Front Cardiovasc Med. 2021 Jul 12;8:675222. doi: 10.3389/fcvm.2021.675222. eCollection 2021.

ABSTRACT

Essential Hypertension (EH) results in the burden of cardiovascular disease (CVD) such as Heart Failure (HF) and Ischemic Stroke (IS). A rapidly emerging field involving the role of Wnt/β-catenin signaling pathway in cardiovascular development and dysfunction has recently drawn extensive attention. In the present study, we conducted a genetic association between genomic variants in Wnt/β-catenin signaling pathway and EH, HF, IS. A total of 95 SNPs in 12 Wnt signaling genes (WNT3A, WNT3, WNT4, DKK1, DKK2, LRP5, LRP6, CTNNB1, APC, FZD1, FRZB, SFRP1) were genotyped in 1,860 participants (440 patients with EH, 535 patients with HF, 421 patients with IS and 464 normal control subjects) using Sequenom MassArray technology. WNT3A rs752107(C > T) was strongly associated with an increased risk of EH, HF and IS. Compared with WNT3A rs752107 CC genotype, the CT genotype carriers had a 48% increased risk of EH (OR = 1.48, 95% CI = 1.12-1.96, P = 0.006), the TT genotype conferred a 139% increased risk of EH (OR = 2.39, 95% CI = 1.32-4.34, P = 0.003). Regarding HF and IS, the risk of HF in the T allele carriers (CT + TT) was nearly increased by 58% (OR = 1.58, 95% CI = 1.22-2.04, P = 4.40 × 10-4) and the risk of IS was increased by 37% (OR = 1.37, 95% CI = 1.04-1.79, P = 0.025). Expression quantitative trait loci (eQTL) analysis indicated that rs752107 C allele corresponded to a significant reduction of WNT3A expression. We described a genetic variant of WNT3A rs752107 in Wnt/β-catenin signaling strongly associated with the risk of EH, HF and IS for the first time.

PMID:34322525 | PMC:PMC8310949 | DOI:10.3389/fcvm.2021.675222

Front Genet. 2021 Jul 12;12:692234. doi: 10.3389/fgene.2021.692234. eCollection 2021.

ABSTRACT

Adverse drug reactions (ADRs) are one of the major causes of morbidity and mortality worldwide. It is well-known that individual genetic make-up is one of the causative factors of ADRs. Approximately 14 million single nucleotide polymorphisms (SNPs) are distributed throughout the entire human genome and every patient has a distinct genetic make-up which influences their response to drug therapy. Cytochrome P450 2B6 (CYP2B6) is involved in the metabolism of antiretroviral, antimalarial, anticancer, and antidepressant drugs. These drug classes are commonly in use worldwide and face specific population variability in side effects and dosing. Parts of this variability may be caused by single nucleotide polymorphisms (SNPs) in the CYP2B6 gene that are associated with altered protein expression and catalytic function. Population variability in the CYP2B6 gene leads to changes in drug metabolism which may result in adverse drug reactions or therapeutic failure. So far more than 30 non-synonymous variants in CYP2B6 gene have been reported. The occurrence of these variants show intra and interpopulation variability, thus affecting drug efficacy at individual and population level. Differences in disease conditions and affordability of drug therapy further explain why some individuals or populations are more exposed to CYP2B6 pharmacogenomics associated ADRs than others. Variabilities in drug efficacy associated with the pharmacogenomics of CYP2B6 have been reported in various populations. The aim of this review is to highlight reports from various ethnicities that emphasize on the relationship between CYP2B6 pharmacogenomics variability and the occurrence of adverse drug reactions. In vitro and in vivo studies evaluating the catalytic activity of CYP2B6 variants using various substrates will also be discussed. While implementation of pharmacogenomic testing for personalized drug therapy has made big progress, less data on pharmacogenetics of drug safety has been gained in terms of CYP2B6 substrates. Therefore, reviewing the existing evidence on population variability in CYP2B6 and ADR risk profiles suggests that, in addition to other factors, the knowledge on pharmacogenomics of CYP2B6 in patient treatment may be useful for the development of personalized medicine with regards to genotype-based prescription.

