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Hernandez-Pacheco N, Gorenjak M, Li J, Repnik K, Vijverberg SJ, Berce V, Jorgensen A, Karimi L, Schieck M, Samedy-Bates LA, Tavendale R, Villar J, Mukhopadhyay S, Pirmohamed M, Verhamme KMC, Kabesch M, Hawcutt DB, Turner S, Palmer CN, Tantisira KG, Burchard EG, Maitland-van der Zee AH, Flores C, Potočnik U, Pino-Yanes M. Identification of ROBO2 as a Potential Locus Associated with Inhaled Corticosteroid Response in Childhood Asthma. J Pers Med 2021; 11:jpm11080733. [PMID: 34442380 PMCID: PMC8399629 DOI: 10.3390/jpm11080733] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
Inhaled corticosteroids (ICS) are the most common asthma controller medication. An important contribution of genetic factors in ICS response has been evidenced. Here, we aimed to identify novel genetic markers involved in ICS response in asthma. A genome-wide association study (GWAS) of the change in lung function after 6 weeks of ICS treatment was performed in 166 asthma patients from the SLOVENIA study. Patients with an improvement in lung function ≥8% were considered as ICS responders. Suggestively associated variants (p-value ≤ 5 × 10−6) were evaluated in an independent study (n = 175). Validation of the association with asthma exacerbations despite ICS use was attempted in European (n = 2681) and admixed (n = 1347) populations. Variants previously associated with ICS response were also assessed for replication. As a result, the SNP rs1166980 from the ROBO2 gene was suggestively associated with the change in lung function (OR for G allele: 7.01, 95% CI: 3.29–14.93, p = 4.61 × 10−7), although this was not validated in CAMP. ROBO2 showed gene-level evidence of replication with asthma exacerbations despite ICS use in Europeans (minimum p-value = 1.44 × 10−5), but not in admixed individuals. The association of PDE10A-T with ICS response described by a previous study was validated. This study suggests that ROBO2 could be a potential novel locus for ICS response in Europeans.
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Affiliation(s)
- Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Carretera General del Rosario 145, 38010 Santa Cruz de Tenerife, Spain;
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Avenida Astrofísico Francisco Sánchez s/n, Faculty of Science, Apartado 456, 38200 San Cristóbal de La Laguna, Spain;
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Avenida de Monforte de Lemos, 5, 28029 Madrid, Spain;
- Correspondence: (N.H.-P.); (U.P.); Tel.: +46-0702983315 (N.H.-P.); +386-22345854 (U.P.)
| | - Mario Gorenjak
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (M.G.); (K.R.); (V.B.)
| | - Jiang Li
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, 75 Francis St, Boston, MA 02115, USA; (J.L.); (K.G.T.)
| | - Katja Repnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (M.G.); (K.R.); (V.B.)
- Laboratory for Biochemistry, Molecular Biology, and Genomics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia
| | - Susanne J. Vijverberg
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (S.J.V.); (A.H.M.-v.d.Z.)
- Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
- Department of Pediatric Respiratory Medicine and Allergy, Emma’s Children Hospital, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Vojko Berce
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (M.G.); (K.R.); (V.B.)
- Department of Pediatrics, University Medical Centre Maribor, Ljubljanska Ulica 5, 2000 Maribor, Slovenia
| | - Andrea Jorgensen
- Department of Biostatistics, University of Liverpool, Crown Street, Liverpool L69 3BX, UK;
| | - Leila Karimi
- Department of Medical Informatics, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (L.K.); (K.M.C.V.)
| | - Maximilian Schieck
- Department of Pediatric Pneumology and Allergy, University Children’s Hospital Regensburg (KUNO), Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany; (M.S.); (M.K.)
- Department of Human Genetics, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Lesly-Anne Samedy-Bates
- Department of Medicine, University of California, San Francisco, CA 94143, USA; (L.-A.S.-B.); (E.G.B.)
- Department of Bioengineering and Therapeutic Sciences, University of California, 533 Parnassus Ave, San Francisco, CA 94143, USA
| | - Roger Tavendale
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital, and Medical School, University of Dundee, Dundee DD1 9SY, UK; (R.T.); (S.M.); (C.N.P.)
| | - Jesús Villar
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Avenida de Monforte de Lemos, 5, 28029 Madrid, Spain;
- Multidisciplinary Organ Dysfunction Evaluation Research Network, Research Unit, Hospital Universitario Dr. Negrín, Calle Barranco de la Ballena s/n, 35019 Las Palmas de Gran Canaria, Spain
- Keenan Research Center for Biomedical Science, Li Ka Shing Knowledge Institute, St Michael’s Hospital, 30 Bond St, Toronto, ON M5B 1W8, Canada
| | - Somnath Mukhopadhyay
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital, and Medical School, University of Dundee, Dundee DD1 9SY, UK; (R.T.); (S.M.); (C.N.P.)
- Academic Department of Paediatrics, Brighton and Sussex Medical School, Royal Alexandra Children’s Hospital, 94 N-S Rd, Falmer, Brighton BN2 5BE, UK
| | - Munir Pirmohamed
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, 200 London Rd, Liverpool L3 9TA, UK;
| | - Katia M. C. Verhamme
- Department of Medical Informatics, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (L.K.); (K.M.C.V.)
| | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children’s Hospital Regensburg (KUNO), Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany; (M.S.); (M.K.)
| | - Daniel B. Hawcutt
- Department of Women’s and Children’s Health, University of Liverpool, Liverpool L69 3BX, UK;
- Alder Hey Children’s Hospital, E Prescot Rd, Liverpool L14 5AB, UK
| | - Steve Turner
- Child Health, University of Aberdeen, King’s College, Aberdeen AB24 3FX, UK;
| | - Colin N. Palmer
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital, and Medical School, University of Dundee, Dundee DD1 9SY, UK; (R.T.); (S.M.); (C.N.P.)
| | - Kelan G. Tantisira
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, 75 Francis St, Boston, MA 02115, USA; (J.L.); (K.G.T.)
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, and Harvard Medical School, 75 Francis St, Boston, MA 02115, USA
| | - Esteban G. Burchard
- Department of Medicine, University of California, San Francisco, CA 94143, USA; (L.-A.S.-B.); (E.G.B.)
- Department of Bioengineering and Therapeutic Sciences, University of California, 533 Parnassus Ave, San Francisco, CA 94143, USA
| | - Anke H. Maitland-van der Zee
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (S.J.V.); (A.H.M.-v.d.Z.)
- Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
- Department of Pediatric Respiratory Medicine and Allergy, Emma’s Children Hospital, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Carretera General del Rosario 145, 38010 Santa Cruz de Tenerife, Spain;
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Avenida de Monforte de Lemos, 5, 28029 Madrid, Spain;
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Polígono Industrial de Granadilla, 38600 Granadilla, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Faculty of Health Sciences, Apartado 456, 38200 San Cristóbal de La Laguna, Spain
| | - Uroš Potočnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; (M.G.); (K.R.); (V.B.)
- Laboratory for Biochemistry, Molecular Biology, and Genomics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia
- Correspondence: (N.H.-P.); (U.P.); Tel.: +46-0702983315 (N.H.-P.); +386-22345854 (U.P.)
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Avenida Astrofísico Francisco Sánchez s/n, Faculty of Science, Apartado 456, 38200 San Cristóbal de La Laguna, Spain;
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Avenida de Monforte de Lemos, 5, 28029 Madrid, Spain;
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Faculty of Health Sciences, Apartado 456, 38200 San Cristóbal de La Laguna, Spain
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2
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Hernandez-Pacheco N, Vijverberg SJ, Herrera-Luis E, Li J, Sio YY, Granell R, Corrales A, Maroteau C, Lethem R, Perez-Garcia J, Farzan N, Repnik K, Gorenjak M, Soares P, Karimi L, Schieck M, Pérez-Méndez L, Berce V, Tavendale R, Eng C, Sardon O, Kull I, Mukhopadhyay S, Pirmohamed M, Verhamme KMC, Burchard EG, Kabesch M, Hawcutt DB, Melén E, Potočnik U, Chew FT, Tantisira KG, Turner S, Palmer CN, Flores C, Pino-Yanes M, Maitland-van der Zee AH. Genome-wide association study of asthma exacerbations despite inhaled corticosteroid use. Eur Respir J 2021; 57:2003388. [PMID: 33303529 PMCID: PMC8122045 DOI: 10.1183/13993003.03388-2020] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 11/09/2020] [Indexed: 02/07/2023]
Abstract
RATIONALE Substantial variability in response to asthma treatment with inhaled corticosteroids (ICS) has been described among individuals and populations, suggesting the contribution of genetic factors. Nonetheless, only a few genes have been identified to date. We aimed to identify genetic variants associated with asthma exacerbations despite ICS use in European children and young adults and to validate the findings in non-Europeans. Moreover, we explored whether a gene-set enrichment analysis could suggest potential novel asthma therapies. METHODS A genome-wide association study (GWAS) of asthma exacerbations was tested in 2681 children of European descent treated with ICS from eight studies. Suggestive association signals were followed up for replication in 538 European asthma patients. Further evaluation was performed in 1773 non-Europeans. Variants revealed by published GWAS were assessed for replication. Additionally, gene-set enrichment analysis focused on drugs was performed. RESULTS 10 independent variants were associated with asthma exacerbations despite ICS treatment in the discovery phase (p≤5×10-6). Of those, one variant at the CACNA2D3-WNT5A locus was nominally replicated in Europeans (rs67026078; p=0.010), but this was not validated in non-European populations. Five other genes associated with ICS response in previous studies were replicated. Additionally, an enrichment of associations in genes regulated by trichostatin A treatment was found. CONCLUSIONS The intergenic region of CACNA2D3 and WNT5A was revealed as a novel locus for asthma exacerbations despite ICS treatment in European populations. Genes associated were related to trichostatin A, suggesting that this drug could regulate the molecular mechanisms involved in treatment response.
