1
|
Tremmel R, Zhou Y, Schwab M, Lauschke VM. Structural variation of the coding and non-coding human pharmacogenome. NPJ Genom Med 2023; 8:24. [PMID: 37684227 PMCID: PMC10491600 DOI: 10.1038/s41525-023-00371-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Genetic variants in drug targets and genes encoding factors involved in drug absorption, distribution, metabolism and excretion (ADME) can have pronounced impacts on drug pharmacokinetics, response, and toxicity. While the landscape of genetic variability at the level of single nucleotide variants (SNVs) has been extensively studied in these pharmacogenetic loci, their structural variation is only poorly understood. Thus, we systematically analyzed the genetic structural variability across 908 pharmacogenes (344 ADME genes and 564 drug targets) based on publicly available whole genome sequencing data from 10,847 unrelated individuals. Overall, we extracted 14,984 distinct structural variants (SVs) ranging in size from 50 bp to 106 Mb. Each individual harbored on average 10.3 and 1.5 SVs with putative functional effects that affected the coding regions of ADME genes and drug targets, respectively. In addition, by cross-referencing pharmacogenomic SVs with experimentally determined binding data of 224 transcription factors across 130 cell types, we identified 1276 non-coding SVs that overlapped with gene regulatory elements. Based on these data, we estimate that non-coding structural variants account for 22% of the genetically encoded pharmacogenomic variability. Combined, these analyses provide the first comprehensive map of structural variability across pharmacogenes, derive estimates for the functional impact of non-coding SVs and incentivize the incorporation of structural genomic data into personalized drug response predictions.
Collapse
Affiliation(s)
- Roman Tremmel
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University Tübingen, Tübingen, Germany
| | - Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Matthias Schwab
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University Tübingen, Tübingen, Germany
- Departments of Clinical Pharmacology and Pharmacy and Biochemistry, University Tübingen, Tübingen, Germany
| | - Volker M Lauschke
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.
- University Tübingen, Tübingen, Germany.
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
2
|
Yang M, Xu X. Important roles of transporters in the pharmacokinetics of anti-viral nucleoside/nucleotide analogs. Expert Opin Drug Metab Toxicol 2022; 18:483-505. [PMID: 35975669 PMCID: PMC9506706 DOI: 10.1080/17425255.2022.2112175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/02/2022] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Nucleoside analogs are an important class of antiviral agents. Due to the high hydrophilicity and limited membrane permeability of antiviral nucleoside/nucleotide analogs (AVNAs), transporters play critical roles in AVNA pharmacokinetics. Understanding the properties of these transporters is important to accelerate translational research for AVNAs. AREAS COVERED The roles of key transporters in the pharmacokinetics of 25 approved AVNAs were reviewed. Clinically relevant information that can be explained by the modulation of transporter functions is also highlighted. EXPERT OPINION Although the roles of transporters in the intestinal absorption and renal excretion of AVNAs have been well identified, more research is warranted to understand their roles in the distribution of AVNAs, especially to immune privileged compartments where treatment of viral infection is challenging. P-gp, MRP4, BCRP, and nucleoside transporters have shown extensive impacts in the disposition of AVNAs. It is highly recommended that the role of transporters should be investigated during the development of novel AVNAs. Clinically, co-administered inhibitors and genetic polymorphism of transporters are the two most frequently reported factors altering AVNA pharmacokinetics. Physiopathology conditions also regulate transporter activities, while their effects on pharmacokinetics need further exploration. Pharmacokinetic models could be useful for elucidating these complicated factors in clinical settings.
