University of Groningen Systematic Prioritization of Candidate Genes in Disease Loci Identifies TRAFD1 as a Master Regulator of IFN gamma Signaling in Celiac Disease BIOS Consortium; van der Graaf, Adriaan; Zorro, Maria M.; Claringbould, Annique; Vosa, Urmo; Aguirre-Gamboa, Raul; Li, Chan; Mooiweer, Joram; Ricano-Ponce, Isis; Borek, Zuzanna Published in: Frontiers in Genetics DOI: 10.3389/fgene.2020.562434 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2021 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): BIOS Consortium, van der Graaf, A., Zorro, M. M., Claringbould, A., Vosa, U., Aguirre-Gamboa, R., Li, C., Mooiweer, J., Ricano-Ponce, I., Borek, Z., Koning, F., Kooy-Winkelaar, Y., Sollid, L. M., Qiao, S-W., Kumar, V., Li, Y., Franke, L., Withoff, S., Wijmenga, C., ... Jonkers, I. (2021). Systematic Prioritization of Candidate Genes in Disease Loci Identifies TRAFD1 as a Master Regulator of IFN gamma Signaling in Celiac Disease. Frontiers in Genetics, 11, 562434. [562434]. https://doi.org/10.3389/fgene.2020.562434 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 28-09-2021 ORIGINAL RESEARCH published: 25 January 2021 doi: 10.3389/fgene.2020.562434 Systematic Prioritization of Candidate Genes in Disease Loci Identifies TRAFD1 as a Master Regulator of IFNγ Signaling in Celiac Edited by: Yue-miao Zhang, Disease Peking University People’s Hospital, China Adriaan van der Graaf 1†, Maria M. Zorro 1†, Annique Claringbould 1, Urmo Võsa 1,2, Reviewed by: Raúl Aguirre-Gamboa 1, Chan Li 1,3, Joram Mooiweer 1, Isis Ricaño-Ponce 1, Jose Ramon Bilbao, 4,5 6 6 3 University of the Basque Zuzanna Borek , Frits Koning , Yvonne Kooy-Winkelaar , Ludvig M. Sollid , 3 1,7 1,7,8 1 1 Country, Spain Shuo-Wang Qiao , Vinod Kumar , Yang Li , Lude Franke , Sebo Withoff , 1,3 1,9 † 1,3 † Jin Xu, Cisca Wijmenga , Serena Sanna * , Iris Jonkers * and BIOS Consortium Ningbo University, China 1 Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands, 2 Estonian *Correspondence: Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia, 3 Department of Immunology, K. G. Jebsen Coeliac Serena Sanna Disease Research Centre, University of Oslo, Oslo, Norway, 4 Deutsches Rheumaforschungszentrum Berlin (DRFZ), An [email protected] Institute of the Leibniz Association, Berlin, Germany, 5 Charité–Universitätsmedizin Berlin, Corporate Member of Freie Iris Jonkers Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gastroenterology, Infectious [email protected] Diseases and Rheumatology, Berlin, Germany, 6 Department of Immunology, Leiden University, Leiden, Netherlands, 7 Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, †These authors have contributed Nijmegen, Netherlands, 8 Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised equally to this work Infection Medicine, Helmholtz Centre for Infection Research, Hannover Medical School, Hanover, Germany, 9 Istituto di Ricerca Genetica e Biomedica (IRGB) del Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy Specialty section: This article was submitted to Genomic Medicine, Celiac disease (CeD) is a complex T cell-mediated enteropathy induced by gluten. a section of the journal Although genome-wide association studies have identified numerous genomic regions Frontiers in Genetics associated with CeD, it is difficult to accurately pinpoint which genes in these loci Received: 10 July 2020 Accepted: 16 December 2020 are most likely to cause CeD. We used four different in silico approaches—Mendelian Published: 25 January 2021 randomization inverse variance weighting, COLOC, LD overlap, and DEPICT—to Citation: integrate information gathered from a large transcriptomics dataset. This identified van der Graaf A, Zorro MM, 118 prioritized genes across 50 CeD-associated regions. Co-expression and pathway Claringbould A, Võsa U, Aguirre-Gamboa R, Li C, Mooiweer J, analysis of these genes indicated an association with adaptive and innate cytokine Ricaño-Ponce I, Borek Z, Koning F, signaling and T cell activation pathways. Fifty-one of these genes are targets of known Kooy-Winkelaar Y, Sollid LM, Qiao S-W, Kumar V, Li Y, Franke L, drug compounds or likely druggable genes, suggesting that our methods can be used to Withoff S, Wijmenga C, Sanna S, pinpoint potential therapeutic targets. In addition, we detected 172 gene combinations Jonkers I and BIOS Consortium that were affected by our CeD-prioritized genes in trans. Notably, 41 of these (2021) Systematic Prioritization of Candidate Genes in Disease Loci trans-mediated genes appear to be under control of one master regulator, TRAF-type Identifies TRAFD1 as a Master zinc finger domain containing 1 (TRAFD1), and were found to be involved in interferon Regulator of IFNγ Signaling in Celiac Disease. Front. Genet. 