1
|
Kim-Hellmuth S, Bechheim M, Pütz B, Mohammadi P, Nédélec Y, Giangreco N, Becker J, Kaiser V, Fricker N, Beier E, Boor P, Castel SE, Nöthen MM, Barreiro LB, Pickrell JK, Müller-Myhsok B, Lappalainen T, Schumacher J, Hornung V. Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations. Nat Commun 2017; 8:266. [PMID: 28814792 PMCID: PMC5559603 DOI: 10.1038/s41467-017-00366-1] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/23/2017] [Indexed: 12/15/2022] Open
Abstract
The immune system plays a major role in human health and disease, and understanding genetic causes of interindividual variability of immune responses is vital. Here, we isolate monocytes from 134 genotyped individuals, stimulate these cells with three defined microbe-associated molecular patterns (LPS, MDP, and 5'-ppp-dsRNA), and profile the transcriptomes at three time points. Mapping expression quantitative trait loci (eQTL), we identify 417 response eQTLs (reQTLs) with varying effects between conditions. We characterize the dynamics of genetic regulation on early and late immune response and observe an enrichment of reQTLs in distal cis-regulatory elements. In addition, reQTLs are enriched for recent positive selection with an evolutionary trend towards enhanced immune response. Finally, we uncover reQTL effects in multiple GWAS loci and show a stronger enrichment for response than constant eQTLs in GWAS signals of several autoimmune diseases. This demonstrates the importance of infectious stimuli in modifying genetic predisposition to disease.Insight into the genetic influence on the immune response is important for the understanding of interindividual variability in human pathologies. Here, the authors generate transcriptome data from human blood monocytes stimulated with various immune stimuli and provide a time-resolved response eQTL map.
Collapse
Affiliation(s)
- Sarah Kim-Hellmuth
- New York Genome Center, New York, NY, 10013, USA.
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
- Institute of Human Genetics, University of Bonn, Bonn, 53127, Germany.
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, 53127, Germany.
| | - Matthias Bechheim
- Institute of Molecular Medicine, University of Bonn, Bonn, 53127, Germany
| | - Benno Pütz
- Statistical Genetics, Max Planck Institute of Psychiatry, Munich, 80804, Germany
| | - Pejman Mohammadi
- New York Genome Center, New York, NY, 10013, USA
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - Yohann Nédélec
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Canada, H3T 1C5
- Department of Biochemistry, University of Montreal, Montreal, Canada, H3C 3J7
| | - Nicholas Giangreco
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - Jessica Becker
- Institute of Human Genetics, University of Bonn, Bonn, 53127, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, 53127, Germany
| | - Vera Kaiser
- Institute of Molecular Medicine, University of Bonn, Bonn, 53127, Germany
| | - Nadine Fricker
- Institute of Human Genetics, University of Bonn, Bonn, 53127, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, 53127, Germany
| | - Esther Beier
- Institute of Molecular Medicine, University of Bonn, Bonn, 53127, Germany
| | - Peter Boor
- Institute of Pathology and Department of Nephrology, University Clinic of RWTH Aachen, Aachen, 52074, Germany
| | - Stephane E Castel
- New York Genome Center, New York, NY, 10013, USA
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, 53127, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, 53127, Germany
| | - Luis B Barreiro
- Department of Genetics, CHU Sainte-Justine Research Center, Montreal, Canada, H3T 1C5
- Department of Pediatrics, University of Montreal, Montreal, Canada, H3T 1C5
| | - Joseph K Pickrell
- New York Genome Center, New York, NY, 10013, USA
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Bertram Müller-Myhsok
- Statistical Genetics, Max Planck Institute of Psychiatry, Munich, 80804, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, 80804, Germany
- Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GL, UK
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, 10013, USA.
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA.
| | - Johannes Schumacher
- Institute of Human Genetics, University of Bonn, Bonn, 53127, Germany.
