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van der Graaf A, Zorro MM, Claringbould A, Võsa U, Aguirre-Gamboa R, Li C, Mooiweer J, Ricaño-Ponce I, Borek Z, Koning F, Kooy-Winkelaar Y, Sollid LM, Qiao SW, Kumar V, Li Y, Franke L, Withoff S, Wijmenga C, Sanna S, Jonkers I. Systematic Prioritization of Candidate Genes in Disease Loci Identifies TRAFD1 as a Master Regulator of IFNγ Signaling in Celiac Disease. Front Genet 2021; 11:562434. [PMID: 33569077 PMCID: PMC7868554 DOI: 10.3389/fgene.2020.562434] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 07/10/2020] [Accepted: 12/16/2020] [Indexed: 12/17/2022] Open
Abstract
Celiac disease (CeD) is a complex T cell-mediated enteropathy induced by gluten. Although genome-wide association studies have identified numerous genomic regions associated with CeD, it is difficult to accurately pinpoint which genes in these loci are most likely to cause CeD. We used four different in silico approaches-Mendelian randomization inverse variance weighting, COLOC, LD overlap, and DEPICT-to integrate information gathered from a large transcriptomics dataset. This identified 118 prioritized genes across 50 CeD-associated regions. Co-expression and pathway analysis of these genes indicated an association with adaptive and innate cytokine signaling and T cell activation pathways. Fifty-one of these genes are targets of known drug compounds or likely druggable genes, suggesting that our methods can be used to pinpoint potential therapeutic targets. In addition, we detected 172 gene combinations that were affected by our CeD-prioritized genes in trans. Notably, 41 of these trans-mediated genes appear to be under control of one master regulator, TRAF-type zinc finger domain containing 1 (TRAFD1), and were found to be involved in interferon (IFN)γ signaling and MHC I antigen processing/presentation. Finally, we performed in vitro experiments in a human monocytic cell line that validated the role of TRAFD1 as an 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.
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Affiliation(s)
- Adriaan van der Graaf
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Maria M. Zorro
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Annique Claringbould
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Urmo Võsa
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Raúl Aguirre-Gamboa
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Chan Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Joram Mooiweer
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Isis Ricaño-Ponce
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Zuzanna Borek
- Deutsches Rheumaforschungszentrum Berlin (DRFZ), An Institute of the Leibniz Association, Berlin, Germany
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Gastroenterology, Infectious Diseases and Rheumatology, Berlin, Germany
| | - Frits Koning
- Department of Immunology, Leiden University, Leiden, Netherlands
| | | | - Ludvig M. Sollid
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Shuo-Wang Qiao
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Vinod Kumar
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
| | - Yang Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
- Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine, Helmholtz Centre for Infection Research, Hannover Medical School, Hanover, Germany
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Sebo Withoff
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Serena Sanna
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Istituto di Ricerca Genetica e Biomedica (IRGB) del Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Iris Jonkers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Immunology, K. G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