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Affiliation(s)
- Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- Genomics and Health Group, Dept of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Susanne J Vijverberg
- Dept of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Dept of Paediatric Respiratory Medicine and Allergy, Emma's Children Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Esther Herrera-Luis
- Genomics and Health Group, Dept of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Jiang Li
- The Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yang Yie Sio
- Dept of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Raquel Granell
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Almudena Corrales
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Cyrielle Maroteau
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Ryan Lethem
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Javier Perez-Garcia
- Genomics and Health Group, Dept of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Niloufar Farzan
- Dept of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Breathomix B.V., El Reeuwijk, The Netherlands
| | - Katja Repnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
- Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Mario Gorenjak
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Patricia Soares
- Academic Dept of Paediatrics, Brighton and Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK
- Escola Nacional de Saúde Pública, Lisboa, Portugal
| | - Leila Karimi
- Dept of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Maximilian Schieck
- Dept of Paediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
- Dept of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Lina Pérez-Méndez
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Dept of Clinic Epidemiology and Biostatistics, Research Unit, Hospital Universitario N.S. de Candelaria, Gerencia de Atención Primaria, Santa Cruz de Tenerife, Spain
| | - Vojko Berce
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
- Dept of Paediatrics, University Medical Centre Maribor, Maribor, Slovenia
| | - Roger Tavendale
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Celeste Eng
- Dept of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Olaia Sardon
- Division of Paediatric Respiratory Medicine, Hospital Universitario Donostia, San Sebastián, Spain
- Dept of Paediatrics, University of the Basque Country (UPV/EHU), San Sebastián, Spain
| | - Inger Kull
- Dept of Clinical Sciences and Education Södersjukhuset, Karolinska Institutet and Sachs' Children's Hospital, Stockholm, Sweden
| | - Somnath Mukhopadhyay
- Academic Dept of Paediatrics, Brighton and Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Munir Pirmohamed
- Dept of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Katia M C Verhamme
- Dept of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Esteban G Burchard
- Dept of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Dept of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Michael Kabesch
- Dept of Paediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
| | - Daniel B Hawcutt
- Dept of Women's and Children's Health, University of Liverpool, Liverpool, UK
- Alder Hey Children's Hospital, Liverpool, UK
| | - Erik Melén
- Dept of Clinical Sciences and Education Södersjukhuset, Karolinska Institutet and Sachs' Children's Hospital, Stockholm, Sweden
- Institute of Environmental Medicine, Karolinska Institutet, Solna, Sweden
| | - Uroš Potočnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
- Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Fook Tim Chew
- Dept of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Kelan G Tantisira
- The Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Steve Turner
- Child Health, University of Aberdeen, Aberdeen, UK
| | - Colin N Palmer
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Maria Pino-Yanes
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- Genomics and Health Group, Dept of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, San Cristóbal de La Laguna, Spain
- These authors contributed equally to this work
| | - Anke H Maitland-van der Zee
- Dept of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Dept of Paediatric Respiratory Medicine and Allergy, Emma's Children Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- These authors contributed equally to this work
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3
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King C, McKenna A, Farzan N, Vijverberg SJ, van der Schee MP, Maitland-van der Zee AH, Arianto L, Bisgaard H, BØnnelykke K, Berce V, PotoČnik U, Repnik K, Carleton B, Daley D, Chew FT, Chiang WC, Sio YY, Cloutier MM, Den Dekker HT, Duijts L, de Jongste JC, Dijk FN, Flores C, Hernandez-Pacheco N, Mukhopadhyay S, Basu K, Tantisira KG, Verhamme KM, Celedón JC, Forno E, Canino G, Francis B, Pirmohamed M, Sinha I, Hawcutt DB. Pharmacogenomic associations of adverse drug reactions in asthma: systematic review and research prioritisation. Pharmacogenomics J 2020; 20:621-628. [PMID: 31949291 PMCID: PMC7502355 DOI: 10.1038/s41397-019-0140-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 11/22/2019] [Accepted: 12/16/2019] [Indexed: 11/16/2022]
Abstract
A systematic review of pharmacogenomic studies capturing adverse drug reactions (ADRs) related to asthma medications was undertaken, and a survey of Pharmacogenomics in Childhood Asthma (PiCA) consortia members was conducted. Studies were eligible if genetic polymorphisms were compared with suspected ADR(s) in a patient with asthma, as either a primary or secondary outcome. Five studies met the inclusion criteria. The ADRs and polymorphisms identified were change in lung function tests (rs1042713), adrenal suppression (rs591118), and decreased bone mineral density (rs6461639) and accretion (rs9896933, rs2074439). Two of these polymorphisms were replicated within the paper, but none had external replication. Priorities from PiCA consortia members (representing 15 institution in eight countries) for future studies were tachycardia (SABA/LABA), adrenal suppression/crisis and growth suppression (corticosteroids), sleep/behaviour disturbances (leukotriene receptor antagonists), and nausea and vomiting (theophylline). Future pharmacogenomic studies in asthma should collect relevant ADR data as well as markers of efficacy.
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Affiliation(s)
- Charlotte King
- Department of Women and Child's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, England
| | - Amanda McKenna
- Department of Women and Child's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, England
| | - Niloufar Farzan
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Susanne J Vijverberg
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Marc P van der Schee
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Anke H Maitland-van der Zee
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Lambang Arianto
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Klaus BØnnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Vojko Berce
- Department of Pediatrics, University Medical Centre Maribor, Maribor, Slovenia
- Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Uros PotoČnik
- Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Katja Repnik
- Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Bruce Carleton
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, BC Children's Hospital and Research Institute, Vancouver, Canada
| | - Denise Daley
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, BC Children's Hospital and Research Institute, Vancouver, Canada
| | - Fook Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore, Singapore
| | - Wen Chin Chiang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore, Singapore
| | - Yang Yie Sio
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore, Singapore
| | - Michelle M Cloutier
- Asthma Center, Connecticut Children's Medical Center, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Herman T Den Dekker
- Department of Pediatrics, Division of Respiratory Medicine & Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Liesbeth Duijts
- Department of Pediatrics, Division of Respiratory Medicine & Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Johan C de Jongste
- Department of Pediatric Pulmonology & Pediatric Allergology, University Medical Center Groningen, University of Groningen, Beatrix Children's Hospital, Groningen, The Netherlands
| | - F Nicole Dijk
- Department of Pediatric Pulmonology & Pediatric Allergology, University Medical Center Groningen, University of Groningen, Beatrix Children's Hospital, Groningen, The Netherlands
- Groningen Research Institute for Asthma & COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Somnath Mukhopadhyay
- Academic Department of Paediatrics, Brighton & Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK
| | - Kaninika Basu
- Academic Department of Paediatrics, Brighton & Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK
| | - Kelan G Tantisira
- The Channing Division of Network Medicine, Department of Medicine, Boston, MA, 02115, USA
- Division of Pulmonary & Critical Care Medicine, Brigham & Women's Hospital & Harvard Medical School, Boston, MA, 02115, USA
| | - Katia M Verhamme
- Department of Medical Informatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Erick Forno
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Glorisa Canino
- Behavioral Sciences Research Institute, University of Puerto Rico, San Juan, Puerto Rico
| | - Ben Francis
- Department of Biostatistics, Institute of Translational Medicine, University of Liverpool, Liverpool, England
| | - Munir Pirmohamed
- Department of Molecular & Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, England
| | - Ian Sinha
- Department of Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, England
| | - Daniel B Hawcutt
- Department of Women and Child's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, England.
- NIHR Alder Hey Clinical Research Facility, Alder Hey Children's Hospital, Liverpool, England.
