Functional Genomics Of Critical Illness

危重疾病的功能基因组学

• 批准号: 8952790
• 负责人: ROBERT L DANNER
• 金额: --
• 依托单位: CLINICAL CENTER
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8952790
• 关键词: Acids; Acute; Adult Respiratory Distress Syndrome; Aerosols; Air; American; Animals; Apoptosis; Arginine; Arteriosclerosis; Ascaridil; Autoimmune Diseases; BMPR2 gene; Bioinformatics; Biological; Biological Markers; Biology; Biotechnology; Bioterrorism; Blood; Blood Circulation; Blood Platelets; Blood Vessels; Bronchoalveolar Lavage; CD40 Ligand; CD8B1 gene; Carbon Monoxide; Cardiac; Categories; Cell Adhesion; Cell Differentiation process; Cell Mobility; Cell Proliferation; Cells; Cellular biology; Chest; Clinical; Complex; Critical Illness; Cytoskeleton; Data Analyses; Databases; Dendritic Cells; Development; Dexamethasone; Diet; Disease; Dose; Endotoxins; Epithelial Cells; Fatigue; Fatty Acids; Gases; Gene Expression; Gene Expression Profile; Gene Expression Profiling; Gene Expression Regulation; Genes; Genetic Programming; Genetic Transcription; Genomics; Goals; HIV; Heart; Heme; Human; Hypersensitivity; Immune; Immune response; Immunity; Inflammation; Inflammatory; Inflammatory Response; Influenza; Inherited; Injury; Intensive Care; Interferon-alpha; Interferons; Intravenous; Investigation; Journals; Kidney; Knockout Mice; Laboratory Procedures; Leptin; Leukocytes; Leukotriene B4; Leukotriene D4; Link; Liquid substance; Liver; Longevity; Lung; Lymphocyte; Malnutrition; Manuscripts; Measures; Mediating; Medicine; Messenger RNA; Metabolic Diseases; Metabolism; MicroRNAs; Microarray Analysis; Mitochondria; Modeling; Molecular Biology; Molecular Profiling; Monkeys; Multiple Organ Failure; Mus; Mutation; Myopathy; Nature; Nitric Oxide; Nuclear Orphan Receptor; Oligonucleotide Microarrays; Organ; Oxidants; Oxygenases; Pathogenesis; Pathway interactions; Patients; Pattern; Pattern Recognition; Peripheral Blood Mononuclear Cell; Pharmaceutical Preparations; Physiological; Play; Pneumocystis; Preparation; Procedures; Prognostic Marker; Proteomics; Ras/Raf; Rattus; Relative (related person); Research; Research Personnel; Reticulocytes; Role; Sampling; Septic Shock; Series; Sickle Cell Anemia; Signal Transduction; Signal Transduction Pathway; Signaling Pathway Gene; Simulate; Societies; Spleen; Staphylococcal Enterotoxin B; Stem cells; Stress; Syndrome; System; T-Lymphocyte; TNF gene; Testing; Thrombosis; Toxic Shock Syndrome; Transcript; Transcription Factor AP-1; Tretinoin; United States National Institutes of Health; Whole Blood; Work; abstracting; apoAI regulatory protein-1; autoimmune lymphoproliferative syndrome; cell motility; cell type; college; cysteinyl leukotriene receptor; drug development; functional genomics; gene induction; genome-wide; in vitro Model; injured; insight; irradiation; meetings; monocyte; neutrophil; new therapeutic target; oxidant stress; polarized cell; programs; pulmonary arterial hypertension; pulmonary artery endothelial cell; research study; respiratory; response; symposium; therapeutic target; tool

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).

