1
|
Kreitmaier P, Park YC, Swift D, Gilly A, Wilkinson JM, Zeggini E. Epigenomic profiling of the infrapatellar fat pad in osteoarthritis. Hum Mol Genet 2024; 33:501-509. [PMID: 37975894 PMCID: PMC10939427 DOI: 10.1093/hmg/ddad198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/13/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023] Open
Abstract
Osteoarthritis is a prevalent, complex disease of the joints, and affects multiple intra-articular tissues. Here, we have examined genome-wide DNA methylation profiles of primary infrapatellar fat pad and matched blood samples from 70 osteoarthritis patients undergoing total knee replacement surgery. Comparing the DNA methylation profiles between these tissues reveal widespread epigenetic differences. We produce the first genome-wide methylation quantitative trait locus (mQTL) map of fat pad, and make the resource available to the wider community. Using two-sample Mendelian randomization and colocalization analyses, we resolve osteoarthritis GWAS signals and provide insights into the molecular mechanisms underpinning disease aetiopathology. Our findings provide the first view of the epigenetic landscape of infrapatellar fat pad primary tissue in osteoarthritis.
Collapse
Affiliation(s)
- Peter Kreitmaier
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine and Health, Ismaninger Str. 22, Munich 81675, Germany
- Graduate School of Experimental Medicine, TUM School of Medicine and Health, Technical University of Munich, Ismaninger Str. 22, Munich 81675, Germany
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstr. 1, Neuherberg 85764, Germany
| | - Young-Chan Park
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstr. 1, Neuherberg 85764, Germany
| | - Diane Swift
- Department of Oncology and Metabolism, The University of Sheffield, Beech Hill Rd, Sheffield S10 2RX, United Kingdom
| | - Arthur Gilly
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstr. 1, Neuherberg 85764, Germany
| | - J Mark Wilkinson
- Department of Oncology and Metabolism, The University of Sheffield, Beech Hill Rd, Sheffield S10 2RX, United Kingdom
| | - Eleftheria Zeggini
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine and Health, Ismaninger Str. 22, Munich 81675, Germany
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstr. 1, Neuherberg 85764, Germany
| |
Collapse
|
2
|
Penner-Goeke S, Bothe M, Rek N, Kreitmaier P, Pöhlchen D, Kühnel A, Glaser LV, Kaya E, Krontira AC, Röh S, Czamara D, Ködel M, Monteserin-Garcia J, Diener L, Wölfel B, Sauer S, Rummel C, Riesenberg S, Arloth-Knauer J, Ziller M, Labeur M, Meijsing S, Binder EB. High-throughput screening of glucocorticoid-induced enhancer activity reveals mechanisms of stress-related psychiatric disorders. Proc Natl Acad Sci U S A 2023; 120:e2305773120. [PMID: 38011552 DOI: 10.1073/pnas.2305773120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/01/2023] [Indexed: 11/29/2023] Open
Abstract
Exposure to stressful life events increases the risk for psychiatric disorders. Mechanistic insight into the genetic factors moderating the impact of stress can increase our understanding of disease processes. Here, we test 3,662 single nucleotide polymorphisms (SNPs) from preselected expression quantitative trait loci in massively parallel reporter assays to identify genetic variants that modulate the activity of regulatory elements sensitive to glucocorticoids, important mediators of the stress response. Of the tested SNP sequences, 547 were located in glucocorticoid-responsive regulatory elements of which 233 showed allele-dependent activity. Transcripts regulated by these functional variants were enriched for those differentially expressed in psychiatric disorders in the postmortem brain. Phenome-wide Mendelian randomization analysis in 4,439 phenotypes revealed potentially causal associations specifically in neurobehavioral traits, including major depression and other psychiatric disorders. Finally, a functional gene score derived from these variants was significantly associated with differences in the physiological stress response, suggesting that these variants may alter disease risk by moderating the individual set point of the stress response.
Collapse
Affiliation(s)
- Signe Penner-Goeke
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- Graduate School of Systemic Neurosciences, Ludwig Maximilian University of Munich, Planegg 82152, Germany
| | - Melissa Bothe
- Department of Computational Molecular Biology, Max Planck Institute of Molecular Genetics, Berlin 14195, Germany
| | - Nils Rek
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Peter Kreitmaier
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg 85764, Germany
| | - Dorothee Pöhlchen
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Anne Kühnel
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Laura V Glaser
- Department of Computational Molecular Biology, Max Planck Institute of Molecular Genetics, Berlin 14195, Germany
| | - Ezgi Kaya
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- Graduate School of Systemic Neurosciences, Ludwig Maximilian University of Munich, Planegg 82152, Germany
| | - Anthi C Krontira
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Simone Röh
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Maik Ködel
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Jose Monteserin-Garcia
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Laura Diener
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Barbara Wölfel
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Susann Sauer
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Christine Rummel
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Stephan Riesenberg
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Janine Arloth-Knauer
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Michael Ziller
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- Department of Psychiatry, University of Muenster, Muenster 48149, Germany
| | - Marta Labeur
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Sebastiaan Meijsing
- Department of Computational Molecular Biology, Max Planck Institute of Molecular Genetics, Berlin 14195, Germany
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| |
Collapse
|
3
|
Abstract
PURPOSE OF REVIEW To provide an overview of recent developments in the field of osteoarthritis research with a focus on insights gleaned from the application of different -omic technologies. RECENT FINDINGS We searched for osteoarthritis-relevant studies focusing on transcriptomics, epigenomics, proteomics and metabolomics, published since November of 2019. Study designs showed a trend towards characterizing the genomic profile of osteoarthritis-relevant tissues with high resolution, for example either by using single-cell technologies or by considering several -omic levels and disease stages. SUMMARY Multitissue interactions (cartilage-subchondral bone; cartilage-synovium) are prevalent in the pathophysiology of osteoarthritis, which is characterized by substantial matrix remodelling in an inflammatory milieu. Subtyping approaches using -omic technologies have contributed to the identification of at least two osteoarthritis endotypes. Studies using data integration approaches have provided molecular maps that are tissue-specific for osteoarthritis and pave the way for expanding these data integration approaches towards a more comprehensive view of disease aetiopathogenesis.
Collapse
Affiliation(s)
- Georgia Katsoula
- Technical University of Munich (TUM), School of Medicine, Graduate School of Experimental Medicine
- Institute of Translational Genomics, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Peter Kreitmaier
- Technical University of Munich (TUM), School of Medicine, Graduate School of Experimental Medicine
- Institute of Translational Genomics, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Eleftheria Zeggini
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine, Munich
- Institute of Translational Genomics, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| |
Collapse
|