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King C, McKenna A, Farzan N, Vijverberg SJ, van der Schee MP, Maitland-van der Zee AH, Arianto L, Bisgaard H, BØnnelykke K, Berce V, PotoČnik U, Repnik K, Carleton B, Daley D, Chew FT, Chiang WC, Sio YY, Cloutier MM, Den Dekker HT, Duijts L, de Jongste JC, Dijk FN, Flores C, Hernandez-Pacheco N, Mukhopadhyay S, Basu K, Tantisira KG, Verhamme KM, Celedón JC, Forno E, Canino G, Francis B, Pirmohamed M, Sinha I, Hawcutt DB. Correction: Pharmacogenomic associations of adverse drug reactions in asthma: systematic review and research prioritization. Pharmacogenomics J 2020; 20:746. [PMID: 32704026 PMCID: PMC7502354 DOI: 10.1038/s41397-020-0178-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Charlotte King
- Department of Women and Child's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, England
| | - Amanda McKenna
- Department of Women and Child's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, England
| | - Niloufar Farzan
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Susanne J Vijverberg
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Marc P van der Schee
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Anke H Maitland-van der Zee
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Lambang Arianto
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Klaus BØnnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Vojko Berce
- Department of Pediatrics, University Medical Centre Maribor, Maribor, Slovenia.,Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Uros PotoČnik
- Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Katja Repnik
- Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Bruce Carleton
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, BC Children's Hospital and Research Institute, Vancouver, Canada
| | - Denise Daley
- Division of Translational Therapeutics, Department of Pediatrics, Faculty of Medicine, University of British Columbia, BC Children's Hospital and Research Institute, Vancouver, Canada
| | - Fook Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore, & the Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore, Singapore
| | - Wen Chin Chiang
- Department of Biological Sciences, National University of Singapore, Singapore, & the Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore, Singapore
| | - Yang Yie Sio
- Department of Biological Sciences, National University of Singapore, Singapore, & the Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore, Singapore
| | - Michelle M Cloutier
- Asthma Center, Connecticut Children's Medical Center, University of Connecticut Health Center, Connecticut, USA
| | - Herman T Den Dekker
- Department of Pediatrics, Division of Respiratory Medicine & Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Liesbeth Duijts
- Department of Pediatrics, Division of Respiratory Medicine & Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Johan C de Jongste
- Department of Pediatric Pulmonology & Pediatric Allergology, University Medical Center Groningen, University of Groningen, Beatrix Children's Hospital, Groningen, The Netherlands
| | - F Nicole Dijk
- Department of Pediatric Pulmonology & Pediatric Allergology, University Medical Center Groningen, University of Groningen, Beatrix Children's Hospital, Groningen, The Netherlands.,Groningen Research Institute for Asthma & COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Somnath Mukhopadhyay
- Academic Department of Paediatrics, Brighton & Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK
| | - Kaninika Basu
- Academic Department of Paediatrics, Brighton & Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK
| | - Kelan G Tantisira
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's Hospital & Harvard Medical School, Boston, MA, 02115, USA.,Division of Pulmonary & Critical Care Medicine, Brigham & Women's Hospital & Harvard Medical School, Boston, MA, 02115, USA
| | - Katia M Verhamme
- Department of Medical Informatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Erick Forno
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Glorisa Canino
- Behavioral Sciences Research Institute, University of Puerto Rico, San Juan, Puerto Rico
| | - Ben Francis
- Department of Biostatistics, Institute of Translational Medicine, University of Liverpool, Liverpool, England
| | - Munir Pirmohamed
- Department of Molecular & Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, England
| | - Ian Sinha
- Department of Respiratory Medicine, Alder Hey Children's Hospital, Liverpool, England
| | - Daniel B Hawcutt
- Department of Women and Child's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, England. .,NIHR Alder Hey Clinical Research Facility, Alder Hey Children's Hospital, Liverpool, England.
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5
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Dijk FN, Vijverberg SJ, Hernandez‐Pacheco N, Repnik K, Karimi L, Mitratza M, Farzan N, Nawijn MC, Burchard EG, Engelkes M, Verhamme KM, Potočnik U, Pino‐Yanes M, Postma DS, Maitland‐van der Zee A, Koppelman GH. IL1RL1 gene variations are associated with asthma exacerbations in children and adolescents using inhaled corticosteroids. Allergy 2020; 75:984-989. [PMID: 31755552 PMCID: PMC7176513 DOI: 10.1111/all.14125] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- F. Nicole Dijk
- Department of Pediatric Pulmonology and Pediatric Allergology Beatrix Children's Hospital Groningen Research Institute for Asthma and COPD (GRIAC) University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Susanne J. Vijverberg
- Department of Respiratory Medicine Amsterdam University Medical Centers University of Amsterdam Amsterdam The Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology Faculty of Science Utrecht University Utrecht The Netherlands
| | - Natalia Hernandez‐Pacheco
- Research Unit Hospital Universitario N.S. de Candelaria Universidad de La Laguna Santa Cruz de Tenerife Spain
- Genomics and Health Group Department of Biochemistry, Microbiology, Cell Biology and Genetics Universidad de La Laguna La Laguna, Tenerife Spain
| | - Katja Repnik
- Center for Human Molecular Genetics and Pharmacogenomics Faculty of Medicine University of Maribor Maribor Slovenia
- Laboratory for Biochemistry Molecular Biology and Genomics Faculty for Chemistry and Chemical Engineering University of Maribor Maribor Slovenia
| | - Leila Karimi
- Department of Medical Informatics Erasmus University Medical Center Rotterdam The Netherlands
| | - Marianna Mitratza
- Division of Pharmacoepidemiology and Clinical Pharmacology Faculty of Science Utrecht University Utrecht The Netherlands
| | - Niloufar Farzan
- Department of Respiratory Medicine Amsterdam University Medical Centers University of Amsterdam Amsterdam The Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology Faculty of Science Utrecht University Utrecht The Netherlands
| | - Martijn C. Nawijn
- Laboratory of Allergology and Pulmonary Diseases, Pathology and Medical Biology Groningen Research Institute for Asthma and COPD (GRIAC) University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Esteban G. Burchard
- Department of Medicine University of California San Francisco CA USA
- Department of Bioengineering and Therapeutic Sciences University of California San Francisco CA USA
| | - Marjolein Engelkes
- Department of Medical Informatics Erasmus University Medical Center Rotterdam The Netherlands
| | - Katia M. Verhamme
- Department of Medical Informatics Erasmus University Medical Center Rotterdam The Netherlands
| | - Uroš Potočnik
- Center for Human Molecular Genetics and Pharmacogenomics Faculty of Medicine University of Maribor Maribor Slovenia
- Laboratory for Biochemistry Molecular Biology and Genomics Faculty for Chemistry and Chemical Engineering University of Maribor Maribor Slovenia
| | - Maria Pino‐Yanes
- Research Unit Hospital Universitario N.S. de Candelaria Universidad de La Laguna Santa Cruz de Tenerife Spain
- Genomics and Health Group Department of Biochemistry, Microbiology, Cell Biology and Genetics Universidad de La Laguna La Laguna, Tenerife Spain
- CIBER de Enfermedades Respiratorias Instituto de Salud Carlos III Madrid Spain
| | - Dirkje S. Postma
- Department of Pulmonary Diseases Groningen Research Institute for Asthma and COPD (GRIAC) University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Anke‐Hilse Maitland‐van der Zee
- Department of Respiratory Medicine Amsterdam University Medical Centers University of Amsterdam Amsterdam The Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology Faculty of Science Utrecht University Utrecht The Netherlands
- Department of Pediatric Respiratory Medicine and Allergy Emma's Children Hospital Academic Medical Center (AMC) University of Amsterdam Amsterdam The Netherlands
| | - Gerard H. Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology Beatrix Children's Hospital Groningen Research Institute for Asthma and COPD (GRIAC) University Medical Center Groningen University of Groningen Groningen The Netherlands
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6
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Maver U, Xhanari K, Žižek M, Gradišnik L, Repnik K, Potočnik U, Finšgar M. Carboxymethyl cellulose/diclofenac bioactive coatings on AISI 316LVM for controlled drug delivery, and improved osteogenic potential. Carbohydr Polym 2020; 230:115612. [DOI: 10.1016/j.carbpol.2019.115612] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/11/2019] [Accepted: 11/12/2019] [Indexed: 12/14/2022]
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Gorenjak M, Repnik K, Jezernik G, Jurgec S, Skok P, Potočnik U. Genetic prediction profile for adalimumab response in Slovenian Crohn's disease patients. Z Gastroenterol 2019; 57:1218-1225. [PMID: 31610585 DOI: 10.1055/a-0981-6516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
INTRODUCTION Response to anti-TNF therapy is crucial for life expectancy and life quality in patients with severe Crohn's disease. We investigated if a previously reported gene expression profile predictive for infliximab response could be also applied to adalimumab response in an independent cohort. METHODS Forty-seven Slovene Crohn's disease patients indicated for adalimumab therapy were enrolled in the study. Inflamed and non-inflamed colon biopsy samples were obtained during routine colonoscopy prior to adalimumab treatment. Response to adalimumab was measured with IBDQ. Gene expression in inflamed and non-inflamed colon biopsy samples was measured with RT-qPCR. Genotypes were extracted from previously available genotype data. Statistical analysis was performed with SPSS software. The R package e1071 was used to train bootstrap aggregated support vector machines (SVM). RESULTS SVM prediction model analysis was used to analyze pooled, non-inflamed, and inflamed colon tissue datasets using IBDQ response after 4, 12, 20 and 30 weeks of adalimumab treatment. The bagging approach was used in an endeavor to obtain 100 % accuracy using 10 × 100 or 100 × 100 iterations. Average adalimumab response prediction accuracy is 75.5 % for pooled samples, 90.5 % for inflamed samples, and 100 % for non-inflamed samples. Moreover, models trained on selected SNPs from analyzed genes had an average accuracy of 92.8 %, confirming the involvement of genetic regions mapping the reported genes. Finally, using combined gene expression and SNP data we observed 100 % adalimumab response prediction accuracy for pooled, inflamed, and non-inflamed datasets. DISCUSSION Our study supports the reported genetic anti-TNF response profile and extends it for adalimumab prediction.