Collapse
Affiliation(s)
- Mengbi Yang
- Drug Metabolism and Pharmacokinetics, Division of Preclinical Innovation (DPI), National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Xin Xu
- Drug Metabolism and Pharmacokinetics, Division of Preclinical Innovation (DPI), National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| |
Collapse
|
3
|
Biswas M, Sawajan N, Rungrotmongkol T, Sanachai K, Ershadian M, Sukasem C. Pharmacogenetics and Precision Medicine Approaches for the Improvement of COVID-19 Therapies. Front Pharmacol 2022; 13:835136. [PMID: 35250581 PMCID: PMC8894812 DOI: 10.3389/fphar.2022.835136] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/24/2022] [Indexed: 01/18/2023] Open
Abstract
Many drugs are being administered to tackle coronavirus disease 2019 (COVID-19) pandemic situations without establishing clinical effectiveness or tailoring safety. A repurposing strategy might be more effective and successful if pharmacogenetic interventions are being considered in future clinical studies/trials. Although it is very unlikely that there are almost no pharmacogenetic data for COVID-19 drugs, however, from inferring the pharmacokinetic (PK)/pharmacodynamic(PD) properties and some pharmacogenetic evidence in other diseases/clinical conditions, it is highly likely that pharmacogenetic associations are also feasible in at least some COVID-19 drugs. We strongly mandate to undertake a pharmacogenetic assessment for at least these drug–gene pairs (atazanavir–UGT1A1, ABCB1, SLCO1B1, APOA5; efavirenz–CYP2B6; nevirapine–HLA, CYP2B6, ABCB1; lopinavir–SLCO1B3, ABCC2; ribavirin–SLC28A2; tocilizumab–FCGR3A; ivermectin–ABCB1; oseltamivir–CES1, ABCB1; clopidogrel–CYP2C19, ABCB1, warfarin–CYP2C9, VKORC1; non-steroidal anti-inflammatory drugs (NSAIDs)–CYP2C9) in COVID-19 patients for advancing precision medicine. Molecular docking and computational studies are promising to achieve new therapeutics against SARS-CoV-2 infection. The current situation in the discovery of anti-SARS-CoV-2 agents at four important targets from in silico studies has been described and summarized in this review. Although natural occurring compounds from different herbs against SARS-CoV-2 infection are favorable, however, accurate experimental investigation of these compounds is warranted to provide insightful information. Moreover, clinical considerations of drug–drug interactions (DDIs) and drug–herb interactions (DHIs) of the existing repurposed drugs along with pharmacogenetic (e.g., efavirenz and CYP2B6) and herbogenetic (e.g., andrographolide and CYP2C9) interventions, collectively called multifactorial drug–gene interactions (DGIs), may further accelerate the development of precision COVID-19 therapies in the real-world clinical settings.
Collapse
Affiliation(s)
- Mohitosh Biswas
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
- Department of Pharmacy, University of Rajshahi, Rajshahi, Bangladesh
| | - Nares Sawajan
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
- Department of Pathology, School of Medicine, Mae Fah Luang University, Chiang Rai, Thailand
| | - Thanyada Rungrotmongkol
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Kamonpan Sanachai
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Maliheh Ershadian
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
| | - Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Laboratory for Pharmacogenomics, Somdech Phra Debaratana Medical Center (SDMC), Ramathibodi Hospital, Bangkok, Thailand
- Pharmacogenomics and Precision Medicine, The Preventive Genomics and Family Check-up Services Center, Bumrungrad International Hospital, Bangkok, Thailand
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- *Correspondence: Chonlaphat Sukasem,
| |
Collapse
|
4
|
Fernandes MR, Rodrigues JCG, Dobbin EAF, Pastana LF, da Costa DF, Barra WF, Modesto AAC, de Assumpção PB, da Costa Silva AL, Dos Santos SEB, Burbano RMR, de Assumpção PP, Dos Santos NPC. Influence of FPGS, ABCC4, SLC29A1, and MTHFR genes on the pharmacogenomics of fluoropyrimidines in patients with gastrointestinal cancer from the Brazilian Amazon. Cancer Chemother Pharmacol 2021; 88:837-844. [PMID: 34331561 DOI: 10.1007/s00280-021-04327-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 06/16/2021] [Indexed: 12/24/2022]
Abstract