PMID:34322158 | PMC:PMC8313315 | DOI:10.3389/fgene.2021.692234

Front Immunol. 2021 Jul 12;12:695933. doi: 10.3389/fimmu.2021.695933. eCollection 2021.

ABSTRACT

Emerging evidence suggests a mechanistic role for myeloid-derived suppressor cells (MDSCs) in lung diseases like asthma. Previously, we showed that adoptive transfer of MDSCs dampens lung inflammation in murine models of asthma through cyclooxygenase-2 and arginase-1 pathways. Here, we further dissected this mechanism by studying the role and therapeutic relevance of the downstream mediator prostaglandin E2 receptor 4 (EP4) in a murine model of asthma. We adoptively transferred MDSCs generated using an EP4 agonist in a murine model of asthma and studied the consequences on airway inflammation. Furthermore, pegylated human arginase-1 was used to model MDSC effector activities. We demonstrate that the selective EP4 agonist L-902,688 increased the number and suppressive activity of MDSCs through arginase-1 and nitric oxide synthase-2. These results showed that adoptive transfer of EP4-primed MDSCs, EP4 agonism alone or arginase-1 administration ameliorated lung inflammatory responses and histopathological changes in asthmatic mice. Collectively, our results provide evidence that MDSCs dampen airway inflammation in murine asthma through a mechanism involving EP4.

PMID:34322123 | PMC:PMC8311661 | DOI:10.3389/fimmu.2021.695933

Front Pharmacol. 2021 Jul 12;12:682020. doi: 10.3389/fphar.2021.682020. eCollection 2021.

ABSTRACT

To elucidate current domestic factors influencing pharmacogenomics (PGx) implementation and its future in China, we conducted a questionnaire survey on PGx applications and testing. A questionnaire-based survey was created on the popular online professional survey platform "Wenjuanxing" (www.wjx.cn) and performed via the social media platform WeChat. Among 422 participants, there were physicians (27.7%), pharmacists (31.3%), and researchers (41.0%). We found that less than 50% of physicians were aware of the importance of PGx in drug therapy, while over 50% of pharmacists and researchers recognized the importance. Only 38.5% of physicians, 40.9% of pharmacists, and 55.5% of researchers concurred that PGx analysis could lower the economic burdens for patients. However, most of the responders affirmed that PGx should be effectively implemented in clinical practices. A lack of sector standards, a lack of clinical research, and a lack of guidelines were found to be the major factors for hindering PGx clinical application. Among drugs associated with PGx assays, the most common were warfarin and clopidogrel. Although PGx research has advanced rapidly in recent years in mainland China, the clinical implementation of PGx has a long way to go.

PMID:34322018 | PMC:PMC8311355 | DOI:10.3389/fphar.2021.682020

Front Neurosci. 2021 Jul 12;15:691244. doi: 10.3389/fnins.2021.691244. eCollection 2021.

ABSTRACT

OBJECTIVE: Neuroimaging measurements of brain structural integrity are thought to be surrogates for brain health, but precise assessments require dedicated advanced image acquisitions. By means of quantitatively describing conventional images, radiomic analyses hold potential for evaluating brain health. We sought to: (1) evaluate radiomics to assess brain structural integrity by predicting white matter hyperintensities burdens (WMH) and (2) uncover associations between predictive radiomic features and clinical phenotypes.

METHODS: We analyzed a multi-site cohort of 4,163 acute ischemic strokes (AIS) patients with T2-FLAIR MR images with total brain and WMH segmentations. Radiomic features were extracted from normal-appearing brain tissue (brain mask-WMH mask). Radiomics-based prediction of personalized WMH burden was done using ElasticNet linear regression. We built a radiomic signature of WMH with stable selected features predictive of WMH burden and then related this signature to clinical variables using canonical correlation analysis (CCA).