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Aguirre-Gamboa R, de Klein N, di Tommaso J, Claringbould A, van der Wijst MG, de Vries D, Brugge H, Oelen R, Võsa U, Zorro MM, Chu X, Bakker OB, Borek Z, Ricaño-Ponce I, Deelen P, Xu CJ, Swertz M, Jonkers I, Withoff S, Joosten I, Sanna S, Kumar V, Koenen HJPM, Joosten LAB, Netea MG, Wijmenga C, Franke L, Li Y. Deconvolution of bulk blood eQTL effects into immune cell subpopulations. BMC Bioinformatics 2020; 21:243. [PMID: 32532224 PMCID: PMC7291428 DOI: 10.1186/s12859-020-03576-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 06/01/2020] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Expression quantitative trait loci (eQTL) studies are used to interpret the function of disease-associated genetic risk factors. To date, most eQTL analyses have been conducted in bulk tissues, such as whole blood and tissue biopsies, which are likely to mask the cell type-context of the eQTL regulatory effects. Although this context can be investigated by generating transcriptional profiles from purified cell subpopulations, current methods to do this are labor-intensive and expensive. We introduce a new method, Decon2, as a framework for estimating cell proportions using expression profiles from bulk blood samples (Decon-cell) followed by deconvolution of cell type eQTLs (Decon-eQTL). RESULTS The estimated cell proportions from Decon-cell agree with experimental measurements across cohorts (R ≥ 0.77). Using Decon-cell, we could predict the proportions of 34 circulating cell types for 3194 samples from a population-based cohort. Next, we identified 16,362 whole-blood eQTLs and deconvoluted cell type interaction (CTi) eQTLs using the predicted cell proportions from Decon-cell. CTi eQTLs show excellent allelic directional concordance with eQTL (≥ 96-100%) and chromatin mark QTL (≥87-92%) studies that used either purified cell subpopulations or single-cell RNA-seq, outperforming the conventional interaction effect. CONCLUSIONS Decon2 provides a method to detect cell type interaction effects from bulk blood eQTLs that is useful for pinpointing the most relevant cell type for a given complex disease. Decon2 is available as an R package and Java application (https://github.com/molgenis/systemsgenetics/tree/master/Decon2) and as a web tool (www.molgenis.org/deconvolution).
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Affiliation(s)
- Raúl Aguirre-Gamboa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Niek de Klein
- Department of Genetics, Oncode Institute, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jennifer di Tommaso
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Annique Claringbould
- Department of Genetics, Oncode Institute, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Monique Gp van der Wijst
- Department of Genetics, Oncode Institute, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Dylan de Vries
- Department of Genetics, Oncode Institute, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Harm Brugge
- Department of Genetics, Oncode Institute, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Roy Oelen
- Department of Genetics, Oncode Institute, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Urmo Võsa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Maria M Zorro
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Xiaojin Chu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Centre for Individualised Infection Medicine (CiiM) & TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Feodor-Lynen-Str. 7, 30625, Hannover, Germany
| | - Olivier B Bakker
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Zuzanna Borek
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Isis Ricaño-Ponce
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Patrick Deelen
- Department of Genetics, Oncode Institute, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Cheng-Jiang Xu
- Centre for Individualised Infection Medicine (CiiM) & TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Feodor-Lynen-Str. 7, 30625, Hannover, Germany
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Morris Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Iris Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sebo Withoff
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Irma Joosten
- Department of Laboratory Medicine, Laboratory for Medical Immunology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Serena Sanna
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Vinod Kumar
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hans J P M Koenen
- Department of Laboratory Medicine, Laboratory for Medical Immunology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Yang Li
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
- Centre for Individualised Infection Medicine (CiiM) & TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Feodor-Lynen-Str. 7, 30625, Hannover, Germany.
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands.