PURPOSE Fluoropyrimidines are one of the most used drug class to treat cancer patients, although they show high levels of associated toxicity. This study analyzed 33 polymorphisms in 17 pharmacogenes involved with the pharmacogenomics of fluoropyrimidines, in gastrointestinal cancer patients undergoing fluoropyrimidine-based treatment in the Brazilian Amazon. METHODS The study population was composed of 216 patients, 92 of whom have an anatomopathological diagnosis of gastric cancer and 124 of colorectal cancer. The single nucleotide polymorphisms (SNP) were genotyped by allelic discrimination using the TaqMan OpenArray Genotyping technology, with a panel of 32 customized assays, run in a QuantStudio ™ 12K Flex Real-Time PCR System (Applied Biosystems, Life Technologies, Carlsbad USA). Ancestry analysis was performed using 61 autosomal ancestry informative markers (AIMs). RESULTS The study population show mean values of 48.1% European, 31.1% Amerindian, and 20.8% African ancestries. A significant risk association for general and severe toxicity was found in the rs4451422 of FPGS (p = 0.001; OR 3.40; CI 95% 1.65-7.00 and p = 0.006; OR 4.63; CI 95% 1.56-13.72, respectively) and the rs9524885 of ABCC4 (p = 0.023; OR 2.74; CI 95% 1.14-6.65 and p = 0.024; OR 5.36; IC 95% 1.24-23.11, respectively) genes. The rs760370 in the SLC29A1 gene (p = 0.009; OR 6.71; CI 95% 1.16-8.21) and the rs1801133 in the MTHFR toxicity (p = 0.023; OR 3.09; CI 95% 1.16-8.21) gene also demonstrated to be significant, although only for severe toxicity. The results found in this study did not have statistics analysis correction. CONCLUSION Four polymorphisms of the ABCC4, FPGS, SLC29A1, and MTHFR genes are likely to be potential predictive biomarkers for precision medicine in fluoropyrimidine-based treatments in the population of the Brazilian Amazon, which is constituted by a unique genetic background.
Collapse
Affiliation(s)
- Marianne Rodrigues Fernandes
- Núcleo de Pesquisas Em Oncologia, Universidade Federal Do Pará, Belém, Pará, Brazil.,Hospital Ophir Loyola, Belém, Pará, Brazil
| | | | | | | | | | | | | | | | - Artur Luiz da Costa Silva
- Centro de Genômica E Biologia de Sistemas, Instituto de Ciências Biológicas, Universidade Federal Do Pará, Belém, Pará, Brazil
| | | | - Rommel Mario Rodriguez Burbano
- Núcleo de Pesquisas Em Oncologia, Universidade Federal Do Pará, Belém, Pará, Brazil.,Hospital Ophir Loyola, Belém, Pará, Brazil
| | | | | |
Collapse
|
5
|
Sakran R, Frisch A, Elias A, Sliman H, Ammuri H, Kurnik D. Acute and severe ribavirin-associated hyperuricemia and acute kidney injury: An underrecognized adverse effect. Am J Health Syst Pharm 2021; 78:794-799. [PMID: 33617629 PMCID: PMC7929397 DOI: 10.1093/ajhp/zxab043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Disclaimer In an effort to expedite the publication of articles related to the COVID-19 pandemic, AJHP is posting these manuscripts online as soon as possible after acceptance. Accepted manuscripts have been peer-reviewed and copyedited, but are posted online before technical formatting and author proofing. These manuscripts are not the final version of record and will be replaced with the final article (formatted per AJHP style and proofed by the authors) at a later time. Purpose To report a case of ribavirin-associated severe hyperuricemia in an immunocompromised patient treated for respiratory syncytial virus (RSV) infection. Summary A 21-year-old male with a past medical history of B-cell acute lymphoblastic leukemia was in full remission after allogenic bone marrow transplantation complicated with chronic graft-versus-host disease. He was hospitalized due to fever, malaise, and respiratory syndromes. A diagnosis of RSV upper respiratory tract infection complicated by secondary pneumonia was made, and oral ribavirin (600 mg in 3 divided doses daily) and intravenous levofloxacin (750 mg once daily) were initiated. On day 2 of the hospital admission, the patient’s uric acid levels had increased from a baseline of 4 to 6 mg/dL to values of 19.3 and 22.2 mg/dL after the fourth and fifth doses of ribavirin, respectively, and his serum creatinine steadily had increased from a baseline of 0.7 to 0.8 mg/dL to a value of 1.6 mg/dL. Ribavirin was discontinued after the sixth dose, and a single dose of intravenous rasburicase (7.5 mg) was administered. On day 3, the patient’s serum uric and creatinine concentrations had decreased to 4.7 mg/dL and 1.1 mg/dL, respectively. He continued to recover on antibiotics and was discharged with normal uric acid and serum creatinine levels. Conclusion We report a case of severe hyperuricemia and acute kidney injury that developed early after initiation of ribavirin for RSV infection and suspected bacterial pneumonia in an immunocompromised patient without hepatitis C, requiring ribavirin discontinuation and rasburicase administration. To our knowledge, this is the first reported case of severe hyperuricemia in a patient treated with ribavirin for RSV infection rather than chronic hepatitis C. Clinicians should be aware of the possibility of acute and severe hyperuricemia following ribavirin administration.