RESULTS: Radiomic features were predictive of WMH burden (R 2 = 0.855 ± 0.011). Seven pairs of canonical variates (CV) significantly correlated the radiomics signature of WMH and clinical traits with respective canonical correlations of 0.81, 0.65, 0.42, 0.24, 0.20, 0.15, and 0.15 (FDR-corrected p-values CV 1 - 6 < 0.001, p-value CV 7 = 0.012). The clinical CV1 was mainly influenced by age, CV2 by sex, CV3 by history of smoking and diabetes, CV4 by hypertension, CV5 by atrial fibrillation (AF) and diabetes, CV6 by coronary artery disease (CAD), and CV7 by CAD and diabetes.

CONCLUSION: Radiomics extracted from T2-FLAIR images of AIS patients capture microstructural damage of the cerebral parenchyma and correlate with clinical phenotypes, suggesting different radiographical textural abnormalities per cardiovascular risk profile. Further research could evaluate radiomics to predict the progression of WMH and for the follow-up of stroke patients' brain health.

PMID:34321995 | PMC:PMC8312571 | DOI:10.3389/fnins.2021.691244

Pharmgenomics Pers Med. 2021 Jul 21;14:893-903. doi: 10.2147/PGPM.S307827. eCollection 2021.

ABSTRACT

BACKGROUND: Complement component 5a (C5a) is a highly potent anaphylatoxin with a variety of pro-inflammatory effects. C5a contributes to progression of atherosclerosis and inhibition of the receptor (C5aR) might offer a therapeutic strategy in this regard. Single nucleotide polymorphisms (SNPs) of the C5 gene may modify protein expression levels and therefore function of C5a and C5aR. This study aimed to examine associations between clinically relevant C5a SNPs and the prognosis of patients with symptomatic coronary artery disease (CAD). Furthermore, we sought to investigate the influence of C5 SNPs on C5aR platelet surface expression and circulating C5a levels.

METHODS: C5 variants (rs25681, rs17611, rs17216529, rs12237774, rs41258306, and rs10985126) were analyzed in a consecutive cohort of 833 patients suffering from symptomatic coronary artery disease (CAD). Circulating C5a levels were determined in 116 patients whereas C5aR platelet surface expression was measured in 473 CAD patients. Endpoints included all-cause mortality, myocardial infarction (MI), and ischemic stroke (IS). Homozygous carriers (HC) of the minor allele (rs10985126) showed significantly higher all-cause mortality than major allele carriers. While we could not find significant associations between rs10985126 allele frequency and C5aR platelet surfazl ce expression, significantly elevated levels of circulating C5a were found in HC of the minor allele of the respective genotype. rs17216529 allele frequency correlated with the composite combined endpoint and bleeding events. However, since the number of HC of the minor allele of this genotype was low, we cannot draw a robust conclusion about the observed associations.

CONCLUSION: In this study, we provide evidence for the prognostic relevance of rs10985126 in CAD patients. C5 rs10985126 may serve as a prognostic biomarker for risk stratification in high-risk CAD patients and consequently promote tailored therapies.

PMID:34321906 | PMC:PMC8312322 | DOI:10.2147/PGPM.S307827

Sci Adv. 2021 Jul 28;7(31):eabf3657. doi: 10.1126/sciadv.abf3657. Print 2021 Jul.

ABSTRACT

Understanding of dedifferentiation, an indicator of poo prognosis for patients with thyroid cancer, has been hampered by imprecise and incomplete characterization of its heterogeneity and its attributes. Using single-cell RNA sequencing, we explored the landscape of thyroid cancer at single-cell resolution with 46,205 cells and delineated its dedifferentiation process and suppressive immune microenvironment. The developmental trajectory indicated that anaplastic thyroid cancer (ATC) cells were derived from a small subset of papillary thyroid cancer (PTC) cells. Moreover, a potential functional role of CREB3L1 on ATC development was revealed by integrated analyses of copy number alteration and transcriptional regulatory network. Multiple genes in differentiation-related pathways (e.g., EMT) were involved as the downstream targets of CREB3L1, increased expression of which can thus predict higher relapse risk of PTC. Collectively, our study provided insights into the heterogeneity and molecular evolution of thyroid cancer and highlighted the potential driver role of CREB3L1 in its dedifferentiation process.

PMID:34321197 | DOI:10.1126/sciadv.abf3657

Pharmacogenet Genomics. 2021 Jul 26. doi: 10.1097/FPC.0000000000000447. Online ahead of print.

