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Sparks R, Rachmaninoff N, Hirsch DC, Bansal N, Lau WW, Martins AJ, Chen J, Liu CC, Cheung F, Failla LE, Biancotto A, Fantoni G, Sellers BA, Chawla DG, Howe KN, Mostaghimi D, Farmer R, Kotliarov Y, Calvo KR, Palmer C, Daub J, Foruraghi L, Kreuzburg S, Treat J, Urban AK, Jones A, Romeo T, Deuitch NT, Moura NS, Weinstein B, Moir S, Ferrucci L, Barron KS, Aksentijevich I, Kleinstein SH, Townsley DM, Young NS, Frischmeyer-Guerrerio PA, Uzel G, Pinto-Patarroyo GP, Cudrici CD, Hoffmann P, Stone DL, Ombrello AK, Freeman AF, Zerbe CS, Kastner DL, Holland SM, Tsang JS. Multiomics integration of 22 immune-mediated monogenic diseases reveals an emergent axis of human immune health. Res Sq 2023:rs.3.rs-2070975. [PMID: 36993430 PMCID: PMC10055521 DOI: 10.21203/rs.3.rs-2070975/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Monogenic diseases are often studied in isolation due to their rarity. Here we utilize multiomics to assess 22 monogenic immune-mediated conditions with age- and sex-matched healthy controls. Despite clearly detectable disease-specific and "pan-disease" signatures, individuals possess stable personal immune states over time. Temporally stable differences among subjects tend to dominate over differences attributable to disease conditions or medication use. Unsupervised principal variation analysis of personal immune states and machine learning classification distinguishing between healthy controls and patients converge to a metric of immune health (IHM). The IHM discriminates healthy from multiple polygenic autoimmune and inflammatory disease states in independent cohorts, marks healthy aging, and is a pre-vaccination predictor of antibody responses to influenza vaccination in the elderly. We identified easy-to-measure circulating protein biomarker surrogates of the IHM that capture immune health variations beyond age. Our work provides a conceptual framework and biomarkers for defining and measuring human immune health.
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Affiliation(s)
- Rachel Sparks
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Nicholas Rachmaninoff
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
- Graduate Program in Biological Sciences, University of Maryland, College Park, MD 20742, USA
| | - Dylan C. Hirsch
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Neha Bansal
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - William W. Lau
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
- Office of Intramural Research, CIT, NIH, Bethesda, MD 20892, USA
| | - Andrew J. Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Jinguo Chen
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Candace C. Liu
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Foo Cheung
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Laura E. Failla
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | | | - Giovanna Fantoni
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Brian A. Sellers
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Daniel G. Chawla
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Katherine N. Howe
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Darius Mostaghimi
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Rohit Farmer
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Yuri Kotliarov
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Katherine R. Calvo
- Hematology Section, Department of Laboratory Medicine, NIH Clinical Center, Bethesda, MD 20892, USA
| | - Cindy Palmer
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Janine Daub
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Ladan Foruraghi
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Samantha Kreuzburg
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Jennifer Treat
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Amanda K. Urban
- Clinical Research Directorate, Frederick National Laboratory for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21701, USA
| | - Anne Jones
- Inflammatory Diseases Section, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Tina Romeo
- Inflammatory Diseases Section, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Natalie T. Deuitch
- Inflammatory Diseases Section, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Natalia Sampaio Moura
- Inflammatory Diseases Section, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Barbara Weinstein
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Susan Moir
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD 20892, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA
| | - Karyl S. Barron
- Divison of Intramural Research, NIAID, NIH, Bethesda, MD 20892, USA
| | - Ivona Aksentijevich
- Inflammatory Diseases Section, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Steven H. Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Danielle M. Townsley
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Neal S. Young
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | | | - Gulbu Uzel
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | | | - Cornelia D. Cudrici
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda MD 20892, USA
| | - Patrycja Hoffmann
- Inflammatory Diseases Section, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Deborah L. Stone
- Inflammatory Diseases Section, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Amanda K. Ombrello
- Inflammatory Diseases Section, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Alexandra F. Freeman
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Christa S. Zerbe
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Daniel L. Kastner
- Inflammatory Diseases Section, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Steven M. Holland
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - John S. Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA
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Franco LM, Gadkari M, Howe KN, Sun J, Kardava L, Kumar P, Kumari S, Hu Z, Fraser IDC, Moir S, Tsang JS, Germain RN. Immune regulation by glucocorticoids can be linked to cell type-dependent transcriptional responses. J Exp Med 2019; 216:384-406. [PMID: 30674564 PMCID: PMC6363437 DOI: 10.1084/jem.20180595] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 10/22/2018] [Accepted: 01/04/2019] [Indexed: 12/13/2022] Open
Abstract
A functional genomics approach uncovers previously undescribed cell type–dependent responses that can be linked to the immunoregulatory actions of glucocorticoids in humans. Glucocorticoids remain the most widely used immunosuppressive and anti-inflammatory drugs, yet substantial gaps exist in our understanding of glucocorticoid-mediated immunoregulation. To address this, we generated a pathway-level map of the transcriptional effects of glucocorticoids on nine primary human cell types. This analysis revealed that the response to glucocorticoids is highly cell type dependent, in terms of the individual genes and pathways affected, as well as the magnitude and direction of transcriptional regulation. Based on these data and given their importance in autoimmunity, we conducted functional studies with B cells. We found that glucocorticoids impair upstream B cell receptor and Toll-like receptor 7 signaling, reduce transcriptional output from the three immunoglobulin loci, and promote significant up-regulation of the genes encoding the immunomodulatory cytokine IL-10 and the terminal-differentiation factor BLIMP-1. These findings provide new mechanistic understanding of glucocorticoid action and emphasize the multifactorial, cell-specific effects of these drugs, with potential implications for designing more selective immunoregulatory therapies.
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Affiliation(s)
- Luis M Franco
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Manasi Gadkari
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Katherine N Howe
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Jing Sun
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Lela Kardava
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Parag Kumar
- Clinical Pharmacokinetics Research Unit, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Sangeeta Kumari
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Zonghui Hu
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Iain D C Fraser
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Susan Moir
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - John S Tsang
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,Center for Human Immunology, National Institutes of Health, Bethesda, MD
| | - Ronald N Germain
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
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