Collapse
Affiliation(s)
- Razan Sakran
- Section of Clinical Pharmacology and Toxicology, Rambam Health Care Campus, Haifa, Israel
| | - Avraham Frisch
- Department of Hematology, Rambam Health Care Campus, Haifa, Israel
| | - Adi Elias
- Department of Internal Medicine, Rambam Health Care Campus, Haifa, Israel
| | - Hend Sliman
- Medical Intensive Care Unit, Rambam Health Care Campus, Haifa, Israel
| | - Hanna Ammuri
- Medical Intensive Care Unit, Rambam Health Care Campus, Haifa, Israel
| | - Daniel Kurnik
- Section of Clinical Pharmacology and Toxicology, Rambam Health Care Campus, Haifa, Israel.,Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| |
Collapse
|
6
|
Takahashi T, Luzum JA, Nicol MR, Jacobson PA. Pharmacogenomics of COVID-19 therapies. NPJ Genom Med 2020; 5:35. [PMID: 32864162 PMCID: PMC7435176 DOI: 10.1038/s41525-020-00143-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/23/2020] [Indexed: 02/06/2023] Open
Abstract
A new global pandemic of coronavirus disease 2019 (COVID-19) has resulted in high mortality and morbidity. Currently numerous drugs are under expedited investigations without well-established safety or efficacy data. Pharmacogenomics may allow individualization of these drugs thereby improving efficacy and safety. In this review, we summarized the pharmacogenomic literature available for COVID-19 drug therapies including hydroxychloroquine, chloroquine, azithromycin, remdesivir, favipiravir, ribavirin, lopinavir/ritonavir, darunavir/cobicistat, interferon beta-1b, tocilizumab, ruxolitinib, baricitinib, and corticosteroids. We searched PubMed, reviewed the Pharmacogenomics Knowledgebase (PharmGKB®) website, Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines, the U.S. Food and Drug Administration (FDA) pharmacogenomics information in the product labeling, and the FDA pharmacogenomics association table. We found several drug-gene variant pairs that may alter the pharmacokinetics of hydroxychloroquine/chloroquine (CYP2C8, CYP2D6, SLCO1A2, and SLCO1B1); azithromycin (ABCB1); ribavirin (SLC29A1, SLC28A2, and SLC28A3); and lopinavir/ritonavir (SLCO1B1, ABCC2, CYP3A). We also identified other variants, that are associated with adverse effects, most notable in hydroxychloroquine/chloroquine (G6PD; hemolysis), ribavirin (ITPA; hemolysis), and interferon β -1b (IRF6; liver toxicity). We also describe the complexity of the risk for QT prolongation in this setting because of additive effects of combining more than one QT-prolonging drug (i.e., hydroxychloroquine/chloroquine and azithromycin), increased concentrations of the drugs due to genetic variants, along with the risk of also combining therapy with potent inhibitors. In conclusion, although direct evidence in COVID-19 patients is lacking, we identified potential actionable genetic markers in COVID-19 therapies. Clinical studies in COVID-19 patients are deemed warranted to assess potential roles of these markers.
