Protein-coding variants contribute to the risk of atopic dermatitis and skin-specific gene expression - 13/12/19

Doi : 10.1016/j.jaci.2019.10.030

Sören Mucha, MSc ^a,^{^{∗
These authors contributed equally to this work.}}, Hansjörg Baurecht, PhD ^b,^c,^{^{∗
These authors contributed equally to this work.}}, Natalija Novak, MD ^d, Elke Rodríguez, PhD ^b, Saptarshi Bej, MSc ^e, Gabriele Mayr, PhD ^a, Hila Emmert, PhD ^b, Dora Stölzl, MD ^b, Sascha Gerdes, MD ^b, Eun Suk Jung, MD ^a,^f, Frauke Degenhardt, MSc ^a, Matthias Hübenthal, PhD ^a,^b, Eva Ellinghaus, PhD ^a, Jan Christian Kässens, PhD ^a, Lars Wienbrandt, PhD ^a, Wolfgang Lieb, MD ^g, Martina Müller-Nurasyid, PhD ^h,^i,^j, Melanie Hotze, PhD ^b, Nick Dand, PhD ^k, Sarah Grosche, PhD ^l,^m, Ingo Marenholz, MD ^l,^m, Andreas Arnold, MD ⁿ, Georg Homuth, PhD ^o, Carsten O. Schmidt, MD ^p, Ulrike Wehkamp, MD ^b, Markus M. Nöthen, MD ^q, Per Hoffmann, PhD ^q, Lavinia Paternoster, PhD ^r, Marie Standl, PhD ^s, on behalf of the
Early Genetics and Lifecourse Epidemiology (EAGLE) Eczema Consortium
Klaus Bønnelykke, MD ^t, Tarunveer S. Ahluwalia, PhD ^t,^u, Hans Bisgaard, MD ^t, Annette Peters, PhD ^s, Christian Gieger, PhD ^v, Melanie Waldenberger, PhD ^v, Holger Schulz, PhD ^s, Konstantin Strauch, PhD ^h,ⁱ, Thomas Werfel, MD ^u,^w, Young-Ae Lee, PhD ^j,^k, Markus Wolfien, MSc ^e, Philip Rosenstiel, MD ^a, Olaf Wolkenhauer, PhD ^e, Stefan Schreiber, MD ^a,^x, Andre Franke, PhD ^a,^{^{‡
These authors jointly supervised this work.}}, Stephan Weidinger, MD ^b,^⁎,^{^{‡
These authors jointly supervised this work.}} , David Ellinghaus, PhD ^a,^⁎,^{^{‡
These authors jointly supervised this work.}}
^a Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
^b Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
^c Department for Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
^d Department of Dermatology and Allergy, University Hospital Bonn, Bonn, Germany
^e Department of Systems Biology and Bioinformatics, University of Rostock, Germany
^f Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
^g Institute of Epidemiology and Biobank PopGen, Christian Albrechts University of Kiel, Kiel, Germany
^h Institute of Genetic Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
ⁱ Chair of Genetic Epidemiology, IBE, Faculty of Medicine, Ludwig-Maximilians-University Munich, Germany
^j Department of Internal Medicine I (Cardiology), Hospital of the Ludwig-Maximilians-University Munich, Munich, Germany
^k School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King’s College London, London, United Kingdom
^l Pediatric Allergology, Experimental and Clinical Research Center, Charité Universitätsmedizin Berlin, Berlin, Germany
^m Max-Delbrück-Centrum (MDC) for Molecular Medicine, Berlin, Germany
ⁿ Clinic and Polyclinic of Dermatology, University Medicine Greifswald, Greifswald, Germany
^o Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
^p Institute for Community Medicine, Study of Health in Pomerania/KEF, University Medicine Greifswald, Greifswald, Germany
^q Institute of Human Genetics, University of Bonn, Bonn, Germany
^r Medical Research Council (MRC) Integrative Epidemiology Unit, Bristol Medical School, and the School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
^s Institute of Epidemiology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
^t Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, Gentofte, Denmark
^u Steno Diabetes Center Copenhagen, Gentofte, Denmark
^v Research Unit of Molecular Epidemiology and Institute of Epidemiology II, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
^w Department of Dermatology and Allergy, Division of Immunodermatology and Allergy Research, Hannover Medical School, Hannover, Germany
^x First Medical Department, University Hospital Schleswig-Holstein, Kiel, Germany

^∗Corresponding authors: Stephan Weidinger, MD, Arnold-Heller-Straße 3, Haus 19, 24105 Kiel, Germany.Arnold-Heller-Straße 3Haus 19Kiel24105Germany^∗∗David Ellinghaus, PhD, Rosalind-Franklin-Str 12, 24105 Kiel, Germany.Rosalind-Franklin-Str 12Kiel24105Germany

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Abstract

Background

Fifteen percent of atopic dermatitis (AD) liability-scale heritability could be attributed to 31 susceptibility loci identified by using genome-wide association studies, with only 3 of them (IL13, IL-6 receptor [IL6R], and filaggrin [FLG]) resolved to protein-coding variants.