ABSTRACT

The cytochrome P450 3A4 (CYP3A4) enzyme is the most abundant drug-metabolizing enzyme in the liver, displaying large inter-person variability with unknown causes. In this study, we found that the expression of CYP3A4 is negatively correlated with AC069294.1 (ENSG00000273407, ENST00000608397.1), a lncRNA generated antisense to CYP3A4. Knockdown of AC069294.1 in Huh7 cells increased CYP3A4 mRNA ~3-fold, whereas overexpression of AC069294.1 decreased CYP3A4 mRNA by 89%. We also observed changes in CYP3A5 expression when AC069294.1 was knocked down or overexpressed, indicating dual effects of AC069294.1 on both CYP3A4 and CYP3A5 expression. Consistently, the expression level of CYP3A5 is also negatively correlated with AC069294.1. Previous studies have shown associations between an intronic single nucleotide polymorphism CYP3A4*1G (rs2242480) and CYP3A metabolism, but the results are inconsistent and the underlying mechanism is unclear. We show here that CYP3A4*1G (rs2242480) is associated with 1.26-fold increased expression of AC069294.1 (P < 0.0001), and decreased expression of CYP3A4 by 31% (P = 0.008) and CYP3A5 by 39% (P = 0.004). CYP3A4*1G is located ~2.7 kb upstream of AC069294.1 and has been previously reported to have increased transcriptional activity in reporter gene assays. Taken together, our results demonstrate the regulation of CYP3A4 and CYP3A5 by a novel lncRNA AC069294.1. Our results also indicate that the clinically observed CYP3A4*1G associations may be caused by its effect on the expression of AC069294.1, and thereby altered expression of both CYP3A4 and CYP3A5. Furthermore, because CYP3A4*1G is in high linkage disequilibrium with CYP3A5*1, increased AC069294.1 expression caused by CYP3A4*1G may decrease expression of the normal-functioning CYP3A5*1, explaining additional inter-person variability of CYP3A5.

PMID:34320606 | DOI:10.1097/FPC.0000000000000447

Pharmacogenet Genomics. 2021 Jul 26. doi: 10.1097/FPC.0000000000000439. Online ahead of print.

ABSTRACT

OBJECTIVE: The aim of this study is to examine the association between genetic variations in deleted in liver cancer 1 (DLC1) gene with progression of the hepatitis B virus (HBV) infection.

METHODS: A total of 623 subjects were included in this study, of whom, 423 were chronic hepatitis B (CHB) patients without liver cirrhosis or hepatocellular carcinoma (HCC), 103 CHB with either liver cirrhosis ± HCC and 97 individuals who had resolved HBV. Two single-nucleotide polymorphisms rs3739298 and rs532841 of DLC1 gene were genotyped using the Sequenom MassARRAY platform.

RESULTS: Our results indicated significant differences between the chronic HBV and resolved HBV groups in genotype and allele frequencies of DLC1-rs3739298 [odds ratio (OR) = 2.23; 95% confidence interval (CI): 1.24-3.99; P = 0.007] and (OR = 1.54; 95% CI: 1.07-2.22; P = 0.021), respectively. Moreover, haplotype analysis revealed significant associations between chronicity of HBV with TG and GA haplotypes (P = 0.041 and P = 0.042), respectively.

CONCLUSION: A significant association exists between the rs3739298 variant and susceptibility to CHB infection.

PMID:34320605 | DOI:10.1097/FPC.0000000000000439

Clin Pharmacol Ther. 2021 Jul 28. doi: 10.1002/cpt.2340. Online ahead of print.

NO ABSTRACT

PMID:34318925 | DOI:10.1002/cpt.2340

PeerJ. 2021 Jul 15;9:e11774. doi: 10.7717/peerj.11774. eCollection 2021.

ABSTRACT

BACKGROUND: Pharmacogenetic variation is important to drug responses through diverse and complex mechanisms. Predictions of the functional impact of missense pharmacogenetic variants primarily rely on the degree of sequence conservation between species as a primary discriminator. However, idiosyncratic or off-target drug-variant interactions sometimes involve effects that are peripheral or accessory to the central systems in which a gene functions. Given the importance of sequence conservation to functional prediction tools-these idiosyncratic pharmacogenetic variants may violate the assumptions of predictive software commonly used to infer their effect.

