Functional Genomics Of Critical Illness

Clinical Center

Investigators

Linked publications, trials & patents

Abstract

Developed laboratory procedures for handling a variety of sample types including neutrophils, peripheral blood mononuclear cells (PBMCs), T-lymphocytes, whole blood, bronchoalveolar lavage, spleen, liver, lung, and heart. Oligonucleotide microarrays for several species including human, monkey, mouse and rat have been performed in our facility for more than a decade. Developed and repeatedly tested a data analysis pipeline including variance stabilized normalization, gene selection and thematic analysis procedures. Established the NIH Bioinformatics Cooperative (http://affylims.cit.nih.gov/) leading to development and dissemination of the MSCL toolbox; construction of a database containing over 4000 microarrays. Founded the NIH-sponsored Symposium on the Functional Genomics of Critical Illness and Injury. The seven meetings in this series (last: December 2009) provided a forum for the presentation of cutting edge research applying high throughput biotechnologies to the study of critical illness and injury. More recently launched the US Critical Illness and Injury Trials Group (USCIITG: http://www.massgeneral.org/research/researchlab.aspx?id=1471), serving first on its Steering Committee and then on its Organizing Committee, as a forum to further investigator-initiated Intensive Care Medicine research on a National scale. Interactions between IFN-alpha and dexamethasone were investigated in primary bronchial epithelial cells (Physiologic Genomics 2005). Dexamethasone was found to broadly suppress late IFN-alpha-induced responses. Global transcriptional analysis of circulating leukocytes highlighted the intense oxidant and inflammatory nature of steady-state sickle cell disease and provided insight into broad compensatory responses to vascular injury (Blood 2004). The human reticulocyte transcriptome was characterized, further extending our understanding of circulating cell-types (Physiol Genomcs 2007). Expression profiling of platelets in sickle cell disease associated circulatory stress in this disorder with abnormalities of arginine metabolism (Circulation 2007). The administration of a single dose of intravenous endotoxin to humans caused extensive changes in the gene expression of circulating cells (Physiol Genomics 2006). These included the induction of genes associated with pattern recognition molecules, intracellular signaling and transcription, cell mobility, and defense function. T lymphocyte-associated genes were repressed, and many genes not previously associated with endotoxin-induced inflammation were differentially regulated during this response. Notably, these alterations in gene expression were rapidly extinguished within 24 h. Gene expression profiling was used to globally identify numerous genes regulated by nitric oxide (NO). This work has led to the discovery of new signal transduction pathways and regulatory mechanisms by which NO influences inflammation and cell proliferation (BMC Genomics 2005; Nuc Acid Res 2006; J Biol Chem 2006). Using expression profiling, a germline activating mutation in NRAS was discovered in a case of human autoimmune lymphoproliferative syndrome (ALPS; PNAS 2007). This finding suggested that RAS-inactivating drugs might be therapeutically useful in human autoimmune disorders. The innate and adaptive immune response to Pneumocystis was characterized in wild type and CD40-ligand knockout mice (J Leukoc Biol 2008). In the field of metabolic diseases, a focused mitochondrial microarray was used to study HIV-associated myopathy/fatigue (Biol Res Nurs 2008; J Infect Dis, 2012; Biol Res Nurs 2013). Genome-wide microarrays also uncovered the importance of leptin and the thermogenic glycerolipid/fatty acid cycling pathway in protecting the heart from diet-induced steatosis (Physiological Genomics 2011). Microarrays were used to globally examine the ability of carbon monoxide, an endogenous messenger produced by heme oxygenase, to suppress LPS-mediated gene induction in human monocytes (PLoS One 2009). Targeted studies of specific inflammatory responses investigated gene regulation mediated by leukotriene D(4) activation of the type I cysteinyl leukotriene receptor (J Allergy Clin Immunol 2008) and the redundancy of leukotriene B(4) and D(4) signaling (Allergy 2011) in human monocytes. Other studies examined the transcriptome of endothelial progenitor cells (Arteriosclerosis Thrombosis and Vascular Biology 2009), animal strain effects on PBMC gene expression in a rat model of acute cardiac rejection (BMC Genomics 2009), and differences between CD4+ and CD8+ effector T cells in antitumor immunity (PNAS 2009). Work on lymphocyte antitumor effects examined TH17 polarized cells, documenting their longevity, plasticity and functionality (Immunity 2011). More recent studies established a critical role for retinoic acid in regulating dendritic cell subsets with implications for the management of immune deficiencies resulting from malnutrition and irradiation (Journal of Experimental Medicine 2013). The effects of O2 (70%) and NO (40 ppm), two gases used in the management of ARDS, were examined in air-liquid interface differentiated normal human bronchial epithelial cells (NHBECs) during an influenza-like inflammatory response (American Thoracic Society abstract 2011). Global gene expression profiling demonstrated that O2 and NO produced highly similar signatures of oxidant stress. Changes in specific miRNAs during human airway epithelial cell differentiation were found to control important gene networks (American Journal of Respiratory Cell and Molecular Biology 2013). The global, host-wide response to Staphylococcal enterotoxin B (SEB) was examined in a lethal murine model that mimics aspects of human toxic shock syndrome and simulates how SEB would likely be deployed (aerosol) in a bioterrorism attack. A shared genetic program was found in circulating leukocytes, spleen, lung, liver, kidney and heart, indicating a dominant IFN-signature that may be central to pathogenesis (PLoS One 2014). Circulating PBMC gene expression signatures in pulmonary arterial hypertension were found to reflect both treatment and disease specific effects (American Thoracic Society abstract 2011). Altered functional gene categories in PAH included inflammation, cell adhesion, motility, the cytoskeleton and apoptosis. Specific genes and canonical pathways overlapped with several previously proposed mechanisms and suggested novel therapeutic targets, such as AP1 signaling (J Am College Cardiol abstract 2014; manuscript in preparation). Global expression profiling of pulmonary artery endothelial cells (PAECs) in which BMPR2 was silenced, an in vitro model of hereditary pulmonary arterial hypertension (PAH), revealed activation of Ras/Raf/Erk/AP1 signaling. Targeting this pathway maybe useful in the treatment of PAH (J Am College Cardiol abstract 2014; manuscript in preparation ). In a knockdown experiment, COUP-TFII, an orphan nuclear receptor highly expressed in the vasculature, was found to broadly modulate the endothelial response to TNF-induced inflammation (American Thoracic Society abstract 2011). COUP-TFII may be a useful therapeutic target in conditions characterized by endothelial inflammation (American Thoracic Society abstract 2011; manuscript in preparation).