Collapse
Affiliation(s)
- Takuto Takahashi
- Department of Experimental and Clinical Pharmacology, College of Pharmacy University of Minnesota, Minneapolis, MN USA
- Division of Hematology/Oncology/Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, MN USA
| | - Jasmine A. Luzum
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI USA
| | - Melanie R. Nicol
- Department of Experimental and Clinical Pharmacology, College of Pharmacy University of Minnesota, Minneapolis, MN USA
| | - Pamala A. Jacobson
- Department of Experimental and Clinical Pharmacology, College of Pharmacy University of Minnesota, Minneapolis, MN USA
| |
Collapse
|
7
|
Abdelkawy KS, El-Haggar SM, Ziada DH, Ebaid NF, El-Magd MA, Elbarbry FA. The effect of genetic variations on ribavirin pharmacokinetics and treatment response in HCV-4 Egyptian patients receiving sofosbuvir/daclatasvir and ribavirin. Biomed Pharmacother 2019; 121:109657. [PMID: 31810127 DOI: 10.1016/j.biopha.2019.109657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/04/2019] [Accepted: 11/06/2019] [Indexed: 12/21/2022] Open
Abstract
PURPOSE This study aimed to investigate the effect of single nucleotide polymorphisms (SNPs) of genes involved in ribavirin (RBV) transport (SLC28A2 gene, ABCB1 gene and ABCB11 gene) on the clinical outcome and pharmacokinetics of ribavirin in HCV- 4 Egyptian patients. METHOD 100 patients treated with sofosbuvir/daclatasvir and ribavirin for 12 weeks. The SNP genotyping was performed by real-time PCR using high resolution melting analysis. Ribavirin plasma trough concentrations were determined at week 4 of therapy using a liquid chromatography/tandem mass spectrometry (LC-MS/MS). For clinical outcomes, sustained virological response (SVR), liver function tests (ALT and AST), total bilirubin, albumin, serum creatinine, hemoglobin, leukocyte count, and platelet count were measured. RESULTS Concerning RBV pharmacokinetics, ABCB1 2677 G > T SNP and ABCB11 1331 T > C SNP were statistically associated with RBV Ctrough levels after 4 weeks of therapy. ABCB11 1331 T > C SNP revealed significant association with clinical outcomes (SVR). SLC28A2-146 A > T SNP has not showed any statistically significant association with RBV plasma levels or response. CONCLUSION SNP genotyping for ABCB1 and ABCB11 genes can help in better personalized medicine for maximizing response for ribavirin as explored by the significant association between polymorphism in ABCB1 and ABCB11 genes and ribavirin pharmacokinetics and the significant association of ABCB11 1331 T > C SNP with clinical response.
Collapse
Affiliation(s)
- K S Abdelkawy
- Clinical Pharmacy, Faculty of Pharmacy, Kafrelsheikh University, Egypt.
| | - S M El-Haggar
- Clinical Pharmacy, Faculty of Pharmacy, Tanta University, Egypt.
| | - D H Ziada
- Tropical Medicine and Infectious Diseases, Faculty of Medicine, Tanta University, Egypt.
| | - N F Ebaid
- Clinical Pharmacy, Faculty of Pharmacy, Kafrelsheikh University, Egypt.
| | - M A El-Magd
- Anatomy and Embryology, Faculty of Veterinary Medicine, Kafrelsheikh University, Egypt.
| | - F A Elbarbry
- Pacific University Oregon School of Pharmacy, 222 SE 8thAve., Hillsboro, OR, 97123, USA.
