are selected. The most significant enriched pathway in module 1 was the mitotic cell cycle. Moreover, six hub genes were selected and validated in clinical sample for further analysis owing to the high degree of connectivity, including CDK1, CCNA2, TOP2A, CCNB1, KIF11, and MELK, and they were all correlated to worse overall survival (OS) in breast cancer. Conclusion: These results revealed that mitotic cell cycle and epithelial-to-mesenchymal transition pathway could be potential pathways accounting for the progression in breast cancer, and CDK1, CCNA2, TOP2A, CCNB1, KIF11, and MELK may be potential crucial genes. Further, it could be utilized as new biomarkers for prognosis and potential new targets for drug synthesis of breast cancer.

PMID: 31428132 [PubMed]

Leveraging Genetic Findings for Precision Medicine in Vasculitis.

Front Immunol. 2019;10:1796

Authors: Acosta-Herrera M, González-Gay MA, Martín J, Márquez A

Abstract
Vasculitides are a heterogeneous group of low frequent disorders, mainly characterized by the inflammation of blood vessels that narrows or occlude the lumen and limits the blood flow, leading eventually to significant tissue and organ damage. These disorders are classified depending on the size of the affected blood vessels in large, medium, and small vessel vasculitis. Currently, it is known that these syndromes show a complex etiology in which both environmental and genetic factors play a major role in their development. So far, these conditions are not curable and the therapeutic approaches are mainly symptomatic. Moreover, a percentage of the patients do not adequately respond to standard treatments. Over the last years, numerous genetic studies have been carried out to identify susceptibility loci and biological pathways involved in vasculitis pathogenesis as well as potential genetic predictors of treatment response. The ultimate goal of these studies is to identify new therapeutic targets and to improve the use of existing drugs to achieve more effective treatments. This review will focus on the main advances made in the field of genetics and pharmacogenetics of vasculitis and their potential application for ameliorating long-term outcomes in patient management and in the development of precision medicine.

PMID: 31428096 [PubMed - in process]

Application of Economic Evaluation to Assess Feasibility for Reimbursement of Genomic Testing as Part of Personalized Medicine Interventions.

Front Pharmacol. 2019;10:830

Authors: Simeonidis S, Koutsilieri S, Vozikis A, Cooper DN, Mitropoulou C, Patrinos GP

Abstract
Background: The incorporation of genomic testing into clinical practice constitutes an opportunity to improve patients' lives, as it makes possible the implementation of innovative, individualized clinical interventions that maximize efficacy and/or minimize the risk of adverse drug reactions. In order to ensure equal access to genomic testing for all patients, the costs associated with these tests should be reimbursed by their respective national healthcare systems. Given that funding for the public health sector is decreasing in real terms, it is of paramount importance that the emerging interventions are thoroughly evaluated both in terms of their clinical effectiveness and their full economic cost. Objective: The aim of this study was to identify those genome-guided interventions that could be adopted and reimbursed by national healthcare systems. Further, we recorded the underlying factors determining the broad adoption of genome-guided interventions in clinical practice, in order to identify potential reimbursement criteria. Methods: We performed a systematic review of published (PubMed-listed) scientific articles on the economic evaluation of those individualized clinical interventions that include genomic tests. Information on genomic tests reimbursed by the US Medicare program was also included. Subsequently, we correlated the regulatory guidance given for the interventions collated in our systematic review with the corresponding economic evaluation results and policies of the Medicare program. Regulatory guidance information was collected from the PharmGKB online knowledgebase and the Clinical Pharmacogenetics Implementation Consortium (CPIC). Results: Most of the included studies constitute cost-utility analyses, in which the outcome of the interventions has been measured in quality-adjusted life years (QALYs) whereas an estimate of the total cost has been based upon direct medical cost data. Favorable economic evaluation results, as well as concrete evidence demonstrating the clinical utility of pre-emptive genotyping, are considered as prerequisites for the broad adoption and reimbursement of the costs incurred during genomic testing. Indicatively, pre-emptive HLA-B*5701 and TPMT testing before administration of abacavir and azathioprine, respectively, is reimbursed by Medicare based on both economic and efficacy evidence. Likewise, the medical necessary screening for MMR and BRCA1/2 genes are reimbursed for high-risk populations. Conclusions: Our findings further underline the need for further cost-utility analyses within different national healthcare systems, in order to promote the reimbursement of the cost of innovative genome-guided therapeutic interventions.