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Affiliation(s)
- Mario Gorenjak
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Slovenia
| | - Katja Repnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Slovenia.,Laboratory of Biochemistry, Molecular biology and Genomics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Slovenia
| | - Gregor Jezernik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Slovenia
| | - Staša Jurgec
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Slovenia.,Laboratory of Biochemistry, Molecular biology and Genomics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Slovenia
| | - Pavel Skok
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Slovenia.,Department of Gastroenterology, University Medical Center Maribor, Slovenia
| | - Uroš Potočnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Slovenia.,Laboratory of Biochemistry, Molecular biology and Genomics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Slovenia
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8
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Hernandez‐Pacheco N, Farzan N, Francis B, Karimi L, Repnik K, Vijverberg SJ, Soares P, Schieck M, Gorenjak M, Forno E, Eng C, Oh SS, Pérez‐Méndez L, Berce V, Tavendale R, Samedy L, Hunstman S, Hu D, Meade K, Farber HJ, Avila PC, Serebrisky D, Thyne SM, Brigino‐Buenaventura E, Rodriguez‐Cintron W, Sen S, Kumar R, Lenoir M, Rodriguez‐Santana JR, Celedón JC, Mukhopadhyay S, Potočnik U, Pirmohamed M, Verhamme KM, Kabesch M, Palmer CNA, Hawcutt DB, Flores C, Maitland‐van der Zee AH, Burchard EG, Pino‐Yanes M. Cover Image. Clin Exp Allergy 2019. [DOI: 10.1111/cea.13414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Hernandez-Pacheco N, Farzan N, Francis B, Karimi L, Repnik K, Vijverberg SJ, Soares P, Schieck M, Gorenjak M, Forno E, Eng C, Oh SS, Pérez-Méndez L, Berce V, Tavendale R, Samedy LA, Hunstman S, Hu D, Meade K, Farber HJ, Avila PC, Serebrisky D, Thyne SM, Brigino-Buenaventura E, Rodriguez-Cintron W, Sen S, Kumar R, Lenoir M, Rodriguez-Santana JR, Celedón JC, Mukhopadhyay S, Potočnik U, Pirmohamed M, Verhamme KM, Kabesch M, Palmer CNA, Hawcutt DB, Flores C, Maitland-van der Zee AH, Burchard EG, Pino-Yanes M. Genome-wide association study of inhaled corticosteroid response in admixed children with asthma. Clin Exp Allergy 2019; 49:789-798. [PMID: 30697902 DOI: 10.1111/cea.13354] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/30/2018] [Accepted: 12/29/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Inhaled corticosteroids (ICS) are the most widely prescribed and effective medication to control asthma symptoms and exacerbations. However, many children still have asthma exacerbations despite treatment, particularly in admixed populations, such as Puerto Ricans and African Americans. A few genome-wide association studies (GWAS) have been performed in European and Asian populations, and they have demonstrated the importance of the genetic component in ICS response. OBJECTIVE We aimed to identify genetic variants associated with asthma exacerbations in admixed children treated with ICS and to validate previous GWAS findings. METHODS A meta-analysis of two GWAS of asthma exacerbations was performed in 1347 admixed children treated with ICS (Hispanics/Latinos and African Americans), analysing 8.7 million genetic variants. Those with P ≤ 5 × 10-6 were followed up for replication in 1697 asthmatic patients from six European studies. Associations of ICS response described in published GWAS were followed up for replication in the admixed populations. RESULTS A total of 15 independent variants were suggestively associated with asthma exacerbations in admixed populations (P ≤ 5 × 10-6 ). One of them, located in the intergenic region of APOBEC3B and APOBEC3C, showed evidence of replication in Europeans (rs5995653, P = 7.52 × 10-3 ) and was also associated with change in lung function after treatment with ICS (P = 4.91 × 10-3 ). Additionally, the reported association of the L3MBTL4-ARHGAP28 genomic region was confirmed in admixed populations, although a different variant was identified. CONCLUSIONS AND CLINICAL RELEVANCE This study revealed the novel association of APOBEC3B and APOBEC3C with asthma exacerbations in children treated with ICS and replicated previously identified genomic regions. This contributes to the current knowledge about the multiple genetic markers determining responsiveness to ICS which could lead in the future the clinical identification of those asthma patients who are not able to respond to such treatment.
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Affiliation(s)
- Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, San Cristóbal de La Laguna, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Niloufar Farzan
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, Netherlands.,Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Ben Francis
- Department of Women's and Children's Health, University of Liverpool, Liverpool, UK
| | - Leila Karimi
- Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Katja Repnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Susanne J Vijverberg
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, Netherlands.,Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Patricia Soares
- Academic Department of Paediatrics, Brighton and Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK
| | - Maximilian Schieck
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany.,Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Mario Gorenjak
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Erick Forno
- Division of Pediatric Pulmonary Medicine, Children's Hospital of Pittsburgh of the University of Pittsburgh, Medical Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, California
| | - Sam S Oh
- Department of Medicine, University of California, San Francisco, California
| | - Lina Pérez-Méndez
- Department of Clinic Epidemiology and Biostatistics, Research Unit, Hospital Universitario N.S. de Candelaria, Gerencia de Atención Primaria, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Vojko Berce
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Department of Pediatrics, University Medical Centre Maribor, Maribor, Slovenia
| | - Roger Tavendale
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Lesly-Anne Samedy
- Department of Medicine, University of California, San Francisco, California.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California
| | - Scott Hunstman
- Department of Medicine, University of California, San Francisco, California
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, California
| | - Kelley Meade
- Children's Hospital and Research Center Oakland, Oakland, California
| | - Harold J Farber
- Department of Pediatrics, Section of Pulmonology, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
| | - Pedro C Avila
- Department of Medicine, Northwestern University, Chicago, Illinois.,Allergy & ENT Associates, The Woodland, Texas
| | | | - Shannon M Thyne
- Department of Pediatrics, University of California, San Francisco, California
| | | | | | - Saunak Sen
- University of Tennessee Health Science Center, Memphis, Tennessee
| | - Rajesh Kumar
- Feinberg School of Medicine's Division of Allergy and Immunology, Northwestern University, Chicago, Illinois.,Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | | | | | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, Children's Hospital of Pittsburgh of the University of Pittsburgh, Medical Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Somnath Mukhopadhyay
- Academic Department of Paediatrics, Brighton and Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK.,Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Uroš Potočnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Munir Pirmohamed
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Katia M Verhamme
- Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
| | - Colin N A Palmer
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Daniel B Hawcutt
- Department of Women's and Children's Health, University of Liverpool, Liverpool, UK.,Alder Hey Children's Hospital, Liverpool, UK
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, San Cristóbal de La Laguna, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Anke H Maitland-van der Zee
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, Netherlands.,Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, Netherlands.,Department of Pediatric Respiratory Medicine and Allergy, Emma's Children Hospital, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, Netherlands
| | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, California.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California
| | - Maria Pino-Yanes
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, San Cristóbal de La Laguna, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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10
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Čuš M, Vlaisavljević V, Repnik K, Potočnik U, Kovačič B. Could polymorphisms of some hormonal receptor genes, involved in folliculogenesis help in predicting patient response to controlled ovarian stimulation? J Assist Reprod Genet 2019; 36:47-55. [PMID: 30406448 PMCID: PMC6338606 DOI: 10.1007/s10815-018-1357-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/22/2018] [Indexed: 01/21/2023] Open
Abstract
PURPOSE The aim of this study was to investigate whether single nucleotide polymorphisms (SNPs) in selected genes, responsible for hormonal regulation of folliculogenesis, are associated with response to controlled ovarian hyperstimulation (COH) and clinical characteristics of women enrolled in in vitro fertilization (IVF) programs. METHODS In a cross-sectional study, 60 (IVF) patients underwent COH by using gonadotropin-releasing hormone (GnRH) antagonist and recombinant follicle-stimulating hormone (rFSH) protocol. Patients were classified into three groups: poor-responders (according to Bologna criteria), normo-responders (≤ 15 oocytes), and hyper-responders (> 15 oocytes). Genotyping of SNPs AMH rs10407022, AMHR rs3741664, FSHR rs1394205 and rs6166, and ESR1 rs2234693 was performed using high-resolution melting analysis (HRMA). Basal FSH (bFSH), estradiol (E2), and anti-Müllerian hormone (AMH) were measured by enzyme-linked immunosorbent assay (ELISA). RESULTS Patients with GG genotype of FSHR rs1394205 had significantly lower AMH level (P = 0.016) and required higher rFSH dose per oocyte compared to women with AA or AG genotype (P = 0.036). We also found higher frequency of GG genotype of FSHR rs1394205 in poor- (76.5%) than in hyper-responders (37.5%, P = 0.002). Patients with AA genotype of FSHR rs6166 had higher level of measured bFSH compared to those with AG or GG genotypes (P = 0.043). Women with GG genotype of AMHR rs3741664 required higher rFSH dose in comparison with patients carrying genotypes AA or AG (P = 0.028). CONCLUSIONS The GG genotype at position rs1394205 is associated with poor ovarian response to COH. Patients with this genotype may require higher doses of rFSH for ovulation induction.