Objective

We examined whether a significant portion of unexplained AD heritability is further explained by low-frequency and rare variants in the gene-coding sequence.

Methods

We evaluated common, low-frequency, and rare protein-coding variants using exome chip and replication genotype data of 15,574 patients and 377,839 control subjects combined with whole-transcriptome data on lesional, nonlesional, and healthy skin samples of 27 patients and 38 control subjects.

Results

An additional 12.56% (SE, 0.74%) of AD heritability is explained by rare protein-coding variation. We identified docking protein 2 (DOK2) and CD200 receptor 1 (CD200R1) as novel genome-wide significant susceptibility genes. Rare coding variants associated with AD are further enriched in 5 genes (IL-4 receptor [IL4R], IL13, Janus kinase 1 [JAK1], JAK2, and tyrosine kinase 2 [TYK2]) of the IL13 pathway, all of which are targets for novel systemic AD therapeutics. Multiomics-based network and RNA sequencing analysis revealed DOK2 as a central hub interacting with, among others, CD200R1, IL6R, and signal transducer and activator of transcription 3 (STAT3). Multitissue gene expression profile analysis for 53 tissue types from the Genotype-Tissue Expression project showed that disease-associated protein-coding variants exert their greatest effect in skin tissues.

Conclusion

Our discoveries highlight a major role of rare coding variants in AD acting independently of common variants. Further extensive functional studies are required to detect all potential causal variants and to specify the contribution of the novel susceptibility genes DOK2 and CD200R1 to overall disease susceptibility.

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Graphical abstract

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Key words : Atopic dermatitis, exome chip association analysis, network analysis, protein sequence and structural domain analysis, RNA sequencing

Abbreviations used : AD, CD200R1, DOK2, EAGLE, GTEx, GWAS, IL6R, LD, MAF, MS, OR, RasGAP, RNA-seq, SNP

Plan

Methods

Study samples and genotyping

Results

Exome chip single-variant association analysis

Exome chip gene-based association analysis

Bayesian fine mapping and functional annotation

Immunohistochemistry and whole-transcriptome mRNA-seq data analysis

In silico variant protein analysis

AD core network construction and differential gene expression analysis of core genes

Pathway and gene expression tissue specificity analysis for exome chip variants

Estimation of liability-heritability from exome chip variants

Discussion

This work was supported by the German Federal Ministry of Education and Research (BMBF) within the framework of the e:Med research and funding concept (SysInflame grant 01ZX1606A and GB-XMAP grant 01ZX1709), as well as the German ELIXIR node de.NBI (de.STAIR grant 031L0106C). The project was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy (EXC 2167-390884018). The project received infrastructure support from the DFG Excellence Cluster no. 306 “Inflammation at Interfaces” and the PopGen Biobank (Kiel, Germany). The Kooperative Gesundheitsforschung in der Region Augsburg (KORA) research platform (Cooperative Research in the Region of Augsburg) was initiated and financed by the Helmholtz Zentrum München–German Research Center for Environmental Health, which is funded by BMBF and the State of Bavaria. Furthermore, KORA research was supported within the Munich Center of Health Sciences (MC Health), Ludwig-Maximilians-Universität, as part of LMUinnovativ. SHIP (Study of Health in Pomerania) is part of the Community Medicine Research net (CMR) of the University of Greifswald, Greifswald, Germany, which is funded by BMBF (grants 01ZZ9603, 01ZZ0103, and 01ZZ0403) and the Ministry of Cultural Affairs, as well as the Social Ministry of the Federal State of Mecklenburg-West Pomerania, and the network “Greifswald Approach to Individualized Medicine (GANI_MED)” funded by BMBF (grant 03IS2061A). Exome chip data have been supported by BMBF (grant no. 03Z1CN22) and the Federal State of Mecklenburg-West Pomerania. L.P. was supported by a UK Medical Research Council fellowship (MR/J012165/1). This work was supported by BIOMAP (Biomarkers in Atopic Dermatitis and Psoriasis), a project funded by the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement no. 821511 and in-kind contributions of the participating pharma companies. The Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation program and EFPIA.

Disclosure of potential conflict of interest: The authors declare that they have no relevant conflicts of interest.