Literature DB >> 31932804

Integration of epidemiologic, pharmacologic, genetic and gut microbiome data in a drug-metabolite atlas.

Jun Liu1,2, Lies Lahousse3,4, Michel G Nivard5,6, Mariska Bot5,6, Lianmin Chen7,8, Jan Bert van Klinken9,10,11, Carisha S Thesing5,6, Marian Beekman12, Erik Ben van den Akker12,13,14, Roderick C Slieker6,15,16, Eveline Waterham17, Carla J H van der Kallen18,19, Irene de Boer20, Ruifang Li-Gao21, Dina Vojinovic3, Najaf Amin3, Djawad Radjabzadeh22, Robert Kraaij22, Louise J M Alferink23, Sarwa Darwish Murad23, André G Uitterlinden3,22, Gonneke Willemsen5,6, Rene Pool5,6, Yuri Milaneschi5,6, Diana van Heemst24, H Eka D Suchiman12, Femke Rutters6,15, Petra J M Elders6,25, Joline W J Beulens6,15, Amber A W A van der Heijden6,25, Marleen M J van Greevenbroek18,19, Ilja C W Arts19,26,27, Gerrit L J Onderwater20, Arn M J M van den Maagdenberg9,20, Dennis O Mook-Kanamori21,28, Thomas Hankemeier29,30, Gisela M Terwindt20, Coen D A Stehouwer18,19, Johanna M Geleijnse17, Leen M 't Hart6,12,15,16, P Eline Slagboom12, Ko Willems van Dijk9,10,31, Alexandra Zhernakova7, Jingyuan Fu7,8, Brenda W J H Penninx5,6, Dorret I Boomsma5,6, Ayşe Demirkan3,7,32, Bruno H C Stricker3,22,33, Cornelia M van Duijn34,35,36.   

Abstract

Progress in high-throughput metabolic profiling provides unprecedented opportunities to obtain insights into the effects of drugs on human metabolism. The Biobanking BioMolecular Research Infrastructure of the Netherlands has constructed an atlas of drug-metabolite associations for 87 commonly prescribed drugs and 150 clinically relevant plasma-based metabolites assessed by proton nuclear magnetic resonance. The atlas includes a meta-analysis of ten cohorts (18,873 persons) and uncovers 1,071 drug-metabolite associations after evaluation of confounders including co-treatment. We show that the effect estimates of statins on metabolites from the cross-sectional study are comparable to those from intervention and genetic observational studies. Further data integration links proton pump inhibitors to circulating metabolites, liver function, hepatic steatosis and the gut microbiome. Our atlas provides a tool for targeted experimental pharmaceutical research and clinical trials to improve drug efficacy, safety and repurposing. We provide a web-based resource for visualization of the atlas (http://bbmri.researchlumc.nl/atlas/).

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Year:  2020        PMID: 31932804     DOI: 10.1038/s41591-019-0722-x

Source DB:  PubMed          Journal:  Nat Med        ISSN: 1078-8956            Impact factor:   53.440


  69 in total

1.  Circulating metabolites and general cognitive ability and dementia: Evidence from 11 cohort studies.

Authors:  Sven J van der Lee; Charlotte E Teunissen; René Pool; Martin J Shipley; Alexander Teumer; Vincent Chouraki; Debora Melo van Lent; Juho Tynkkynen; Krista Fischer; Jussi Hernesniemi; Toomas Haller; Archana Singh-Manoux; Aswin Verhoeven; Gonneke Willemsen; Francisca A de Leeuw; Holger Wagner; Jenny van Dongen; Johannes Hertel; Kathrin Budde; Ko Willems van Dijk; Leonie Weinhold; M Arfan Ikram; Maik Pietzner; Markus Perola; Michael Wagner; Nele Friedrich; P Eline Slagboom; Philip Scheltens; Qiong Yang; Robert E Gertzen; Sarah Egert; Shuo Li; Thomas Hankemeier; Catharina E M van Beijsterveldt; Ramachandran S Vasan; Wolfgang Maier; Carel F W Peeters; Hans Jörgen Grabe; Alfredo Ramirez; Sudha Seshadri; Andres Metspalu; Mika Kivimäki; Veikko Salomaa; Ayşe Demirkan; Dorret I Boomsma; Wiesje M van der Flier; Najaf Amin; Cornelia M van Duijn
Journal:  Alzheimers Dement       Date:  2018-01-06       Impact factor: 21.566

Review 2.  Metabolite changes in risk of type 2 diabetes mellitus in cohort studies: A systematic review and meta-analysis.