11:562434. (IFN)γ signaling and MHC I antigen processing/presentation. Finally, we performed in doi: 10.3389/fgene.2020.562434 vitro experiments in a human monocytic cell line that validated the role of TRAFD1 as an Frontiers in Genetics | www.frontiersin.org 1 January 2021 | Volume 11 | Article 562434 van der Graaf et al. TRAFD1 Is Trans-Regulator in CeD immune regulator acting in trans. Our strategy confirmed the role of adaptive immunity in CeD and revealed a genetic link between CeD and IFNγ signaling as well as with MHC I antigen processing, both major players of immune activation and CeD pathogenesis. Keywords: celiac disease, gene prioritization, expression quantitative trait locus (eQTL), TRAFD1, trans regulation INTRODUCTION between the genes that surround the GWAS locus (Pers et al., 2015). Unfortunately, there is no current “gold standard” method Celiac disease (CeD) is an autoimmune disease in which patients for finding the causal gene behind a GWAS hit, as all the methods experience severe intestinal inflammation upon ingestion of discussed here are subject to their respective assumptions, gluten peptides. CeD has a large genetic component, with drawbacks, and caveats. However, it is worthwhile to use all these heritability estimated to be ∼75% (Kuja-Halkola et al., 2016). methods in parallel to find the most likely causal genes for CeD. The largest CeD-impacting locus is the human leukocyte antigen Here, we systematically applied four prioritization methods (HLA) region, which contributes ∼40% of CeD heritability to the latest meta-analysis for CeD that we have performed (Bevan et al., 1999). While the individual impacts of CeD- previously (Ricaño-Ponce et al., 2020) and coupled them with associated genes outside the HLA region are smaller, they jointly eQTL results from the Biobank Integrative Omics Study (BIOS) account for an additional 20% of heritability. Previous genome- cohort (Zhernakova et al., 2017), one of the largest cohorts wide association studies (GWASs) have identified 42 non-HLA for which there is genotype and RNA sequencing (RNA-seq) genomic loci associated with CeD. Yet, identification of these expression data of peripheral blood mononuclear cells. We non-HLA genetic components and an understanding of the focused on 58 CeD-associated loci (p < 5 × 10−6) outside the molecular perturbations associated with them are necessary to HLA region. Our approach prioritized 118 genes in 50 loci and understand CeD pathophysiology. identified one gene, TRAF-type zinc finger domain containing Understanding the biological mechanisms of non-HLA CeD 1 (TRAFD1), as a master regulator of trans-effects. We then loci is difficult: only three of these loci point to single- experimentally validated the role of TRAFD1-mediated genes nucleotide polymorphisms (SNPs) located in protein-coding using a TRAFD1 knockdown through RNA-seq in a disease- regions (Trynka et al., 2011). The other CeD-risk loci cannot relevant cell type. Our study yields novel insights into the genetics be explained by missense mutations, making it necessary to of CeD and is proof-of-concept for a systematic approach that look at other biological mechanisms such as gene expression can be applied to other complex diseases. A schematic overview to explain their role in CeD pathogenicity. Several studies of our study is shown in Supplementary Figure 1A. have been performed to integrate expression quantitative trait loci (eQTLs) with CeD GWAS associations (Dubois et al., 2010; Kumar et al., 2015; Ricaño-Ponce et al., 2016), and NOMENCLATURE several candidate genes, including UBASH3A, CD274, SH2B3, and STAT4 (Zhernakova et al., 2011), have been identified, Underlined words are definitions that have been explained in