PMID: 31427963 [PubMed]

Absolute quantitation of drug metabolizing cytochrome P450 enzymes and accessory proteins in dog liver microsomes using label-free standard-free analysis reveals inter-breed variability.

Drug Metab Dispos. 2019 Aug 19;:

Authors: Martinez SE, Shi J, Zhu HJ, Perez Jimenez TE, Zhu Z, Court MH

Abstract
Dogs are commonly used in human and veterinary pharmaceutical development. Physiologically based pharmacokinetic modeling using recombinant cytochrome P450 (CYP) enzymes requires accurate estimates of CYP abundance, particularly in liver. However, such estimates are currently available for only seven CYPs, which were determined in a limited number of livers from one dog breed (Beagle). Here, we used a label-free shotgun proteomics method to quantitate eleven CYPs, (including four CYPs not previously measured), cytochrome P450 oxidoreductase, and cytochrome b5 in liver microsomes from 59 dogs representing four different breeds and mixed-breed dogs. Validation included showing correlation with CYP marker activities, immunoquantified protein, as well as CYP1A2 and CYP2C41 null allele genotypes. Abundance values largely agreed with those previously published. Average CYP abundance was highest (>120 pmol/mg protein) for CYP2D15 and CYP3A12; intermediate (40-89 pmol/mg) for CYP1A2, CYP2B11, CYP2E1, CYP2C21; and lowest (<12 pmol/mg) for CYP2A13, CYP2A25, CYP2C41, CYP3A26, and CYP1A1. The CYP2C41 gene was detected in 12 of 58 (21%) livers. CYP2C41 protein abundance averaged 8.2 pmol/mg in those livers, and was highest (19 pmol/mg) in the only liver with two CYP2C41 gene copies. CYP1A2 protein was not detected in the only liver homozygous for the CYP1A2 stop codon mutation. Large breed-associated differences were observed for CYP2B11 (P<0.0001; ANOVA) but not for other CYPs. Research Hounds and Beagles had the highest CYP2B11 abundance; mixed-breed dogs and Chihuahua were intermediate; while Greyhounds had the lowest abundance. These results provide the most comprehensive estimates to date of CYP abundance and variability in canine liver. SIGNIFICANCE STATEMENT: This work provides the most comprehensive quantitative analysis to date of the drug metabolizing cytochrome P450 proteome in dogs that will serve as a valuable reference for physiologically based scaling and modeling used in drug development and research. This study also revealed high interindividual variation and dog breed-associated differences in drug metabolizing cytochrome P450 expression that may be important for predicting drug disposition variability among a genetically diverse canine population.

PMID: 31427433 [PubMed - as supplied by publisher]

Baseline Genomic Features in BRAFV600-Mutated Metastatic Melanoma Patients Treated with BRAF Inhibitor + MEK Inhibitor in Routine Care.

Cancers (Basel). 2019 Aug 18;11(8):

Authors: Louveau B, Jouenne F, Reger de Moura C, Sadoux A, Baroudjian B, Delyon J, Herms F, De Masson A, Da Meda L, Battistella M, Dumaz N, Lebbe C, Mourah S

Abstract
In BRAFV600mut metastatic melanoma, the combination of BRAF and MEK inhibitors (BRAFi, MEKi) has undergone multiple resistance mechanisms, limiting its clinical benefit and resulting in the need for response predicting biomarkers. Based on phase III clinical trial data, several studies have previously explored baseline genomic features associated with response to BRAFi + MEKi. Using a targeted approach that combines the examination of mRNA expression and DNA alterations in a subset of genes, we performed an analysis of baseline genomic alterations involved in MAPK inhibitors' resistance in a real-life cohort of BRAFV600mut metastatic melanoma patients. Twenty-seven patients were included in this retrospective study, and tumor samples were analyzed when the BRAFi + MEKi therapy was initiated. The clinical characteristics of our cohort were consistent with previously published studies. The BRAFi + MEKi treatment was initiated in seven patients as a following-line treatment, and had a specific transcriptomic profile exhibiting 14 genes with lower mRNA expression. However, DNA alterations in CCND1, RB1, and MET were only observed in patients who received BRAFi + MEKi as the first-line treatment. Furthermore, KIT mRNA expression was significantly higher in patients showing clinical benefit from the combined therapy, emphasizing the tumor-suppressor role of KIT already described within the context of BRAF-mutant melanoma.