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Affiliation(s)
- Maruška Čuš
- Department of Reproductive Medicine and Gynecological Endocrinology, University Medical Centre Maribor, Ljubljanska ulica 5, 2000, Maribor, Slovenia
| | | | - Katja Repnik
- Center for human molecular genetics and pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
- Faculty for Chemistry & Chemical Engineering, University of Maribor, Smetanova 17, Maribor, Slovenia
| | - Uroš Potočnik
- Center for human molecular genetics and pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
- Faculty for Chemistry & Chemical Engineering, University of Maribor, Smetanova 17, Maribor, Slovenia
| | - Borut Kovačič
- Department of Reproductive Medicine and Gynecological Endocrinology, University Medical Centre Maribor, Ljubljanska ulica 5, 2000, Maribor, Slovenia.
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11
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Farzan N, Vijverberg SJ, Hernandez‐Pacheco N, Bel EHD, Berce V, Bønnelykke K, Bisgaard H, Burchard EG, Canino G, Celedón JC, Chew FT, Chiang WC, Cloutier MM, Forno E, Francis B, Hawcutt DB, Herrera‐Luis E, Kabesch M, Karimi L, Melén E, Mukhopadhyay S, Merid SK, Palmer CN, Pino‐Yanes M, Pirmohamed M, Potočnik U, Repnik K, Schieck M, Sevelsted A, Sio YY, Smyth RL, Soares P, Söderhäll C, Tantisira KG, Tavendale R, Tse SM, Turner S, Verhamme KM, Maitland‐van der Zee A. 17q21 variant increases the risk of exacerbations in asthmatic children despite inhaled corticosteroids use. Allergy 2018; 73:2083-2088. [PMID: 29885281 PMCID: PMC6220986 DOI: 10.1111/all.13499] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- N. Farzan
- Division of Pharmacoepidemiology and Clinical Pharmacology Faculty of Science Utrecht University Utrecht The Netherlands
- Department of Respiratory Medicine Academic Medical Center (AMC) University of Amsterdam Amsterdam The Netherlands
| | - S. J. Vijverberg
- Division of Pharmacoepidemiology and Clinical Pharmacology Faculty of Science Utrecht University Utrecht The Netherlands
- Department of Respiratory Medicine Academic Medical Center (AMC) University of Amsterdam Amsterdam The Netherlands
| | - N. Hernandez‐Pacheco
- Research Unit Hospital Universitario N.S. de Candelaria Universidad de La Laguna Santa Cruz de Tenerife Spain
- Genomics and Health Group Department of Biochemistry, Microbiology, Cell Biology and Genetics Universidad de La Laguna La Laguna, Tenerife Spain
| | - E. H. D. Bel
- Department of Respiratory Medicine Academic Medical Center (AMC) University of Amsterdam Amsterdam The Netherlands
| | - V. Berce
- Centre for Human Molecular Genetics and Pharmacogenomics Faculty of Medicine University of Maribor Maribor Slovenia
- Clinic of Pediatrics University Medical Centre Maribor Maribor Slovenia
| | - K. Bønnelykke
- COPSAC Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital University of Copenhagen Copenhagen Denmark
| | - H. Bisgaard
- COPSAC Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital University of Copenhagen Copenhagen Denmark
| | - E. G. Burchard
- Departments of Medicine, Bioengineering and Therapeutic Sciences University of California San Francisco CA USA
| | - G. Canino
- Behavioral Sciences Institute University of Puerto Rico Medical Sciences Campus San Juan Puerto Rico
| | - J. C. Celedón
- Division of Pulmonary Medicine, Allergy, and Immunology Children's Hospital of Pittsburgh of the University of Pittsburgh Medical Center University of Pittsburgh Pittsburgh PA USA
| | - F. T. Chew
- Department of Biological Sciences National University of Singapore Singapore Singapore
- The Allergy & Immunology Division Department of Paediatric Medicine KK Children's Hospital Singapore Singapore
| | - W. C. Chiang
- The Allergy & Immunology Division Department of Paediatric Medicine KK Children's Hospital Singapore Singapore
| | - M. M. Cloutier
- Asthma Center Connecticut Children's Medical Center University of Connecticut Health Center Hartford CT USA
| | - E. Forno
- Division of Pulmonary Medicine, Allergy, and Immunology Children's Hospital of Pittsburgh of the University of Pittsburgh Medical Center University of Pittsburgh Pittsburgh PA USA
| | - B. Francis
- Department of Women's and Children's Health University of Liverpool Liverpool UK
| | - D. B. Hawcutt
- Department of Women's and Children's Health University of Liverpool Liverpool UK
- Alder Hey Children's Hospital Liverpool UK
| | - E. Herrera‐Luis
- Genomics and Health Group Department of Biochemistry, Microbiology, Cell Biology and Genetics Universidad de La Laguna La Laguna, Tenerife Spain
| | - M. Kabesch
- Department of Pediatric Pneumology and Allergy University Children's Hospital Regensburg (KUNO) Regensburg Germany
| | - L. Karimi
- Deptartment of Medical Informatics Erasmus University Medical Center Rotterdam The Netherlands
| | - E. Melén
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
- Department of Pediatrics Sachs’ Children's Hospital Stockholm Sweden
| | - S. Mukhopadhyay
- Academic Department of Paediatrics Brighton and Sussex Medical School Royal Alexandra Children's Hospital Brighton UK
- Division of Molecular & Clinical Medicine School of Medicine University of Dundee Dundee UK
| | - S. K. Merid
- Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden
| | - C. N. Palmer
- Division of Molecular & Clinical Medicine School of Medicine University of Dundee Dundee UK
| | - M. Pino‐Yanes
- Research Unit Hospital Universitario N.S. de Candelaria Universidad de La Laguna Santa Cruz de Tenerife Spain
- Genomics and Health Group Department of Biochemistry, Microbiology, Cell Biology and Genetics Universidad de La Laguna La Laguna, Tenerife Spain
- CIBER de Enfermedades Respiratorias Instituto de Salud Carlos III Madrid Spain
| | - M. Pirmohamed
- Department of Molecular and Clinical Pharmacology Institute of Translational Medicine University of Liverpool Liverpool UK
| | - U. Potočnik
- Centre for Human Molecular Genetics and Pharmacogenomics Faculty of Medicine University of Maribor Maribor Slovenia
- Faculty for Chemistry and Chemical Engineering University of Maribor Maribor Slovenia
| | - K. Repnik
- Centre for Human Molecular Genetics and Pharmacogenomics Faculty of Medicine University of Maribor Maribor Slovenia
- Faculty for Chemistry and Chemical Engineering University of Maribor Maribor Slovenia
| | - M. Schieck
- Department of Pediatric Pneumology and Allergy University Children's Hospital Regensburg (KUNO) Regensburg Germany
- Department of Human Genetics Hannover Medical School Hannover Germany
| | - A. Sevelsted
- COPSAC Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital University of Copenhagen Copenhagen Denmark
| | - Y. Y. Sio
- Department of Biological Sciences National University of Singapore Singapore Singapore
- The Allergy & Immunology Division Department of Paediatric Medicine KK Children's Hospital Singapore Singapore
| | - R. L. Smyth
- Institute of Child Health University College London London UK
| | - P. Soares
- Academic Department of Paediatrics Brighton and Sussex Medical School Royal Alexandra Children's Hospital Brighton UK
| | - C. Söderhäll
- Department of Women's and Children's Health Karolinska Institutet Stockholm Sweden
- Department of Biosciences and Nutrition Karolinska Institutet Stockholm Sweden
| | - K. G. Tantisira
- The Channing Division of Network Medicine Department of Medicine Brigham and Women's Hospital and Harvard Medical School Boston MA USA
- Division of Pulmonary and Critical Care Medicine Brigham and Women's Hospital and Harvard Medical School Boston MA USA
| | - R. Tavendale
- Division of Molecular & Clinical Medicine School of Medicine University of Dundee Dundee UK
| | - S. M. Tse
- Division of Respiratory Medicine Department of Pediatrics Sainte‐Justine University Hospital Center and University of Montreal Montreal QC Canada
| | - S. Turner
- Child Health University of Aberdeen Aberdeen UK
| | - K. M. Verhamme
- Deptartment of Medical Informatics Erasmus University Medical Center Rotterdam The Netherlands
| | - A.‐H. Maitland‐van der Zee
- Division of Pharmacoepidemiology and Clinical Pharmacology Faculty of Science Utrecht University Utrecht The Netherlands
- Department of Respiratory Medicine Academic Medical Center (AMC) University of Amsterdam Amsterdam The Netherlands
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12
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Pernat Drobež C, Ferkolj I, Potočnik U, Repnik K. Crohn's Disease Candidate Gene Alleles Predict Time to Progression from Inflammatory B1 to Stricturing B2, or Penetrating B3 Phenotype. Genet Test Mol Biomarkers 2018; 22:143-151. [PMID: 29446656 DOI: 10.1089/gtmb.2017.0210] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