Authors:  Jeong-Eun Park; Hye Rin Lim; Jun Woo Kim; Kwang-Hee Shin
Journal:  Diabetes Res Clin Pract       Date:  2018-04-04       Impact factor: 5.602

3.  A Mendelian Randomization Study of Metabolite Profiles, Fasting Glucose, and Type 2 Diabetes.

Authors:  Jun Liu; Jan Bert van Klinken; Sabina Semiz; Ko Willems van Dijk; Aswin Verhoeven; Thomas Hankemeier; Amy C Harms; Eric Sijbrands; Nuala A Sheehan; Cornelia M van Duijn; Ayşe Demirkan
Journal:  Diabetes       Date:  2017-08-28       Impact factor: 9.461

4.  Plasma phospholipids identify antecedent memory impairment in older adults.

Authors:  Mark Mapstone; Amrita K Cheema; Massimo S Fiandaca; Xiaogang Zhong; Timothy R Mhyre; Linda H MacArthur; William J Hall; Susan G Fisher; Derick R Peterson; James M Haley; Michael D Nazar; Steven A Rich; Dan J Berlau; Carrie B Peltz; Ming T Tan; Claudia H Kawas; Howard J Federoff
Journal:  Nat Med       Date:  2014-03-09       Impact factor: 53.440

Review 5.  Innovation: Metabolomics: the apogee of the omics trilogy.

Authors:  Gary J Patti; Oscar Yanes; Gary Siuzdak
Journal:  Nat Rev Mol Cell Biol       Date:  2012-03-22       Impact factor: 94.444

6.  Evidence that asthma is a developmental origin disease influenced by maternal diet and bacterial metabolites.

Authors:  Alison N Thorburn; Craig I McKenzie; Sj Shen; Dragana Stanley; Laurence Macia; Linda J Mason; Laura K Roberts; Connie H Y Wong; Raymond Shim; Remy Robert; Nina Chevalier; Jian K Tan; Eliana Mariño; Rob J Moore; Lee Wong; Malcolm J McConville; Dedreia L Tull; Lisa G Wood; Vanessa E Murphy; Joerg Mattes; Peter G Gibson; Charles R Mackay
Journal:  Nat Commun       Date:  2015-06-23       Impact factor: 14.919

7.  Metabolite profiles and the risk of developing diabetes.

Authors:  Thomas J Wang; Martin G Larson; Ramachandran S Vasan; Susan Cheng; Eugene P Rhee; Elizabeth McCabe; Gregory D Lewis; Caroline S Fox; Paul F Jacques; Céline Fernandez; Christopher J O'Donnell; Stephen A Carr; Vamsi K Mootha; Jose C Florez; Amanda Souza; Olle Melander; Clary B Clish; Robert E Gerszten
Journal:  Nat Med       Date:  2011-03-20       Impact factor: 53.440

Review 8.  Cardiovascular Metabolomics.

Authors:  Robert W McGarrah; Scott B Crown; Guo-Fang Zhang; Svati H Shah; Christopher B Newgard
Journal:  Circ Res       Date:  2018-04-27       Impact factor: 17.367

9.  A genome-wide perspective of genetic variation in human metabolism.

Authors:  Thomas Illig; Christian Gieger; Guangju Zhai; Werner Römisch-Margl; Rui Wang-Sattler; Cornelia Prehn; Elisabeth Altmaier; Gabi Kastenmüller; Bernet S Kato; Hans-Werner Mewes; Thomas Meitinger; Martin Hrabé de Angelis; Florian Kronenberg; Nicole Soranzo; H-Erich Wichmann; Tim D Spector; Jerzy Adamski; Karsten Suhre
Journal:  Nat Genet       Date:  2009-12-27       Impact factor: 38.330

10.  Linoleic acid metabolite drives severe asthma by causing airway epithelial injury.

Authors:  Ulaganathan Mabalirajan; Rakhshinda Rehman; Tanveer Ahmad; Sarvesh Kumar; Suchita Singh; Geeta D Leishangthem; Jyotirmoi Aich; Manish Kumar; Kritika Khanna; Vijay P Singh; Amit K Dinda; Shyam Biswal; Anurag Agrawal; Balaram Ghosh
Journal:  Sci Rep       Date:  2013       Impact factor: 4.379