METHODS: Here we exhaustively assess the effectiveness of eleven missense mutation functional inference tools on all known pharmacogenetic missense variants contained in the Pharmacogenomics Knowledgebase (PharmGKB) repository. We categorize PharmGKB entries into sub-classes to catalog likely off-target interactions, such that we may compare predictions across different variant annotations.

RESULTS: As previously demonstrated, functional inference tools perform variably across the complete set of PharmGKB variants, with large numbers of variants incorrectly classified as 'benign'. However, we find substantial differences amongst PharmGKB variant sub-classes, particularly in variants known to cause off-target, type B adverse drug reactions, that are largely unrelated to the main pharmacological action of the drug. Specifically, variants associated with off-target effects (hence referred to as off-target variants) were most often incorrectly classified as 'benign'. These results highlight the importance of understanding the underlying mechanism of pharmacogenetic variants and how variants associated with off-target effects will ultimately require new predictive algorithms.

CONCLUSION: In this work we demonstrate that functional inference tools perform poorly on pharmacogenetic variants, particularly on subsets enriched for variants causing off-target, type B adverse drug reactions. We describe how to identify variants associated with off-target effects within PharmGKB in order to generate a training set of variants that is needed to develop new algorithms specifically for this class of variant. Development of such tools will lead to more accurate functional predictions and pave the way for the increased wide-spread adoption of pharmacogenetics in clinical practice.

PMID:34316407 | PMC:PMC8286708 | DOI:10.7717/peerj.11774

Sci Rep. 2021 Jul 27;11(1):15304. doi: 10.1038/s41598-021-94700-9.

ABSTRACT

Weight gain is a frequent and severe adverse reaction in patients taking antipsychotics. The objective was to further investigate in a natural setting influential risk factors associated with clinically significant weight gain. An observational follow-up study was conducted. Patients when initiating treatment with whatever antipsychotic were included; a structured questionnaire was applied at baseline, 3 and 6 months later; a blood sample was obtained. In a nested case-control approach, patients with an increase ≥ 7% of their initial weight were considered as cases, the remaining, as controls. The results showed that, out of 185 patients, 137 completed the 6-month follow-up (cases, 38; controls, 99). Weight gain gradually and significantly increased in cases (baseline, 65.0 kg; 6 months, 74.0 kg) but not in controls (65.6 kg and 65.8 kg, respectively). Age (adjusted OR = 0.97, 95% CI = 0.96-0.99, p = 0.004), olanzapine (adjusted OR = 2.98, 95% CI = 1.13-7.80, p = 0.027) and quetiapine (adjusted OR = 0.25, 95% = 0.07-0.92, p = 0.037) significantly associated with weight gain. An association was also found for the CNR1 (rs1049353) and INSIG2 (rs7566605) polymorphisms. In conclusion, an increased risk of antipsychotics-induced weight gain was observed for younger age and olanzapine, and a relative lower risk for quetiapine. A potential role of CNR1 rs1049353 and INSIG2 rs7566605 polymorphisms is suggested.

PMID:34315947 | DOI:10.1038/s41598-021-94700-9

BMC Med Genomics. 2021 Jul 27;14(1):190. doi: 10.1186/s12920-021-01042-6.

ABSTRACT

BACKGROUND: Brachydactyly type A1 (BDA1) is an autosomal dominant disorder characterized by uniform shortening of the middle phalanges in all digits. It is associated with variants in the Indian Hedgehog (IHH) gene, which plays a key role in endochondral ossification. To date, heterozygous pathogenic IHH variants involving several codons, which are restricted to a specific region of the N-terminal active fragment of IHH, have been reported. The purpose of this study was to identify the pathogenic variant in a Japanese family with BDA1 and to evaluate its pathogenesis with regard to previous reports.