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, 53127, Germany.
| | - Veit Hornung
- Institute of Molecular Medicine, University of Bonn, Bonn, 53127, Germany
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität Munich, Munich, 81377, Germany
- Center for Integrated Protein Science (CIPSM), Ludwig-Maximilians-Universität Munich, Munich, 81377, Germany
| |
Collapse
|
2
|
Kim S, Becker J, Bechheim M, Kaiser V, Noursadeghi M, Fricker N, Beier E, Klaschik S, Boor P, Hess T, Hofmann A, Holdenrieder S, Wendland JR, Fröhlich H, Hartmann G, Nöthen MM, Müller-Myhsok B, Pütz B, Hornung V, Schumacher J. Characterizing the genetic basis of innate immune response in TLR4-activated human monocytes. Nat Commun 2014; 5:5236. [PMID: 25327457 DOI: 10.1038/ncomms6236] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 09/11/2014] [Indexed: 12/18/2022] Open
Abstract
Toll-like receptors (TLRs) play a key role in innate immunity. Apart from their function in host defense, dysregulation in TLR signalling can confer risk to autoimmune diseases, septic shock or cancer. Here we report genetic variants and transcripts that are active only during TLR signalling and contribute to interindividual differences in immune response. Comparing unstimulated versus TLR4-stimulated monocytes reveals 1,471 expression quantitative trait loci (eQTLs) that are unique to TLR4 stimulation. Among these we find functional SNPs for the expression of NEU4, CCL14, CBX3 and IRF5 on TLR4 activation. Furthermore, we show that SNPs conferring risk to primary biliary cirrhosis (PBC), inflammatory bowel disease (IBD) and celiac disease are immune response eQTLs for PDGFB and IL18R1. Thus, PDGFB and IL18R1 represent plausible candidates for studying the pathophysiology of these disorders in the context of TLR4 activation. In summary, this study presents novel insights into the genetic basis of the innate immune response and exemplifies the value of eQTL studies in the context of exogenous cell stimulation.
Collapse
Affiliation(s)
- Sarah Kim
- 1] Institute of Human Genetics, University of Bonn, Bonn 53127, Germany [2] Department of Genomics, Life &Brain Center, University of Bonn, Bonn 53127, Germany [3] Institute of Molecular Medicine, University of Bonn, Bonn 53127, Germany
| | - Jessica Becker
- 1] Institute of Human Genetics, University of Bonn, Bonn 53127, Germany [2] Department of Genomics, Life &Brain Center, University of Bonn, Bonn 53127, Germany
| | - Matthias Bechheim
- Institute of Molecular Medicine, University of Bonn, Bonn 53127, Germany
| | - Vera Kaiser
- Institute of Molecular Medicine, University of Bonn, Bonn 53127, Germany
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Nadine Fricker
- 1] Institute of Human Genetics, University of Bonn, Bonn 53127, Germany [2] Department of Genomics, Life &Brain Center, University of Bonn, Bonn 53127, Germany
| | - Esther Beier
- Institute of Molecular Medicine, University of Bonn, Bonn 53127, Germany
| | - Sven Klaschik
- Department for Anesthesiology and Intensive Care Medicine, University of Bonn, Bonn 53127, Germany
| | - Peter Boor
- Institute of Pathology and Department of Nephrology, University Clinic of RWTH Aachen, Aachen 52074, Germany
| | - Timo Hess
- 1] Institute of Human Genetics, University of Bonn, Bonn 53127, Germany [2] Department of Genomics, Life &Brain Center, University of Bonn, Bonn 53127, Germany
| | - Andrea Hofmann
- 1] Institute of Human Genetics, University of Bonn, Bonn 53127, Germany [2] Department of Genomics, Life &Brain Center, University of Bonn, Bonn 53127, Germany
| | - Stefan Holdenrieder
- Institute for Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn 53127, Germany
| | - Jens R Wendland
- Worldwide R&D, Pfizer Inc., Cambridge, Massachusetts 02139, USA
| | - Holger Fröhlich
- Bonn-Aachen International Center for IT (B-IT), University of Bonn, Bonn 53113, Germany