AIM Crohn's disease (CD) patients are mostly diagnosed with the uncomplicated inflammatory form of disease; however, the majority will progress to complicated stricturing or penetrating disease over time. It is important to identify patients at risk for disease progression at an early stage. The aim of our study was to examine the role of 33 candidate CD genes as possible predictors of disease progression and their influence on time to progression from an inflammatory to a stricturing or penetrating phenotype. METHODS Patients with an inflammatory phenotype at diagnosis were followed for 10 years and 33 CD-associated polymorphisms were genotyped. To test for association with CD, 449 healthy individuals were analyzed as the control group. RESULTS Ten years after diagnosis, 39.1% of patients had not progressed beyond an inflammatory phenotype, but 60.9% had progressed to complicated disease, with average time to progression being 5.91 years. Association analyses of selected single nucleotide polymorphisms (SNPs) confirmed associations with CD for 12 SNPs. Furthermore, seven loci were associated with disease progression, out of which SNP rs4263839 in the gene TNFSF15 showed the strongest association with disease progression and the frameshift mutation rs2066847 in the gene NOD2 showed the strongest association with time to progression. CONCLUSIONS The results of our study identified specific genetic biomarkers as useful predictors of both disease progression and speed of disease progression in patients with CD.
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Affiliation(s)
- Cvetka Pernat Drobež
- 1 Department of Gastroenterology, University Medical Centre Maribor , Maribor, Slovenia
| | - Ivan Ferkolj
- 2 Department of Gastroenterology, Division of Internal Medicine, University Medical Centre Ljubljana , Ljubljana, Slovenia
| | - Uroš Potočnik
- 3 Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor , Maribor, Slovenia .,4 Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor , Maribor, Slovenia
| | - Katja Repnik
- 3 Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor , Maribor, Slovenia .,4 Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor , Maribor, Slovenia
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13
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Vijverberg SJH, Hernandez-Pacheco N, Farzan N, Francis B, Flores C, Schieck M, Soares P, Karimi L, Tavendale R, Berce V, Repnik K, Verhamme K, PotočNik U, Mukhopadhyay S, Pirmohamed M, Palmer C, Turner S, Hawcutt D, Kabesch M, Pino-Yanes M, Maitland-Van Der Zee AH. Genome-wide association study of asthma exacerbations in European children treated with inhaled corticosteroids. Genes Environ 2017. [DOI: 10.1183/1393003.congress-2017.pa1817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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14
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Farzan N, Vijverberg SJ, Andiappan AK, Arianto L, Berce V, Blanca-López N, Bisgaard H, Bønnelykke K, Burchard EG, Campo P, Canino G, Carleton B, Celedón JC, Chew FT, Chiang WC, Cloutier MM, Daley D, Den Dekker HT, Dijk FN, Duijts L, Flores C, Forno E, Hawcutt DB, Hernandez-Pacheco N, de Jongste JC, Kabesch M, Koppelman GH, Manolopoulos VG, Melén E, Mukhopadhyay S, Nilsson S, Palmer CN, Pino-Yanes M, Pirmohamed M, Potočnik U, Raaijmakers JA, Repnik K, Schieck M, Sio YY, Smyth RL, Szalai C, Tantisira KG, Turner S, van der Schee MP, Verhamme KM, Maitland-van der Zee AH. Rationale and design of the multiethnic Pharmacogenomics in Childhood Asthma consortium. Pharmacogenomics 2017. [PMID: 28639505 DOI: 10.2217/pgs-2017-0035] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
AIM International collaboration is needed to enable large-scale pharmacogenomics studies in childhood asthma. Here, we describe the design of the Pharmacogenomics in Childhood Asthma (PiCA) consortium. MATERIALS & METHODS Investigators of each study participating in PiCA provided data on the study characteristics by answering an online questionnaire. RESULTS A total of 21 studies, including 14,227 children/young persons (58% male), from 12 different countries are currently enrolled in the PiCA consortium. Fifty six percent of the patients are Caucasians. In total, 7619 were inhaled corticosteroid users. Among patients from 13 studies with available data on asthma exacerbations, a third reported exacerbations despite inhaled corticosteroid use. In the future pharmacogenomics studies within the consortium, the pharmacogenomics analyses will be performed separately in each center and the results will be meta-analyzed. CONCLUSION PiCA is a valuable platform to perform pharmacogenetics studies within a multiethnic pediatric asthma population.
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Affiliation(s)
- Niloufar Farzan
- Division of Pharmacoepidemiology & Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands.,Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Susanne J Vijverberg
- Division of Pharmacoepidemiology & Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands.,Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Anand K Andiappan
- Singapore Immunology Network, Agency for Science, Technology & Research, Singapore 138648, Singapore
| | - Lambang Arianto
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Vojko Berce
- Department of Pediatrics, University Medical Centre Maribor, Maribor, Slovenia.,Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | | | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev & Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Esteban G Burchard
- Departments of Medicine, Bioengineering & Therapeutic Sciences University of California, San Francisco, CA 94110, USA
| | - Paloma Campo
- Allergy Unit, IBIMA, Regional University Hospital of Malaga, Malaga, Spain
| | - Glorisa Canino
- Behavioral Sciences institute, University of Puerto Rico, Medical Sciences Campus, San Juan, Puerto Rico
| | - Bruce Carleton
- Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Juan C Celedón
- Division of Pulmonary Medicine, Allergy, & Immunology, Children's Hospital of Pittsburgh of the University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Fook Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore, & the Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore
| | - Wen Chin Chiang
- Department of Biological Sciences, National University of Singapore, Singapore, & the Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore
| | - Michelle M Cloutier
- Asthma Center, Connecticut Children's Medical Center, University of Connecticut Health Center, CT 06106, USA
| | - Denis Daley
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Herman T Den Dekker
- Department of Pediatrics, Division of Respiratory Medicine & Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - F Nicole Dijk
- Department of Pediatric Pulmonology & Pediatric Allergology, University Medical Center Groningen, University of Groningen, Beatrix Children's Hospital, Groningen, The Netherlands.,Groningen Research Institute for Asthma & COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Liesbeth Duijts
- Department of Pediatrics, Division of Respiratory Medicine & Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pediatrics, Division of Neonatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Carlos Flores
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Erick Forno
- Division of Pulmonary Medicine, Allergy, & Immunology, Children's Hospital of Pittsburgh of the University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Daniel B Hawcutt
- Alder Hey Children's Hospital, Liverpool, UK.,Department of Women's & Children's Health, University of Liverpool, Liverpool, UK
| | - Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Johan C de Jongste
- Department of Pediatrics, Division of Respiratory Medicine & Allergology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Michael Kabesch
- Department of Pediatric Pneumology & Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology & Pediatric Allergology, University Medical Center Groningen, University of Groningen, Beatrix Children's Hospital, Groningen, The Netherlands.,Groningen Research Institute for Asthma & COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Vangelis G Manolopoulos
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre of Occupational & Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Somnath Mukhopadhyay
- Academic Department of Paediatrics, Brighton & Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK.,Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital & Medical School University of Dundee, Dundee, UK
| | - Sara Nilsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre of Occupational & Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Colin N Palmer
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital & Medical School University of Dundee, Dundee, UK
| | - Maria Pino-Yanes
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Munir Pirmohamed
- Department of Molecular & Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Uros Potočnik
- Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Faculty for Chemistry & Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Jan A Raaijmakers
- Division of Pharmacoepidemiology & Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Katja Repnik