| |
Collapse
|
8
|
Wang X, Shen W, Zhang X, Guo S, Gao Y, Li X, Feng F, Yang G. Indirect Electrochemical Determination of Ribavirin Using Boronic Acid-Diol Recognition on a 3-Aminophenylboronic Acid-Electrochemically Reduced Graphene Oxide Modified Glassy Carbon Electrode (APBA/ERGO/GCE). ANAL LETT 2019. [DOI: 10.1080/00032719.2019.1576716] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Xiaoyan Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Weiyang Shen
- School of Science, China Pharmaceutical University, Nanjing, P.R. China
| | - Xiaolei Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Siyan Guo
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Ye Gao
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xiaotong Li
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Fang Feng
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Gongjun Yang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| |
Collapse
|
9
|
Eektimmerman F, Swen JJ, Böhringer S, Aslibekyan S, Allaart CF, Guchelaar HJ. SLC04A1, SLC22A2 and SLC28A2 variants not related to methotrexate efficacy or toxicity in rheumatoid arthritis patients. Pharmacogenomics 2018; 19:613-619. [PMID: 29701127 DOI: 10.2217/pgs-2018-0021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
AIM A third of rheumatoid arthritis patients discontinue methotrexate treatment due to inefficacy or toxic side effects. Recently, an association between SLC04A1 rs2236553, SLC22A2 rs624249 and rs316019, and SLC28A2 rs10519020 and rs1060896 with the efficacy and toxicity of methotrexate was reported. This study aims to replicate these findings in an independent cohort (n = 324). METHODS Regression analyses tested the associations between genotype and methotrexate response or toxicity. RESULTS In the discovery study, there was a significant association between toxicity and rs624249, and rs1060896. These associations were not replicated in the independent cohort. Neither study observed an association between methotrexate efficacy and SLC04A1, SLC22A2 or SLC28A2 variants. CONCLUSION Current evidence does not support associations between variants in SLC04A1, SLC22A2 and SLC28A2 with methotrexate efficacy or toxicity.
Collapse
Affiliation(s)
- Frank Eektimmerman
- Clinical Pharmacy & Toxicology, Leiden University Medical Center, Leiden, The Netherlands.,Leiden Network for Personalised Therapeutics (LNPT), Leiden, The Netherlands
| | - Jesse J Swen
- Clinical Pharmacy & Toxicology, Leiden University Medical Center, Leiden, The Netherlands.,Leiden Network for Personalised Therapeutics (LNPT), Leiden, The Netherlands
| | - Stefan Böhringer
- Department of Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, 1665 University Blvd, Birmingham, AL 35205, USA
| | - Cornelia F Allaart
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Henk-Jan Guchelaar
- Clinical Pharmacy & Toxicology, Leiden University Medical Center, Leiden, The Netherlands.,Leiden Network for Personalised Therapeutics (LNPT), Leiden, The Netherlands
| |
Collapse
|
10
|
Latek D. Rosetta Broker for membrane protein structure prediction: concentrative nucleoside transporter 3 and corticotropin-releasing factor receptor 1 test cases. BMC STRUCTURAL BIOLOGY 2017; 17:8. [PMID: 28774292 PMCID: PMC5543540 DOI: 10.1186/s12900-017-0078-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 07/26/2017] [Indexed: 02/12/2023]
Abstract
Background Membrane proteins are difficult targets for structure prediction due to the limited structural data deposited in Protein Data Bank. Most computational methods for membrane protein structure prediction are based on the comparative modeling. There are only few de novo methods targeting that distinct protein family. In this work an example of such de novo method was used to structurally and functionally characterize two representatives of distinct membrane proteins families of solute carrier transporters and G protein-coupled receptors. The well-known Rosetta program and one of its protocols named Broker was used in two test cases. The first case was de novo structure prediction of three N-terminal transmembrane helices of the human concentrative nucleoside transporter 3 (hCNT3) homotrimer belonging to the solute carrier 28 family of transporters (SLC28). The second case concerned the large scale refinement of transmembrane helices of a homology model of the corticotropin-releasing factor receptor 1 (CRFR1) belonging to the G protein-coupled receptors family. Results The inward-facing model of the hCNT3 homotrimer was used to propose the functional impact of its single nucleotide polymorphisms. Additionally, the 100 ns molecular dynamics simulation of the unliganded hCNT3 model confirmed its validity and revealed mobility of the selected binding site and homotrimer interface residues. The large scale refinement of transmembrane helices of the CRFR1 homology model resulted in the significant improvement of its accuracy with respect to the crystal structure of CRFR1, especially in the binding site area. Consequently, the antagonist CP-376395 could be docked with Autodock VINA to the CRFR1 model without any steric clashes. Conclusions The presented work demonstrated that Rosetta Broker can be a versatile tool for solving various issues referring to protein biology. Two distinct examples of de novo membrane protein structure prediction presented here provided important insights into three major areas of protein biology. Namely, the dynamics of the inward-facing hCNT3 homotrimer system, the structural changes of the CRFR1 receptor upon the antagonist binding and finally, the role of single nucleotide polymorphisms in both, hCNT3 and CRFR1 proteins, were investigated. Electronic supplementary material The online version of this article (doi:10.1186/s12900-017-0078-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Dorota Latek
- Faculty of Chemistry, University of Warsaw, Pasteur St. 1, 02-093, Warsaw, Poland.
