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Bronchial airway inducible expression and methylation QTL mapping identifies a single nucleotide polymorphism predicting inhaled corticosteroids response heterogeneity

Elise M.A. Slob, Alen Faiz, Susanne Vijverberg, Cristina Longo, Merve Kutlu, Patricia Soares, Fook Tim Chew, Esther Herrera-Luis, Antonio Espuela Ortiz, Maria Del Pino Yanes, Esteban Burchard, Uroš Potočnik, Colin Palmer, Cyrielle Maroteau, Steve Turner, Katia Verhamme, Leila Karimi, Somnath Mukhopadhyay, Wim Timens, Pieter Hiemstra, Mariëlle Pijnenburg, Maarten Van Den Berge, Anke-Hilse Maitland-Van Der Zee, Gerard Koppelman
European Respiratory Journal 2020 56: 4920; DOI: 10.1183/13993003.congress-2020.4920
Elise M.A. Slob
1Department of Respiratory Disease and Paediatric Pulmonology, AmsterdamUMC, Amsterdam, Netherlands
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  • For correspondence: e.m.slob@amc.nl
Alen Faiz
2Respiratory Bioinformatics and Molecular Biology, School of Life Sciences, University of Technology Sydney, Sydney, Australia
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Susanne Vijverberg
1Department of Respiratory Disease and Paediatric Pulmonology, AmsterdamUMC, Amsterdam, Netherlands
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Cristina Longo
1Department of Respiratory Disease and Paediatric Pulmonology, AmsterdamUMC, Amsterdam, Netherlands
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Merve Kutlu
1Department of Respiratory Disease and Paediatric Pulmonology, AmsterdamUMC, Amsterdam, Netherlands
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Patricia Soares
3Dept. of Paediatrics, Royal Alexandra Children’s Hospital, Brighton, United Kingdom
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Fook Tim Chew
4Dept. of Biological Science, National University of Singapore, Singapore, Singapore
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Esther Herrera-Luis
5Dept. of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
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Antonio Espuela Ortiz
5Dept. of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
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Maria Del Pino Yanes
5Dept. of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
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Esteban Burchard
6Department of Medicine, University of California San Francisco, San Francisco, United States of America
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Uroš Potočnik
7Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
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Colin Palmer
814Population Pharmacogenetics Group, Biomedical Research Institute, University of Dundee, Dundee, United Kingdom
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Cyrielle Maroteau
9Population Pharmacogenetics Group, Biomedical Research Institute, University of Dundee, Dundee, United Kingdom
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Steve Turner
10Child Health, University of Aberdeen, Aberdeen, United Kingdom
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Katia Verhamme
11Dept. of Medical Informatics, Erasmus Medical Center, Rotterdam, Netherlands
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Leila Karimi
11Dept. of Medical Informatics, Erasmus Medical Center, Rotterdam, Netherlands
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Somnath Mukhopadhyay
3Dept. of Paediatrics, Royal Alexandra Children’s Hospital, Brighton, United Kingdom
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Wim Timens
12University of Groningen, University Medical Center Groningen, Dept. of Pathology and Medical Biology, Groningen, Netherlands
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Pieter Hiemstra
13Dept. of Pulmonology, Leiden University Medical Center, Leiden, Netherlands
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Mariëlle Pijnenburg
14Dept. of Pediatrics, Pediatric Pulmonology & Allergology, Erasmus Medical Center- Sophia Children’s Hospital, Rotterdam, Netherlands
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Maarten Van Den Berge
1520Dept. of Pulmonology, University of Groningen, University Medical Center Groningen, GRIAC research Institute, Groningen, Netherlands
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Anke-Hilse Maitland-Van Der Zee
1Department of Respiratory Disease and Paediatric Pulmonology, AmsterdamUMC, Amsterdam, Netherlands
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Gerard Koppelman
16Dept. of Pediatric Pulmonology & Allergology, University Medical Center Groningen, GRIAC research Institute, Groningen, Groningen, Netherlands
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Abstract

Objectives: We aimed to identify genetic variants affecting gene expression and methylation changes in airway wall biopsies before and after ICS and investigate whether these are associated with poor response to ICS.