- Centre for Human Molecular Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Faculty for Chemistry & Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Maximilian Schieck
- Department of Pediatric Pneumology & Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany.,Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Yang Yie Sio
- Department of Biological Sciences, National University of Singapore, Singapore, & the Allergy & Immunology Division, Department of Paediatric Medicine, KK Children's Hospital, Singapore
| | - Rosalind L Smyth
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Csaba Szalai
- Department of Genetics, Cell & Immuno-biology, Semmelweis University, Budapest, Hungary.,Central Laboratory, Heim Pal Children Hospital, Budapest, Hungary
| | - Kelan G Tantisira
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's hospital & Harvard Medical School, Boston, MA 02115, USA.,Division of Pulmonary & Critical Care Medicine, Brigham & Women's Hospital & Harvard Medical School, Boston, MA 02115, USA
| | - Steve Turner
- Child Health, University of Aberdeen, Aberdeen, UK
| | - Marc P van der Schee
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Katia M Verhamme
- Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anke H Maitland-van der Zee
- Division of Pharmacoepidemiology & Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands.,Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
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15
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Horvat M, Potocnik U, Repnik K, Kavalar R, Zadnik V, Potrc S, Stabuc B. Single Nucleotide Polymorphisms in Genes MACC1, RAD18, MMP7 and SDF-1a As Prognostic Factors in Resectable Colorectal Cancer. Radiol Oncol 2016; 51:151-159. [PMID: 28740450 PMCID: PMC5514655 DOI: 10.1515/raon-2016-0043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/27/2016] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) represents one of the most common malignancies worldwide. Research has indicated that functional gene changes such as single nucleotide polymorphism (SNP) influence carcinogenesis and metastasis and might have an influence on disease relapse. The aim of our study was to evaluate the role of SNPs in selected genes as prognostic markers in resectable CRC. PATIENTS AND METHODS In total, 163 consecutive patients treated surgically for CRC of stages I, II and III at the University Medical Centre in Maribor in 2007 and 2008 were investigated. DNA was isolated from formalin-fixed paraffin-embedded CRC tissue from the Department of Pathology and SNPs in genes SDF-1a, MMP7, RAD18 and MACC1 were genotyped using polymerase chain reaction followed by high resolution melting curve analysis or restriction fragment length polymorphism. RESULTS We found worse disease-free survival (DFS) for patients with TT genotype of SNP rs1990172 in gene MACC1 (p = 0.029). Next, we found worse DFS for patients with GG genotype for SNP rs373572 in gene RAD18 (p = 0.020). Higher frequency of genotype GG of MMP7 SNP rs11568818 was found in patients with T3/T4 stage (p = 0.014), N1/N2 stage (p = 0.041) and with lymphovascular invasion (p = 0.018). For MACC1 rs1990172 SNP we found higher frequency of genotype TT in patients with T3/T4 staging (p = 0.024). Higher frequency of genotype GG of RAD18 rs373572 was also found in patients with T1/T2 stage with disease relapse (p = 0.041). CONCLUSIONS Our results indicate the role of SNPs as prognostic factors in resectable CRC.
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Affiliation(s)
- Matej Horvat
- Department of Oncology, University Medical Centre Maribor, Maribor, Slovenia
| | - Uros Potocnik
- Centre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Katja Repnik
- Centre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Rajko Kavalar
- Department of Pathology, University Medical Centre Maribor, Maribor, Slovenia
| | - Vesna Zadnik
- Epidemiology and Cancer Registry, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Stojan Potrc
- Department of General and Abdominal Surgery, University Medical Centre Maribor, Maribor, Slovenia
| | - Borut Stabuc
- Department of Gastroenterology, University Medical Centre Ljubljana, Ljubljana, Slovenia
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16
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Repnik K, Koder S, Skok P, Ferkolj I, Potočnik U. Transferrin Level Before Treatment and Genetic Polymorphism in HFE Gene as Predictive Markers for Response to Adalimumab in Crohn’s Disease Patients. Biochem Genet 2016; 54:476-486. [DOI: 10.1007/s10528-016-9734-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/13/2016] [Indexed: 12/19/2022]
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17
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Deželak M, Repnik K, Koder S, Ferkolj I, Potočnik U. A Prospective Pharmacogenomic Study of Crohn's Disease Patients during Routine Therapy with Anti-TNF-α Drug Adalimumab: Contribution of ATG5, NFKB1, and CRP Genes to Pharmacodynamic Variability. OMICS 2016; 20:296-309. [PMID: 27096233 DOI: 10.1089/omi.2016.0005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Crohn's disease is often treated with the anti-tumor necrosis factor-α drug adalimumab. However, about 20%-40% of patients do not display adequate therapeutic response. We prospectively evaluated, during a routine therapy of Crohn's disease patients, the candidate autophagy-related genes ATG12 and ATG5 and the inflammation-related genes NFKB1, NFKBIA, and CRP as potential predictors of adalimumab treatment response (pharmacodynamics). The associations of haplotypes and SNPs in these genes with response to drug therapy, biochemical parameters, and body mass were determined at baseline and after 4, 12, 20, and 30 weeks of therapy. Association analysis showed that haplotypes defined with the SNPs rs9373839 and rs510432 in ATG5 gene were significantly associated with positive response to therapy (p < 0.002). In addition, allele C and genotypes CC and CT of the rs1130864 in the CRP gene were positively associated with therapeutic response (p < 0.002). To the best of our knowledge, this is the first report that supports the association of SNPs in ATG5 and CRP genes with response to adalimumab therapy in Crohn's disease. Further study of these biological pathways in larger and independent clinical samples is warranted as novel streams of research on precision medicine and diagnostics for Crohn's disease.
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Affiliation(s)
- Matjaž Deželak
- 1 Centre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor , Maribor, Slovenia
| | - Katja Repnik
- 1 Centre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor , Maribor, Slovenia .,2 Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor , Maribor, Slovenia
| | - Silvo Koder
- 3 University Medical Centre Maribor , Maribor, Slovenia
| | - Ivan Ferkolj
- 4 University Medical Centre Ljubljana , Ljubljana, Slovenia
| | - Uroš Potočnik
- 1 Centre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor , Maribor, Slovenia .,2 Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor , Maribor, Slovenia
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18
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Zupančič K, Skok K, Repnik K, Weersma RK, Potočnik U, Skok P. Multi-locus genetic risk score predicts risk for Crohn’s disease in Slovenian population. World J Gastroenterol 2016; 22:3777-3784. [PMID: 27076762 PMCID: PMC4814740 DOI: 10.3748/wjg.v22.i14.3777] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 03/01/2016] [Accepted: 03/14/2016] [Indexed: 02/07/2023] Open
Abstract
AIM: To develop a risk model for Crohn’s disease (CD) based on homogeneous population.
METHODS: In our study were included 160 CD patients and 209 healthy individuals from Slovenia. The association study was performed for 112 single nucleotide polymorphisms (SNPs). We generated genetic risk scores (GRS) based on the number of risk alleles using weighted additive model. Discriminatory accuracy was measured by area under ROC curve (AUC). For risk evaluation, we divided individuals according to positive and negative likelihood ratios (LR) of a test, with LR > 5 for high risk group and LR < 0.20 for low risk group.
RESULTS: The highest accuracy, AUC of 0.78 was achieved with GRS combining 33 SNPs with optimal sensitivity and specificity of 75.0% and 72.7%, respectively. Individuals with the highest risk (GRS > 5.54) showed significantly increased odds of developing CD (OR = 26.65, 95%CI: 11.25-63.15) compared to the individuals with the lowest risk (GRS < 4.57) which is a considerably greater risk captured than in one SNP with the highest effect size (OR = 3.24). When more than 33 SNPs were included in GRS, discriminatory ability was not improved significantly; AUC of all 74 SNPs was 0.76.
CONCLUSION: The authors proved the possibility of building accurate genetic risk score based on 33 risk variants on Slovenian CD patients which may serve as a screening tool in the targeted population.