METHODS: The proband, a 9-year-old boy, his siblings, and his father had shortened digits and a short stature of variable severity. Based on physical examinations, radiographic findings and family history, they were diagnosed with BDA1. This family is the first case of an isolated malformation in Japan. Sanger sequencing of IHH was performed on these individuals and on the proband's unaffected mother. The significance of the variants was assessed using three-dimensional analysis methods.

RESULTS: Sanger sequencing showed a novel IHH heterozygous variant, NM_002181.4:c.544_549delTCAAAG(p.Ser182Lys183del) [NC_000002.12:g.219057461_219057466del].. These two residues are located outside the cluster region considered a hotspot of pathogenic variants. Three-dimensional modelling showed that S182 and K183 are located on the same surface as other residues associated with BDA1. Analysis of residue interactions across the interface between IHH and its interacting receptor protein revealed the presence of hydrogen bonds between them.

CONCLUSIONS: We report a novel variant, NM_002181.4:c.544_549delTCAAAG (p.Ser182Lys183del) [NC_000002.12:g.219057461_219057466del] in a Japanese family with BDA1. Indeed, neither variations in codons 182 or 183 nor with such two-amino-acid deletions in IHH have been reported previously. Although these two residues are located outside the cluster region considered a hotspot of pathogenic variants, we speculate that this variant causes BDA1 through impaired interactions between IHH and target receptor proteins in the same manner as other pathogenic variants located in the cluster region. This report expands the genetic spectrum of BDA1.

PMID:34315464 | DOI:10.1186/s12920-021-01042-6

Curr Drug Saf. 2021 Jul 27. doi: 10.2174/1574886316666210727155227. Online ahead of print.

ABSTRACT

AIMS: The aim of this study was to determine if there are discrepancies among various agency-approved labels for the same active ingredient and where the labels approved by the Turkish Medicines and Medical Devices Agency (TMMDA) stand regarding the inclusion of PGx and discuss these ethical implications.

BACKGROUND: The efficacy and safety of drugs can be improved by rational prescription and personalization of medicine for each patient. Pharmacogenomics information (PGx) in drug labels (DL) is one of the important tools for the personalization of medications because genetic differences may affect both drug efficacy and safety. Providing adequate PGx to patients has ethical implications.

OBJECTIVE: To evaluate PGx in the DLs approved by TMMDA and other national agencies provided by the Pharmacogenomics Knowledgebase.

METHODS: DL annotations from the Pharmacogenomics Knowledgebase and DLs approved by the TMMDA were analyzed according to information and action levels, which are "testing required", "testing recommended", "actionable", and "informative".

RESULTS: There are 381 drugs listed in PharmGKB drug label annotations with pharmacogenomics information and 278 of these have biomarkers. A total of 242 (63.5%) drugs are approved and available in Turkey. Of these, 207 (85.5%) contain the same information as in or similar to that in the labels approved by the other agencies. The presence and level of information varied among the DLs approved by different agencies. The inconsistencies may have an important effect on the efficacy and the safety of drugs.

CONCLUSION: These findings suggest a need for the standardization of PGx information globally because it may not only affect the efficacy and safety of medications but also essential ethical rules regarding patient rights by violating not sufficiently sharing all available information.

PMID:34315387 | DOI:10.2174/1574886316666210727155227

Trials. 2021 Jul 26;22(1):487. doi: 10.1186/s13063-021-05458-4.

ABSTRACT

BACKGROUND: There is an urgent unmet clinical need for the identification of novel therapeutics for the treatment of COVID-19. A number of COVID-19 late phase trial platforms have been developed to investigate (often repurposed) drugs both in the UK and globally (e.g. RECOVERY led by the University of Oxford and SOLIDARITY led by WHO). There is a pressing need to investigate novel candidates within early phase trial platforms, from which promising candidates can feed into established later phase platforms. AGILE grew from a UK-wide collaboration to undertake early stage clinical evaluation of candidates for SARS-CoV-2 infection to accelerate national and global healthcare interventions.