| | - Gunther Hartmann
- Institute for Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn 53127, Germany
| | - Markus M Nöthen
- 1] Institute of Human Genetics, University of Bonn, Bonn 53127, Germany [2] Department of Genomics, Life &Brain Center, University of Bonn, Bonn 53127, Germany
| | - Bertram Müller-Myhsok
- 1] Statistical Genetics, Max Planck Institute of Psychiatry, Munich 80804, Germany [2] Munich Cluster for Systems Neurology (SyNergy), Munich 80804, Germany [3] Institute of Translational Medicine, University of Liverpool, Liverpool L69 3GL, UK
| | - Benno Pütz
- Statistical Genetics, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Veit Hornung
- Institute of Molecular Medicine, University of Bonn, Bonn 53127, Germany
| | - Johannes Schumacher
- 1] Institute of Human Genetics, University of Bonn, Bonn 53127, Germany [2] Department of Genomics, Life &Brain Center, University of Bonn, Bonn 53127, Germany
| |
Collapse
|
3
|
Kim S, Kaiser V, Beier E, Bechheim M, Guenthner-Biller M, Ablasser A, Berger M, Endres S, Hartmann G, Hornung V. Self-priming determines high type I IFN production by plasmacytoid dendritic cells. Eur J Immunol 2014; 44:807-818. [PMID: 24338737 DOI: 10.1002/eji.201343806] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 11/05/2013] [Accepted: 12/06/2013] [Indexed: 12/19/2022]
Abstract
Plasmacytoid dendritic cells (pDCs) are responsible for the robust and immediate production of type I IFNs during viral infection. pDCs employ TLR7 and TLR9 to detect RNA and CpG motifs present in microbial genomes. CpG-A was the first synthetic stimulus available that induced large amounts of IFN-α (type I IFN) in pDCs. CpG-B, however, only weakly activates pDCs to produce IFN-α. Here, we demonstrate that differences in the kinetics of TLR9 activation in human pDCs are essential for the understanding of the functional difference between CpG-A and CpG-B. While CpG-B quickly induces IFN-α production in pDCs, CpG-A stimulation results in delayed yet maximal IFN-α induction. Constitutive production of low levels of type I IFN in pDCs, acting in a paracrine and autocrine fashion, turned out to be the key mechanism responsible for this phenomenon. At high cell density, pDC-derived, constitutive type I IFN production primes pDCs for maximal TLR responsiveness. This accounts for the high activity of higher structured TLR agonists that trigger type I IFN production in a delayed fashion. Altogether, these data demonstrate that high type I IFN production by pDCs cannot be simply ascribed to cell-autonomous mechanisms, yet critically depends on the local immune context.
Collapse
Affiliation(s)
- Sarah Kim
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, 53105 Bonn, Germany
| | - Vera Kaiser
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, 53105 Bonn, Germany
| | - Esther Beier
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, 53105 Bonn, Germany
| | - Matthias Bechheim
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, 53105 Bonn, Germany
| | - Margit Guenthner-Biller
- Center of Integrated Protein Science (CIPS-M), Division of Clinical Pharmacology, Medizinische Klinik und Poliklinik IV, University of Munich, 80336 Munich, Germany
| | - Andrea Ablasser
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, 53105 Bonn, Germany
| | - Michael Berger
- Center of Integrated Protein Science (CIPS-M), Division of Clinical Pharmacology, Medizinische Klinik und Poliklinik IV, University of Munich, 80336 Munich, Germany
| | - Stefan Endres
- Center of Integrated Protein Science (CIPS-M), Division of Clinical Pharmacology, Medizinische Klinik und Poliklinik IV, University of Munich, 80336 Munich, Germany
| | - Gunther Hartmann
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, 53105 Bonn, Germany
| | - Veit Hornung
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, 53105 Bonn, Germany
| |
Collapse
|