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Bernal CE, Zorro MM, Sierra J, Gilchrist K, Botero JH, Baena A, Ramirez-Pineda JR. Encephalitozoon intestinalis Inhibits Dendritic Cell Differentiation through an IL-6-Dependent Mechanism. Front Cell Infect Microbiol 2016; 6:4. [PMID: 26870700 PMCID: PMC4735406 DOI: 10.3389/fcimb.2016.00004] [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: 11/30/2015] [Accepted: 01/12/2016] [Indexed: 01/03/2023] Open
Abstract
Microsporidia are a group of intracellular pathogens causing self-limited and severe diseases in immunocompetent and immunocompromised individuals, respectively. A cellular type 1 adaptive response, mediated by IL-12, IFNγ, CD4+, and CD8+ T cells has been shown to be essential for host resistance, and dendritic cells (DC) play a key role at eliciting anti-microsporidial immunity. We investigated the in vitro response of DC and DC precursors/progenitors to infection with Encephalitozoon intestinalis (Ei), a common agent of human microsporidosis. Ei-exposed DC cultures up-regulated the surface expression of MHC class II and the costimulatory molecules CD86 and CD40, only when high loads of spores were used. A vigorous secretion of IL-6 but not of IL-1β or IL-12p70 was also observed in these cultures. Ei-exposed DC cultures consisted of immature infected and mature bystander DC, as assessed by MHC class II and costimulatory molecules expression, suggesting that intracellular Ei spores deliver inhibitory signals in DC. Moreover, Ei selectively inhibited the secretion of IL-12p70 in LPS-stimulated DC. Whereas Ei-exposed DC promoted allogeneic naïve T cell proliferation and IL-2 and IFNγ secretion in DC-CD4+ T cell co-cultures, separated co-cultures with bystander or infected DCs showed stimulation or inhibition of IFNγ secretion, respectively. When DC precursors/progenitors were exposed to Ei spores, a significant inhibition of DC differentiation was observed without shifting the development toward cells phenotypically or functionally compatible with myeloid-derived suppressor cells. Neutralization experiments demonstrated that this inhibitory effect is IL-6-dependent. Altogether this investigation reveals a novel potential mechanism of immune escape of microsporidian parasites through the modulation of DC differentiation and maturation.
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Affiliation(s)
- Carmen E Bernal
- Grupo Inmunomodulación, Universidad de AntioquiaMedellín, Colombia; Grupo de Parasitología, Universidad de AntioquiaMedellín, Colombia
| | - Maria M Zorro
- Grupo Inmunomodulación, Universidad de Antioquia Medellín, Colombia
| | - Jelver Sierra
- Grupo Inmunomodulación, Universidad de Antioquia Medellín, Colombia
| | | | - Jorge H Botero
- Grupo de Parasitología, Universidad de Antioquia Medellín, Colombia
| | - Andres Baena
- Grupo de Inmunología Celular e Inmunogenética, Universidad de AntioquiaMedellín, Colombia; Departamento de Microbiología y Parasitología, Universidad de AntioquiaMedellín, Colombia
| | - Jose R Ramirez-Pineda
- Grupo Inmunomodulación, Universidad de AntioquiaMedellín, Colombia; Corporación Académica para el Estudio de Patologías Tropicales, Facultad de Medicina, Universidad de AntioquiaMedellín, Colombia
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Stachurska A, Zorro MM, van der Sijde MR, Withoff S. Small and Long Regulatory RNAs in the Immune System and Immune Diseases. Front Immunol 2014; 5:513. [PMID: 25368617 PMCID: PMC4202709 DOI: 10.3389/fimmu.2014.00513] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [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: 07/24/2014] [Accepted: 10/02/2014] [Indexed: 12/14/2022] Open
Abstract
Cellular differentiation is regulated on the level of gene expression, and it is known that dysregulation of gene expression can lead to deficiencies in differentiation that contribute to a variety of diseases, particularly of the immune system. Until recently, it was thought that the dysregulation was governed by changes in the binding or activity of a class of proteins called transcription factors. However, the discovery of micro-RNAs and recent descriptions of long non-coding RNAs (lncRNAs) have given enormous momentum to a whole new field of biology: the regulatory RNAs. In this review, we describe these two classes of regulatory RNAs and summarize what is known about how they regulate aspects of the adaptive and innate immune systems. Finally, we describe what is known about the involvement of micro-RNAs and lncRNAs in three different autoimmune diseases (celiac disease, inflammatory bowel disease, and multiple sclerosis).
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Affiliation(s)
- Anna Stachurska
- Department of Genetics, University Medical Center Groningen, University of Groningen , Groningen , Netherlands
| | - Maria M Zorro
- Department of Genetics, University Medical Center Groningen, University of Groningen , Groningen , Netherlands
| | - Marijke R van der Sijde
- Department of Genetics, University Medical Center Groningen, University of Groningen , Groningen , Netherlands
| | - Sebo Withoff
- Department of Genetics, University Medical Center Groningen, University of Groningen , Groningen , Netherlands
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