METHODS/DESIGN: AGILE is a seamless phase I/IIa platform study to establish the optimum dose, determine the activity and safety of each candidate and recommend whether it should be evaluated further. Each candidate is evaluated in its own trial, either as an open label single arm healthy volunteer study or in patients, randomising between candidate and control usually in a 2:1 allocation in favour of the candidate. Each dose is assessed sequentially for safety usually in cohorts of 6 patients. Once a phase II dose has been identified, efficacy is assessed by seamlessly expanding into a larger cohort. AGILE is completely flexible in that the core design in the master protocol can be adapted for each candidate based on prior knowledge of the candidate (i.e. population, primary endpoint and sample size can be amended). This information is detailed in each candidate specific trial protocol of the master protocol.

DISCUSSION: Few approved treatments for COVID-19 are available such as dexamethasone, remdesivir and tocilizumab in hospitalised patients. The AGILE platform aims to rapidly identify new efficacious and safe treatments to help end the current global COVID-19 pandemic. We currently have three candidate specific trials within this platform study that are open to recruitment.

TRIAL REGISTRATION: EudraCT Number: 2020-001860-27 14 March 2020 ClinicalTrials.gov Identifier: NCT04746183 19 February 2021 ISRCTN reference: 27106947.

PMID:34311777 | PMC:PMC8311065 | DOI:10.1186/s13063-021-05458-4

Am J Hum Genet. 2021 Jul 21:S0002-9297(21)00269-X. doi: 10.1016/j.ajhg.2021.07.001. Online ahead of print.

ABSTRACT

CYP2C9 encodes a cytochrome P450 enzyme responsible for metabolizing up to 15% of small molecule drugs, and CYP2C9 variants can alter the safety and efficacy of these therapeutics. In particular, the anti-coagulant warfarin is prescribed to over 15 million people annually and polymorphisms in CYP2C9 can affect individual drug response and lead to an increased risk of hemorrhage. We developed click-seq, a pooled yeast-based activity assay, to test thousands of variants. Using click-seq, we measured the activity of 6,142 missense variants in yeast. We also measured the steady-state cellular abundance of 6,370 missense variants in a human cell line by using variant abundance by massively parallel sequencing (VAMP-seq). These data revealed that almost two-thirds of CYP2C9 variants showed decreased activity and that protein abundance accounted for half of the variation in CYP2C9 function. We also measured activity scores for 319 previously unannotated human variants, many of which may have clinical relevance.

PMID:34314704 | DOI:10.1016/j.ajhg.2021.07.001

Clin Pharmacol Ther. 2021 Jul 27. doi: 10.1002/cpt.2379. Online ahead of print.

ABSTRACT

MiRNAs regulate the expression of hepatic genes involved in pharmacokinetics and pharmacodynamics. Genetic variants affecting miRNA binding (mirSNPs) have been associated with altered drug response, but previously used methods to identify miRNA binding sites and functional mirSNPs in pharmacogenes are indirect and limited by low throughput. We utilized the high-throughput chimeric-eCLIP assay to directly map thousands of miRNA-mRNA interactions and define the miRNA binding sites in primary hepatocytes. We then used the high-throughput PASSPORT-seq assay to functionally test 262 potential mirSNPs with coordinates overlapping the identified miRNA binding sites. Using chimeric-eCLIP, we identified a network of 448 miRNAs that collectively target 11,263 unique genes in primary hepatocytes pooled from 100 donors. Our data provide an extensive map of miRNA binding of each gene, including pharmacogenes, expressed in primary hepatocytes. For example, we identified the hsa-mir-27b-DPYD interaction at a previously validated binding site. A second example is our identification of 19 unique miRNAs that bind to CYP2B6 across 20 putative binding sites on the transcript. Using PASSPORT-seq, we then identified twenty-four mirSNPs that functionally impacted reporter mRNA levels. To our knowledge this is the most comprehensive identification of miRNA binding sites in pharmacogenes. Combining chimeric-eCLIP with PASSPORT-seq successfully identified functional mirSNPs in pharmacogenes that may affect transcript levels through altered miRNA binding. These results provide additional insights into potential mechanisms contributing to interindividual variability in drug response.

PMID:34314509 | DOI:10.1002/cpt.2379

IEEE J Biomed Health Inform. 2021 Jul 27;PP. doi: 10.1109/JBHI.2021.3100424. Online ahead of print.

