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      A genomic storm in critically injured humans

      research-article
      1 , 4 , 4 , 4 , 9 , 8 , 4 , 6 , 9 , 10 , 11 , 12 , 10 , 13 , 14 , 13 , 15 , 16 , 5 , 8 , 17 , 18 , 8 , 9 , 19 , 9 , 11 , 4 , 4 , 20 , 5 , 2 , 21 , 3 , 2 , 8 , 17 , 20 , 9 , 4 , 1 , 7
      The Journal of Experimental Medicine
      The Rockefeller University Press

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          Abstract

          Critical injury in humans induces a genomic storm with simultaneous changes in expression of innate and adaptive immunity genes.

          Abstract

          Human survival from injury requires an appropriate inflammatory and immune response. We describe the circulating leukocyte transcriptome after severe trauma and burn injury, as well as in healthy subjects receiving low-dose bacterial endotoxin, and show that these severe stresses produce a global reprioritization affecting >80% of the cellular functions and pathways, a truly unexpected “genomic storm.” In severe blunt trauma, the early leukocyte genomic response is consistent with simultaneously increased expression of genes involved in the systemic inflammatory, innate immune, and compensatory antiinflammatory responses, as well as in the suppression of genes involved in adaptive immunity. Furthermore, complications like nosocomial infections and organ failure are not associated with any genomic evidence of a second hit and differ only in the magnitude and duration of this genomic reprioritization. The similarities in gene expression patterns between different injuries reveal an apparently fundamental human response to severe inflammatory stress, with genomic signatures that are surprisingly far more common than different. Based on these transcriptional data, we propose a new paradigm for the human immunological response to severe injury.

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          Most cited references27

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          Systematic determination of genetic network architecture.

          Technologies to measure whole-genome mRNA abundances and methods to organize and display such data are emerging as valuable tools for systems-level exploration of transcriptional regulatory networks. For instance, it has been shown that mRNA data from 118 genes, measured at several time points in the developing hindbrain of mice, can be hierarchically clustered into various patterns (or 'waves') whose members tend to participate in common processes. We have previously shown that hierarchical clustering can group together genes whose cis-regulatory elements are bound by the same proteins in vivo. Hierarchical clustering has also been used to organize genes into hierarchical dendograms on the basis of their expression across multiple growth conditions. The application of Fourier analysis to synchronized yeast mRNA expression data has identified cell-cycle periodic genes, many of which have expected cis-regulatory elements. Here we apply a systematic set of statistical algorithms, based on whole-genome mRNA data, partitional clustering and motif discovery, to identify transcriptional regulatory sub-networks in yeast-without any a priori knowledge of their structure or any assumptions about their dynamics. This approach uncovered new regulons (sets of co-regulated genes) and their putative cis-regulatory elements. We used statistical characterization of known regulons and motifs to derive criteria by which we infer the biological significance of newly discovered regulons and motifs. Our approach holds promise for the rapid elucidation of genetic network architecture in sequenced organisms in which little biology is known.
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            Cell death.

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              • Record: found
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              Gene expression during the life cycle of Drosophila melanogaster.

              Molecular genetic studies of Drosophila melanogaster have led to profound advances in understanding the regulation of development. Here we report gene expression patterns for nearly one-third of all Drosophila genes during a complete time course of development. Mutations that eliminate eye or germline tissue were used to further analyze tissue-specific gene expression programs. These studies define major characteristics of the transcriptional programs that underlie the life cycle, compare development in males and females, and show that large-scale gene expression data collected from whole animals can be used to identify genes expressed in particular tissues and organs or genes involved in specific biological and biochemical processes.
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                Author and article information

                Journal
                J Exp Med
                J. Exp. Med
                jem
                The Journal of Experimental Medicine
                The Rockefeller University Press
                0022-1007
                1540-9538
                19 December 2011
                : 208
                : 13
                : 2581-2590
                Affiliations
                [1 ]Department of Surgery , [2 ]Department of Medicine , and [3 ]Department of Anesthesiology, Critical Care Medicine, and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
                [4 ]Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304
                [5 ]Department of Surgery and [6 ]Department of Medicine , [7 ]Massachusetts General Hospital, Boston, MA 02114
                [8 ]Department of Surgery, University of Florida College of Medicine, Gainesville, FL 32610
                [9 ]Department of Surgery, Harborview Medical Center, University of Washington School of Medicine, Seattle, WA 98104
                [10 ]Department of Surgery, University of Colorado Denver–Anschutz Medical Campus, Denver, CO 80045
                [11 ]Department of Surgery, Parkland Memorial Hospital, University of Texas Southwestern Medical Center, Dallas, TX 75390
                [12 ]Department of Surgery, University of Rochester Medical Center, Rochester, NY 14642
                [13 ]Department of Surgery, University of Pittsburgh Medical Center Presbyterian University Hospital, Pittsburgh, PA 15213
                [14 ]Department of Surgery, St. Michael’s Hospital, Toronto, Ontario M5B 1W8, Canada
                [15 ]Department of Surgery, San Francisco General Hospital, University of California, San Francisco, San Francisco, CA 94110
                [16 ]Department of Surgery, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
                [17 ]Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555
                [18 ]Division of Plastic and Reconstructive Surgery, Department of Surgery, University of Toronto, Toronto, Ontario M5G 1L5, Canada
                [19 ]Department of Surgery, Stritch School of Medicine, Loyola University, Maywood, IL 60153
                [20 ]Department of Surgery, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, New Brunswick, NJ 08901
                [21 ]Department of Molecular Biology, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
                Author notes
                CORRESPONDENCE Ronald G. Tompkins: rtompkins@ 123456partners.org

                Dr. Lowry died on 4 June 2011.

                W. Xiao, M.N. Mindrinos, J. Seok, and J. Cuschieri contributed equally to this paper.

                Article
                20111354
                10.1084/jem.20111354
                3244029
                22110166
                09669f79-fd77-40b2-a7d2-2331c3bd6410
                © 2011 Xiao et al.

                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 3.0 Unported license, as described at http://creativecommons.org/licenses/by-nc-sa/3.0/).

                History
                : 1 July 2011
                : 19 October 2011
                Categories
                Brief Definitive Report

                Medicine
                Medicine

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