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      Immune regulation by glucocorticoids can be linked to cell type–dependent transcriptional responses

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          Abstract

          A functional genomics approach uncovers previously undescribed cell type–dependent responses that can be linked to the immunoregulatory actions of glucocorticoids in humans.

          Abstract

          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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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            Autoreactive B cell responses to RNA-related antigens due to TLR7 gene duplication.

            Antibodies against nuclear self-antigens are characteristic of systemic autoimmunity, although mechanisms promoting their generation and selection are unclear. Here, we report that B cells containing the Y-linked autoimmune accelerator (Yaa) locus are intrinsically biased toward nucleolar antigens because of increased expression of TLR7, a single-stranded RNA-binding innate immune receptor. The TLR7 gene is duplicated in Yaa mice because of a 4-Megabase expansion of the pseudoautosomal region. These results reveal high divergence in mouse Y chromosomes and represent a good example of gene copy number qualitatively altering a polygenic disease manifestation.
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              A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics

              Pseudogenes are thought to be inactive gene sequences, but recent evidence of extensive pseudogene transcription raised the question of potential function. Here we discover and characterize the sets of mouse lncRNAs induced by inflammatory signaling via TNFα. TNFα regulates hundreds of lncRNAs, including 54 pseudogene lncRNAs, several of which show exquisitely selective expression in response to specific cytokines and microbial components in a NF-κB-dependent manner. Lethe, a pseudogene lncRNA, is selectively induced by proinflammatory cytokines via NF-κB or glucocorticoid receptor agonist, and functions in negative feedback signaling to NF-κB. Lethe interacts with NF-κB subunit RelA to inhibit RelA DNA binding and target gene activation. Lethe level decreases with organismal age, a physiological state associated with increased NF-κB activity. These findings suggest that expression of pseudogenes lncRNAs are actively regulated and constitute functional regulators of inflammatory signaling. DOI: http://dx.doi.org/10.7554/eLife.00762.001
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                Author and article information

                Journal
                J Exp Med
                J. Exp. Med
                jem
                jem
                The Journal of Experimental Medicine
                Rockefeller University Press
                0022-1007
                1540-9538
                04 February 2019
                : 216
                : 2
                : 384-406
                Affiliations
                [1 ]Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
                [2 ]Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
                [3 ]Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
                [4 ]Clinical Pharmacokinetics Research Unit, Clinical Center, National Institutes of Health, Bethesda, MD
                [5 ]Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
                [6 ]Center for Human Immunology, National Institutes of Health, Bethesda, MD
                Author notes
                Correspondence to Luis M. Franco: luis.franco@ 123456nih.gov
                [*]

                R.N. Germain and J.S. Tsang contributed equally to this work.

                P. Kumar’s present address is Otsuka American Pharmaceutical, Rockville, MD.

                S. Kumari’s present address is American Type Culture Collection, Gaithersburg, MD.

                Author information
                http://orcid.org/0000-0002-0540-5942
                http://orcid.org/0000-0002-5814-2795
                http://orcid.org/0000-0001-9135-6026
                http://orcid.org/0000-0002-0163-6911
                Article
                20180595
                10.1084/jem.20180595
                6363437
                30674564
                b8718e1f-2b6b-46d6-b43e-32a9f19163a5
                This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.

                This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.rupress.org/terms/). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 4.0 International license, as described at https://creativecommons.org/licenses/by-nc-sa/4.0/).

                History
                : 27 March 2018
                : 22 October 2018
                : 04 January 2019
                Funding
                Funded by: Division of Intramural Research, NIAID., DOI https://doi.org/10.13039/100006492;
                Categories
                Research Articles
                Article
                311

                Medicine
                Medicine

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