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  10 in total

1.  The human microbiome and genetic disease: towards the integration of metagenomic and multi-omics data.

Authors:  Huiying Zhao
Journal:  Hum Genet       Date:  2021-05       Impact factor: 4.132

2.  Metabolomic and microbiome profiling reveals personalized risk factors for coronary artery disease.

Authors:  Yeela Talmor-Barkan; Noam Bar; Aviv A Shaul; Nir Shahaf; Anastasia Godneva; Yuval Bussi; Maya Lotan-Pompan; Adina Weinberger; Alon Shechter; Chava Chezar-Azerrad; Ziad Arow; Yoav Hammer; Kanta Chechi; Sofia K Forslund; Sebastien Fromentin; Marc-Emmanuel Dumas; S Dusko Ehrlich; Oluf Pedersen; Ran Kornowski; Eran Segal
Journal:  Nat Med       Date:  2022-02-17       Impact factor: 87.241

3.  A reference map of potential determinants for the human serum metabolome.

Authors:  Noam Bar; Tal Korem; Omer Weissbrod; David Zeevi; Daphna Rothschild; Sigal Leviatan; Noa Kosower; Maya Lotan-Pompan; Adina Weinberger; Caroline I Le Roy; Cristina Menni; Alessia Visconti; Mario Falchi; Tim D Spector; Jerzy Adamski; Paul W Franks; Oluf Pedersen; Eran Segal
Journal:  Nature       Date:  2020-11-11       Impact factor: 49.962

4.  Plasma metabolites to profile pathways in noncommunicable disease multimorbidity.

Authors:  Maik Pietzner; Isobel D Stewart; Johannes Raffler; Kay-Tee Khaw; Gregory A Michelotti; Gabi Kastenmüller; Nicholas J Wareham; Claudia Langenberg
Journal:  Nat Med       Date:  2021-03-11       Impact factor: 53.440

Review 5.  The Exposome and Toxicology: A Win-Win Collaboration.

Authors:  Robert Barouki; Karine Audouze; Christel Becker; Ludek Blaha; Xavier Coumoul; Spyros Karakitsios; Jana Klanova; Gary W Miller; Elliott J Price; Denis Sarigiannis
Journal:  Toxicol Sci       Date:  2022-02-28       Impact factor: 4.109

6.  An Inductive Logistic Matrix Factorization Model for Predicting Drug-Metabolite Association With Vicus Regularization.

Authors:  Yuanyuan Ma; Lifang Liu; Qianjun Chen; Yingjun Ma
Journal:  Front Microbiol       Date:  2021-04-01       Impact factor: 5.640

7.  A multi-omics study of circulating phospholipid markers of blood pressure.

Authors:  Jun Liu; Paul S de Vries; Fabiola Del Greco M; Åsa Johansson; Katharina E Schraut; Caroline Hayward; Ko Willems van Dijk; Oscar H Franco; Andrew A Hicks; Veronique Vitart; Igor Rudan; Harry Campbell; Ozren Polašek; Peter P Pramstaller; James F Wilson; Ulf Gyllensten; Cornelia M van Duijn; Abbas Dehghan; Ayşe Demirkan
Journal:  Sci Rep       Date:  2022-01-12       Impact factor: 4.996

8.  Blood metabolites predicting mild cognitive impairment in the study of Latinos-investigation of neurocognitive aging (HCHS/SOL).

Authors:  Shan He; Einat Granot-Hershkovitz; Ying Zhang; Jan Bressler; Wassim Tarraf; Bing Yu; Tianyi Huang; Donglin Zeng; Sylvia Wassertheil-Smoller; Melissa Lamar; Martha Daviglus; Maria J Marquine; Jianwen Cai; Thomas Mosley; Robert Kaplan; Eric Boerwinkle; Myriam Fornage; Charles DeCarli; Bruce Kristal; Hector M Gonzalez; Tamar Sofer
Journal:  Alzheimers Dement (Amst)       Date:  2022-02-23

Review 9.  Gut Microbes and Neuropathology: Is There a Causal Nexus?

Authors:  Katherine Dinan; Timothy G Dinan
Journal:  Pathogens       Date:  2022-07-14

Review 10.  Dual and mutual interaction between microbiota and viral infections: a possible treat for COVID-19.

Authors:  Taha Baghbani; Hossein Nikzad; Javid Azadbakht; Fatemeh Izadpanah; Hamed Haddad Kashani
Journal:  Microb Cell Fact       Date:  2020-11-26       Impact factor: 5.328

  10 in total

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