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Repnik K, Potočnik U. eQTL analysis links inflammatory bowel disease associated 1q21 locus to ECM1 gene. J Appl Genet 2016; 57:363-72. [PMID: 26738999 DOI: 10.1007/s13353-015-0334-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 12/16/2015] [Accepted: 12/18/2015] [Indexed: 12/11/2022]
Abstract
Genome-wide association studies (GWAS) have been highly successful in inflammatory bowel disease (IBD) with 163 confirmed associations so far. We used expression quantitative trait loci (eQTL) mapping to analyze IBD associated regions for which causative gene from the region is still unknown. First, we performed an extensive literature search and in silico analysis of published GWAS in IBD and eQTL studies and extracted 402 IBD associated SNPs assigned to 208 candidate loci, and 9562 eQTL correlations. When crossing GWA and eQTL data we found that for 50 % of loci there is no eQTL gene, while for 31.2 % we can determine one gene, for 11.1 % two genes and for the remaining 7.7 % three or more genes. Based on that we selected loci with one, two, and three or more eQTL genes and analyzed them in peripheral blood lymphocytes and intestine tissue samples of 606 Slovene patients with IBD and in 449 controls. Association analysis of selected SNPs showed statistical significance for three (rs2631372 and rs1050152 on 5q locus and rs13294 on 1q locus) out of six selected SNPs with at least one phenotype. Furthermore, with eQTL analysis of selected chromosomal regions, we confirmed a link between SNP and gene for four (SLC22A5 on 5q, ECM1 on 1q, ORMDL3 on 17q, and PUS10 on 2p locus) out of five selected regions. For 1q21 loci, we confirmed gene ECM1 as the most plausible gene from this region to be involved in pathogenesis of IBD and thereby contributed new eQTL correlation from this genomic region.
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Affiliation(s)
- Katja Repnik
- Faculty of Medicine, Center for Human Molecular Genetics and Pharmacogenomics, University of Maribor, Taborska ulica 8, 2000, Maribor, Slovenia.,Faculty for Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Uroš Potočnik
- Faculty of Medicine, Center for Human Molecular Genetics and Pharmacogenomics, University of Maribor, Taborska ulica 8, 2000, Maribor, Slovenia. .,Faculty for Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia.
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Koder S, Repnik K, Ferkolj I, Pernat C, Skok P, Weersma RK, Potočnik U. Genetic polymorphism in ATG16L1 gene influences the response to adalimumab in Crohn's disease patients. Pharmacogenomics 2015; 16:191-204. [PMID: 25712183 DOI: 10.2217/pgs.14.172] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
AIM To see if SNPs could help predict response to biological therapy using adalimumab (ADA) in Crohn's disease (CD). MATERIALS & METHODS IBDQ index and CRP levels were used to monitor therapy response. We genotyped 31 CD-associated genes in 102 Slovenian CD patients. RESULTS The strongest association for treatment response defined as decrease in CRP levels was found for ATG16L1 SNP rs10210302. Additional SNPs in 7 out of 31 tested CD-associated genes (PTGER4, CASP9, IL27, C11orf30, CCNY, IL13, NR1I2) showed suggestive association with ADA response. CONCLUSION Our results suggest ADA response in CD patients is genetically predisposed by SNPs in CD risk genes and suggest ATG16L1 as most promising candidate gene for drug response in ADA treatment. Original submitted 24 September 2014; Revision submitted 1 December 2014.
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Affiliation(s)
- Silvo Koder
- University Medical Centre Maribor, Ljubljanska 5, Maribor, Slovenia
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Repnik K, Potočnik U. Haplotype in the IBD5 region is associated with refractory Crohn's disease in Slovenian patients and modulates expression of the SLC22A5 gene. J Gastroenterol 2011; 46:1081-91. [PMID: 21695374 DOI: 10.1007/s00535-011-0426-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Accepted: 05/27/2011] [Indexed: 02/06/2023]
Abstract
BACKGROUND The IBD5 locus (OMIM ID 606348) on chromosome 5 was suggested to be one of the most important genetic factors involved in the pathogenesis of inflammatory bowel diseases (IBDs). However the main contributor from this region is still unknown. METHODS We investigated the possible association of the IBD5 locus with IBD in Slovenian patients and correlation between disease-associated single nucleotide polymorphisms (SNPs) and quantitative gene expression (eQTL) of candidate genes from the IBD5 locus in peripheral blood lymphocytes and colon tissue biopsies from IBD patients. We genotyped SNPs from the IBD5 locus in 312 healthy controls and 632 IBD patients. RESULTS We found statistically significant association of polymorphisms rs1050152 in gene SLC22A4 (p = 0.005, OR = 2.177, 95% CI = 1.270-3.526) and rs2631372 in gene SLC22A5 (p = 0.001, OR = 0.473, 95% CI = 0.307-0.731) and TC haplotype of both polymorphisms (p = 0.006, OR = 1,541, 95% CI = 1.130-2.100) with refractory Crohn's disease (CD) in Slovenian patients who do not respond to standard therapy, including patients who develop fistulas. We found decreased expression of SLC22A4 and SLC22A5 genes in peripheral blood lymphocytes from IBD patients compared to control group and decreased expression of SLC22A5 gene in inflamed tissue biopsies compared to noninflamed colon (p = 0.009). We found lower expression of SLC22A5 gene in IBD patients with disease-susceptible genotypes for both disease-associated SNPs. CONCLUSIONS Our data suggest that SNPs and haplotype in the IBD5 SLC22A4/SLC22A5 region contribute to the development of particularly refractory Crohn's disease in the Slovenian population, and expression studies in blood lymphocytes and colon tissue biopsies and eQTL analysis suggest that SLC22A5 is the main gene in the IBD5 region contributing to the IBD pathogenesis.
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Affiliation(s)
- Katja Repnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Slomškov Trg 15, 2000 Maribor, Slovenia
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Repnik K, Potocnik U. CTLA4 CT60 single-nucleotide polymorphism is associated with Slovenian inflammatory bowel disease patients and regulates expression of CTLA4 isoforms. DNA Cell Biol 2010; 29:603-10. [PMID: 20491567 DOI: 10.1089/dna.2010.1021] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
We have evaluated functional polymorphism (rs3087243; in literature known also as CTLA4 CT60) in the cytotoxic T lymphocyte antigen 4 (CTLA4) gene, previously associated with several autoimmune diseases, for potential association with inflammatory bowel diseases (IBD). In addition, we investigated correlations between CTLA4 CT60 polymorphism and CTLA4 gene expression in peripheral blood lymphocytes and colon biopsies from IBD patients. We genotyped CTLA4 CT60 polymorphism in 266 healthy control subjects and 481 IBD patients and found statistically lower frequency of CTLA4 CT60 AA genotype in IBD patients (13.72%) compared to control subjects (23.31%; p = 0.001, odds ratio [OR] = 0.504) as well as lower allele frequency of minor A allele in IBD patients (0.346) compared to control subjects (0.461, p < 0.001, OR = 0.623). The association was confirmed with both major forms of IBD, Crohn's disease, and ulcerative colitis (UC), but was slightly stronger in UC patients, particularly when we compared allele frequency of A allele in UC patients (0.299) and control subjects (0.461, p < 0.001, OR = 0.500). We found lower expression of the CTLA4 gene in blood lymphocytes from IBD patients compared to control subjects (p < 0.001) and higher CTLA4 expression in biopsies taken from inflamed part of the colon compared to noninflamed part of the colon (p = 0.021). We found lower expression of soluble CTLA4 isoform than membrane-bound full-length isoform in peripheral blood lymphocytes from IBD patients compared to control subjects (p = 0.010) and in lymphocytes from IBD patients with CTLA4 CT60 GG genotype compared to IBD patients with AA genotype (p = 0.034). Our genotype and gene expression data suggest that CTLA4 plays a role in IBD pathogenesis. Polymorphism CTLA4 CT60 contributes to genetic susceptibility to IBD in Slovenian population and regulates expression of CTLA4 isoforms.
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Affiliation(s)
- Katja Repnik
- Faculty of Medicine, Center for Human Molecular Genetics and Pharmacogenomics, University of Maribor, Maribor, Slovenia
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Abstract
Asthma is one of the most common chronic diseases of childhood. Asthma results from the interaction of several genes and environmental influences. Viral infections are common triggers of asthma attacks, especially in nonatopic asthmatics. CCR5 is a chemokine receptor involved in the immune response against a number of viruses. A 32 base pair deletion (delta32) in the CCR5 receptor gene causes loss of gene function and is associated with several chronic diseases due to the resulting altered immunity. The results of the association studies exploring the role of the CCR5 receptor gene in asthma pathogenesis are contradictory. We studied 111 children aged between 5 and 18 years with mild or moderate persistent asthma; 75 of them were atopic and 36 had nonatopic asthma. We carried out allergy and spirometry tests, a bronchoprovocation test with methacholine and performed measurement of exhaled nitric oxide and genotyping for CCR5-delta32 mutation. Compared with 365 nonatopic, nonasthmatic controls we found significantly lower CCR5-delta32 allelic frequency in nonatopic asthmatics (p = 0.016, OR 0.139, 95% CI 0.02 to 0.984) but not in atopic asthmatics. CCR5-delta32 mutation protects against nonatopic asthma. This association offers new insights into the pathogenesis of an important asthma phenotype and could serve as useful information for the future research of new asthma management strategies.
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Affiliation(s)
- Vojko Berce
- Department of Pediatrics, General Hospital Murska Sobota, Murska Sobota, Slovenia
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