| |
Collapse
|
11
|
Estimated glomerular filtration rate but not solute carrier polymorphisms influences anemia in HIV-hepatitis C virus coinfected patients treated with boceprevir or telaprevir-based therapy. AIDS 2016; 30:2085-90. [PMID: 27149089 DOI: 10.1097/qad.0000000000001143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Ribavirin (RBV) induced anemia may be influenced by host genetic factors affecting RBV transport solute carrier (SLC) or metabolism inosine triphosphatase (ITPA), as already reported. We investigated the influence of single nucleotide polymorphisms (SNPs) on SLC genes on anemia, RBV trough concentration (Ctrough) and response in HIV-hepatitis C virus coinfected patients receiving triple therapy with boceprevir or telaprevir. METHODS Patients from the ANRS HC26/HC27 studies were genotyped for SLC28A3 SNPs (rs10868138 and rs56350726) and SL29A1 SNPs (rs760370). Hemoglobin (Hb) decline was collected at baseline day 0 (D0), week 4 (W4) and week 8 (W8), and RBV Ctrough was measured at W4 and W8 by HPLC. A multivariate analysis including SLC SNPs, estimated glomerular filtration rate (eGFR), ITPA deficiency and RBV Ctrough was performed to determine predictive factors of anemia and response. RESULTS SLC genotyping was performed in 130 patients. Neither SLC28A3 nor SLC29A1 SNPs were associated with Hb decline both at W4 and W8. No association was found between SLC polymorphisms and RBV Ctrough. Independent predictive factors of Hb decline at W4 were D0 Hb, ITPA deficiency and W4 RBV Ctrough in the multivariate analysis (P < 0.05). Only D0 Hb, W4 RBV Ctrough and eGFRD0-W8 were predictive of anemia at W8 (P < 0.05). Response was not influenced by SLC SNPs. CONCLUSION eGFR, but not SLC polymorphisms, influences anemia in HIV-hepatitis C virus coinfected patients receiving boceprevir-based or telaprevir-based therapy. RBV is still a cornerstone of hepatitis C treatment, thus renal function and RBV Ctrough should be monitored in patients receiving RBV regimen combined with first-generation direct-acting antiviral agent.