ABSTRACT

The identification of mutation markers and the selection of appropriate treatment for patients with specific genome mutations are important steps in the development of targeted therapies and the realization of precision medicine for human cancers. To investigate the baseline characteristics of drug sensitivity markers and develop computational methods of mutation effect prediction, we presented a manually curated online- based database of mutation Markers for anti-Cancer drug Sensitivity (dbMCS). Currently, dbMCS contains 1271 mutations and 4427 mutation-disease-drug associations (3151 and 1276 for sensitivity and resistance, respectively) with their PubMed indexed articles. By comparing the mutations in dbMCS with the putative neutral polymorphisms, we investigated the characteristics of drug sensitivity markers. We found that the mutation markers tend to significantly impact on high-conservative regions both in DNA sequences and protein domains. And some of them presented pleiotropic effects depending on the tumor context, appearing concurrently in the sensitivity and resistance categories. In addition, we preliminarily explored the machine learning-based methods for identifying mutation markers of anti-cancer drug sensitivity and produced optimistic results, which suggests that a reliable dataset may provide new insights and essential clues for future cancer pharmacogenomics studies. dbMCS is available at http://bioinfo.aielab.cc/dbMCS/.

PMID:34314366 | DOI:10.1109/JBHI.2021.3100424

Dig Dis Sci. 2021 Jul 27. doi: 10.1007/s10620-021-07177-x. Online ahead of print.

ABSTRACT

BACKGROUND: Sex and gender refer to biological and social differences between men and women. While well-evaluated in other disciplines, their roles in inflammatory bowel disease (IBD) are not well-defined. This study aimed to characterize differences in healthcare outcomes in men and women with IBD.

METHODS: A retrospective single-centre cohort study was conducted to evaluate differences between men and women receiving care for Crohn's disease (CD) and ulcerative colitis (UC) at the Western University Personalized Medicine Clinic from March 2012 to September 2019. The primary endpoint was the proportion of IBD drugs used for all drug classes. Additional outcomes in healthcare utilization and disease phenotype were assessed. Student's t test and Fisher's exact test were used to assess differences RESULTS: A total of 1015 participants were included (CD = 656; UC = 359). In UC and CD, 47.9% and 59.0% were women, respectively. Overall, women were more likely prescribed budesonide than men (23.6% vs. 13.4%; p < 0.0001), while more men were exposed to prednisone for IBD management (73.5% vs. 67.4%; p = 0.04). Immunomodulator use was higher in men with CD versus women (86.6% vs. 78.3%; p = 0.008) and of those exposed, women more commonly experienced ADRs (29.5% vs. 21.2%; p = 0.01). Though no sex-related difference was identified, age was a predictor of biologic exposure in women with CD and men with UC, with those > 55 being less likely to receive biologics.

CONCLUSIONS: These findings highlight differences in disease course and treatment approaches between men and women with IBD and support the consideration of sex and gender when researching disease outcomes.

PMID:34313923 | DOI:10.1007/s10620-021-07177-x

Mol Genet Genomic Med. 2021 Jul 27:e1766. doi: 10.1002/mgg3.1766. Online ahead of print.

ABSTRACT

BACKGROUND: Genome sequencing (GS) of individuals without a medical indication, known as elective GS, is now available at a number of centers around the United States. Here we report the results of elective GS and pharmacogenetic panel testing in 52 individuals at a private genomics clinic in Alabama.

METHODS: Individuals seeking elective genomic testing and pharmacogenetic testing were recruited through a private genomics clinic in Huntsville, AL. Individuals underwent clinical genome sequencing with a separate pharmacogenetic testing panel.

RESULTS: Six participants (11.5%) had pathogenic or likely pathogenic variants that may explain one or more aspects of their medical history. Ten participants (19%) had variants that altered the risk of disease in the future, including two individuals with clonal hematopoiesis of indeterminate potential. Forty-four participants (85%) were carriers of a recessive or X-linked disorder. All individuals with pharmacogenetic testing had variants that affected current and/or future medications.

CONCLUSION: Our study highlights the importance of collecting detailed phenotype information to interpret results in elective GS.

PMID:34313030 | DOI:10.1002/mgg3.1766