PMID: 31426590 [PubMed]

Improving the Utility of the Tox21 Dataset by Deep Metadata Annotations and Constructing Reusable Benchmarked Chemical Reference Signatures.

Molecules. 2019 Apr 23;24(8):

Authors: Cooper DJ, Schürer S

Abstract
The Toxicology in the 21st Century (Tox21) project seeks to develop and test methods for high-throughput examination of the effect certain chemical compounds have on biological systems. Although primary and toxicity assay data were readily available for multiple reporter gene modified cell lines, extensive annotation and curation was required to improve these datasets with respect to how FAIR (Findable, Accessible, Interoperable, and Reusable) they are. In this study, we fully annotated the Tox21 published data with relevant and accepted controlled vocabularies. After removing unreliable data points, we aggregated the results and created three sets of signatures reflecting activity in the reporter gene assays, cytotoxicity, and selective reporter gene activity, respectively. We benchmarked these signatures using the chemical structures of the tested compounds and obtained generally high receiver operating characteristic (ROC) scores, suggesting good quality and utility of these signatures and the underlying data. We analyzed the results to identify promiscuous individual compounds and chemotypes for the three signature categories and interpreted the results to illustrate the utility and re-usability of the datasets. With this study, we aimed to demonstrate the importance of data standards in reporting screening results and high-quality annotations to enable re-use and interpretation of these data. To improve the data with respect to all FAIR criteria, all assay annotations, cleaned and aggregate datasets, and signatures were made available as standardized dataset packages (Aggregated Tox21 bioactivity data, 2019).

PMID: 31018579 [PubMed - indexed for MEDLINE]

Pharmacogenes (PGx-genes): Current understanding and future directions.

Gene. 2019 Aug 16;:144050

Authors: Katara P, Yadav A

Abstract
Individual specific variable drug response against similar drugs raises a significant challenge for the effective and safe treatment of many human diseases. Pharmacogenomics is the branch which try to deal with these challenge by relating drug response to patient specific genome in orders to better customize patient treatments. Pharmacogenomics based research focus on the whole genome, but since last few years after realizing the importance, it mainly centralized towards genes of pharmacological importance called pharmacogenes, and try to explore association between their variants and variable drug response in world's different population. This research was initiated with the resulted data from human genome based research projects and later on assisted by exome sequencing projects. Simultaneously, it was boost-up with the participation of various pharmacogenomics groups lead by PGRN. By realizing the significance of pharmacogenes, and their variant related information, in health science, scientific communities are already started to look for genes of pharmacogenomics importance with different aspect. This article aims to provide an inclusive insight on current state of knowledge of pharmacogenes, recent trends and progress in the understanding of the pharmacogenes and the implications for personalized medicine.

PMID: 31425740 [PubMed - as supplied by publisher]

Therapeutic drug monitoring of olanzapine and cytochrome P450 genotyping in non-smoking subjects.

Ther Drug Monit. 2019 Aug 14;:

Authors: Miroshnichenko II, Pozhidaev IV, Ivanova SA, Baymeeva NV

Abstract
BACKGROUND: The relationship between a daily dose of olanzapine, its serum concentration, and the genotype of young non-smoking males treated for schizophrenia or schizophreniform disorder was investigated in day-to-day clinical practice. Pharmacogenetics was also examined for the selected patients.
METHODS: A total of 49 participants were recruited as in-patients at the Mental Health Research Center (Moscow, Russia). Inclusion criteria were patients who had been diagnosed with schizophrenia or schizoaffective disorder (following DSM-IV guidelines) and were being treated with OLZ. A prospective, observational, open-study design was implemented. In line with the literature, patients were only included if they attained steady-state OLZ concentrations lasting for at least 8 days. An LC-MS/MS method was developed for analyzing OLZ in human serum. The single cytochrome P450 polymorphisms were genotyped using an amplifier Real-Time PCR System following standard protocols.
RESULTS: Evidence indicating that CYP2D6 polymorphism has a significant (p=0.046) effect on the pharmacokinetics of olanzapine was obtained, confirming the beneficial effects of therapeutic drug monitoring for olanzapine.
CONCLUSION: TDM should therefore be used as a standard care during olanzapine therapy. TDM is also useful in assessing adherence and may have a role in limiting olanzapine dosage geared at minimizing the risk of long-term toxicity.

PMID: 31425442 [PubMed - as supplied by publisher]