Collapse
|
12
|
Mei R, Chi X, Wu R, Xu H, Wang X, Gao X, Sun H, Lv J, Yu G, Kong F, Jiang J, Sun B, Zhong J, Pan Y, Niu J. Sustained viral response and treatment-induced cytopenia correlate with SLCs and KLF12 genotypes in interferon/ribavirin-treated Chinese chronic hepatitis C patients. J Gastroenterol Hepatol 2016; 31:1489-97. [PMID: 26750805 DOI: 10.1111/jgh.13290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/01/2016] [Accepted: 01/06/2016] [Indexed: 01/14/2023]
Abstract
BACKGROUND AND AIM Genetic variations in solute carrier (SLC) genes are associated with liver diseases, and Kruppel-like factor 12 (KLF12) affects the b chain of hemoglobin. We investigated possible correlations of SLC and KLF12 polymorphisms with viral clearance (spontaneous and treatment-induced) and adverse effects in Chinese chronic hepatitis C (CHC) patients. METHODS We genotyped the single nucleotide polymorphisms in 525 CHC patients, 137 patients with spontaneous clearance, and 207 healthy controls. Three hundred fifty-seven CHC patients received recombinant interferon-alpha2b/ribavirin (IFN-α2b/RBV) treatment, and 175 patients were chosen for analysis of drug-induced cytopenia. All raw P-values were corrected by the Bonferroni method. RESULTS A higher rate of sustained viral response was detected in patients with SLC4A11 rs3810560 CC variant versus TT/TC variant (76.9% vs 59.2%; OR, 2.42; 95% CI, 1.06-5.56, P = 0.037 after adjustment), but there was no significant difference among different hepatitis C virus genotypes. RBV-induced anemia was independently correlated with SLC29A1 rs760370 AA genotype (OR, 2.90; 95% CI, 1.29-6.54, P = 0.010), and the severity of IFN-induced thrombocytopenia was related to GG genotype (OR, 4.98; 95% CI, 1.27-19.61; P = 0.021); the detected effects held true for HCV-2a patients but weakened in HCV-1b patients. A reactive increase in platelet count was closely associated with KLF12 rs9543524 TT variant. CONCLUSION SLC4A11 rs3810560 polymorphism independently affected the sustained viral response rates in CHC patients, whereas SLC29A1 rs760370 and KLF12 rs9543524 single nucleotide polymorphisms correlated with treatment-induced adverse events. Clearly, the predictive power varied with HCV genotypes and the reason for genotype-dependent discrepancy was not fully understood.
Collapse
Affiliation(s)
- Ruqi Mei
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Xiumei Chi
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Ruihong Wu
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Hongqin Xu
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Xiaomei Wang
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Xiuzhu Gao
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Haibo Sun
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Juan Lv
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Ge Yu
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Fei Kong
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Jing Jiang
- Department of Clinical Epidemiology, First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Bing Sun
- Institute Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jin Zhong
- Institute Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu Pan
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province, China
| | - Junqi Niu
- Department of Hepatology, First Hospital of Jilin University, Changchun, Jilin Province, China
| |
Collapse
|
13
|
D'Avolio A, Cusato J, De Nicolò A, Allegra S, Di Perri G. Pharmacogenetics of ribavirin-induced anemia in HCV patients. Pharmacogenomics 2016; 17:925-41. [PMID: 27248282 DOI: 10.2217/pgs.16.22] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Dual therapy (pegylated interferon plus ribavirin) was considered the standard of care for hepatitis C virus (HCV) treatment until 2011, when the first-wave direct-acting antivirals were added to this regimen for HCV genotype-1 patients to increase the sustained virological response rate. The second-wave direct-acting antivirals entered the clinical use also in some ribavirin (RBV)- and/or interferon-free combinations. Nevertheless, since some of the new therapeutic regimens also include RBV and its use results still associated with hemolytic anemia, this requires countermeasures to be prevented. These include the identification of several host predictive factors involved in RBV absorption, distribution, metabolism, elimination and many others that might influence this toxic effect. For this reason, we provided an overview of the potential role of pharmacogenomics in predisposing RBV-treated HCV patients to anemia.
Collapse
Affiliation(s)
- Antonio D'Avolio
- Unit of Infectious Diseases, Department of Medical Sciences, Amedeo di Savoia Hospital, University of Turin, Turin, Italy
| | - Jessica Cusato
- Unit of Infectious Diseases, Department of Medical Sciences, Amedeo di Savoia Hospital, University of Turin, Turin, Italy
| | - Amedeo De Nicolò
- Unit of Infectious Diseases, Department of Medical Sciences, Amedeo di Savoia Hospital, University of Turin, Turin, Italy
| | - Sarah Allegra
- Unit of Infectious Diseases, Department of Medical Sciences, Amedeo di Savoia Hospital, University of Turin, Turin, Italy
| | - Giovanni Di Perri
- Unit of Infectious Diseases, Department of Medical Sciences, Amedeo di Savoia Hospital, University of Turin, Turin, Italy
| |
Collapse
|