Methods: Quantitative Trait Locus (QTL) Mapping profiling of paired bronchial biopsies from 42 COPD patients, was performed prior to and 6 months post ICS use. The window size was 1Mb flanking gene limits and the false discovery rate was used to adjust for multiple comparisons. Association between SNPs and gene expression (eQTL) or gene methylation (meQTL) changes upon ICS use was evaluated. Subsequently, a candidate-gene study was conducted in asthma patients treated with ICS to investigate whether these SNPs are associated with ICS response. Poor ICS response was defined as presence of exacerbations despite ICS use in the last 6-12 months. Logistic regressions were used to test the association and Bonferroni correction was applied.

Results: 18 eQTL and 57 meQTL SNPs were associated with ICS response. When these SNPs were tested in asthma patients (3,722 children for eQTL and 1,166 children for meQTL), the only significant variant was the meQTL SNP rs7220099, an intergenic variant at locus 17q12 with an allele frequency of 33% and a lung eQTL for TBC1 domain family member 3D. The G allele increased the risk of exacerbations (pooled OR: 1.39 95%CI 1.19-1.63, p-value = 2.4 x 10-5).

Conclusions: Our results show that gene expression and methylation profiling prior and post ICS use are quite different between asthma and COPD but still may help to find functional SNPs predicting ICS response.

  • Genetics
  • Pharmacology
  • Personalised medicine

Footnotes

Cite this article as: European Respiratory Journal 2020; 56: Suppl. 64, 4920.

This abstract was presented at the 2020 ERS International Congress, in session “Respiratory viruses in the "pre COVID-19" era”.

This is an ERS International Congress abstract. No full-text version is available. Further material to accompany this abstract may be available at www.ers-education.org (ERS member access only).

  • Copyright ©the authors 2020
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Bronchial airway inducible expression and methylation QTL mapping identifies a single nucleotide polymorphism predicting inhaled corticosteroids response heterogeneity
Elise M.A. Slob, Alen Faiz, Susanne Vijverberg, Cristina Longo, Merve Kutlu, Patricia Soares, Fook Tim Chew, Esther Herrera-Luis, Antonio Espuela Ortiz, Maria Del Pino Yanes, Esteban Burchard, Uroš Potočnik, Colin Palmer, Cyrielle Maroteau, Steve Turner, Katia Verhamme, Leila Karimi, Somnath Mukhopadhyay, Wim Timens, Pieter Hiemstra, Mariëlle Pijnenburg, Maarten Van Den Berge, Anke-Hilse Maitland-Van Der Zee, Gerard Koppelman
European Respiratory Journal Sep 2020, 56 (suppl 64) 4920; DOI: 10.1183/13993003.congress-2020.4920

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Bronchial airway inducible expression and methylation QTL mapping identifies a single nucleotide polymorphism predicting inhaled corticosteroids response heterogeneity
Elise M.A. Slob, Alen Faiz, Susanne Vijverberg, Cristina Longo, Merve Kutlu, Patricia Soares, Fook Tim Chew, Esther Herrera-Luis, Antonio Espuela Ortiz, Maria Del Pino Yanes, Esteban Burchard, Uroš Potočnik, Colin Palmer, Cyrielle Maroteau, Steve Turner, Katia Verhamme, Leila Karimi, Somnath Mukhopadhyay, Wim Timens, Pieter Hiemstra, Mariëlle Pijnenburg, Maarten Van Den Berge, Anke-Hilse Maitland-Van Der Zee, Gerard Koppelman
European Respiratory Journal Sep 2020, 56 (suppl 64) 4920; DOI: 10.1183/13993003.congress-2020.4920
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