开发了用于处理各种样本类型的实验室程序，包括中性粒细胞，外周血单核细胞（PBMC），T淋巴细胞，全血，支气管肺泡灌洗，脾，肝，肺和心脏。多种物种的寡核苷酸微阵列在我们的设施中已经进行了十多年的时间。 开发并反复测试了数据分析管道，包括方差稳定归一化，基因选择和主题分析程序。建立了NIH生物信息学合作社（http://affylims.cit.nih.gov/），导致MSCL工具箱的开发和传播；构建包含4000多个微阵列的数据库。 建立了关于重症疾病和损伤功能基因组学的NIH赞助的研讨会。本系列的七次会议（上次：2009年12月）为尖端研究提供了一个论坛，将高通量生物技术应用于重症疾病和伤害的研究。 最近，启动了美国重症疾病和伤害试验小组（USCIITG：http：//www.massgeneral.org/research/research/researchlab.aspx?id=1471），在其指导委员会中首先任职于其组织委员会，然后在其组织委员会任职，作为一个论坛，以进一步研究人对全国规模进行研究的强化医学研究。 在原发性支气管上皮细胞中研究了IFN-α和地塞米松之间的相互作用（生理基因组学，2005年）。发现地塞米松广泛抑制了IFN-Alpha诱导的晚期反应。 循环白细胞的全球转录分析强调了稳态镰状细胞疾病的强烈氧化剂和炎症性质，并深入了解了对血管损伤的广泛补偿性反应（Blood 2004）。人类的网状细胞转录组的表征进一步扩展了我们对循环细胞类型的理解（Physiol Genomcs 2007）。镰状细胞疾病中血小板与精氨酸代谢异常的循环应激相关的循环应激的表达分析（Circulation 2007）。 单剂量静脉内毒素对人的给药引起了循环细胞基因表达的广泛变化（Physiol Genomics 2006）。其中包括诱导与模式识别分子，细胞内信号传导和转录，细胞迁移率和防御功能相关的基因。抑制与T淋巴细胞相关的基因，并且在此反应期间，许多与内毒素诱导的炎症相关的基因都受到差异调节。值得注意的是，这些基因表达的改变在24小时内迅速消失。 基因表达分析用于全球鉴定由一氧化氮调节（NO）调节的许多基因。这项工作导致发现了新的信号转导途径和调节机制，从而没有影响炎症和细胞增殖（BMC Genomics 2005; Nic Acid Res 2006; J Biol Chem 2006）。 使用表达分析，在人类自身免疫性淋巴增生综合征的情况下发现了NRA中的种系激活突变（ALPS; PNAS 2007）。这一发现表明，RAS灭活药物可能在人类自身免疫性疾病中有用。 野生型和CD40-Ligand敲除小鼠的先天和适应性免疫反应是对肺囊肿的（J Leukoc Biol 2008）。 在代谢性疾病领域，使用重点的线粒体微阵列来研究与HIV相关的肌病/疲劳（Biol Res Nurs 2008; J Infect Dis，2012; Biol Res Nurs 2013）。全基因组微阵列还发现了瘦素和热甘油/脂肪酸循环途径在保护心脏免受饮食诱发的脂肪变性方面的重要性（生理基因组学2011）。 微阵列用于全局检查一氧化碳（由血红素加氧酶产生的内源性信使碳二氧化碳抑制人类单核细胞中LPS介导的基因诱导的能力（PLOS One 2009）。 对人类单型介导的特异性炎症反应的针对研究研究了由白三苯D（4）激活I型西胱烷基体白细胞受体介导的基因调控（J Allergy Clin Immunol 2008）和白细胞三烯B（4）和D（4）信号（4）信号（Alrergy 2011）的冗余性。 其他研究检查了内皮祖细胞细胞的转录组（动脉粥样硬化血栓形成和血管生物学2009），动物菌株对PBMC基因表达的影响在急性心脏排斥大鼠模型中（BMC Genomics 2009），以及CD4+和CD8+效应T细胞之间抗源性免疫免疫的差异（PNAS 2009）。淋巴细胞抗肿瘤作用的工作检查了Th17极化细胞，记录了其寿命，可塑性和功能（Immunity 2011）。最近的研究确定了视黄酸在调节树突细胞亚群中的关键作用，对营养不良和辐照引起的免疫缺陷的治疗产生了影响（实验医学杂志，2013年）。 在流感样炎症反应期间，在空气界面中检查了O2（70％）和NO（40 ppm）的ARDS管理中使用的两种气体（NHBEC）的正常人支气管上皮细胞（NHBEC）的影响（American Thoracic Society Abstract 2011）。全球基因表达分析表明，O2和NO产生了高度相似的氧化应激特征。发现人类气道上皮细胞分化过程中特定miRNA的变化可控制重要的基因网络（《美国呼吸细胞和分子生物学杂志》，2013年）。 在一个致命的鼠模型中检查了对葡萄球菌肠毒素B（SEB）的全球范围范围反应，该模型模仿了人类有毒休克综合征的各个方面，并模拟了在生物恐怖袭击中如何在生物恐怖攻击中部署SEB（气溶胶）。在循环白细胞，脾，肺，肝，肾脏和心脏中发现了一个共同的遗传程序，表明可能是发病机理核心的IFN签名（PLOS One 2014）。 发现肺动脉高压中的循环PBMC基因表达特征反映了治疗和特定疾病的影响（美国胸腔学会摘要2011）。 PAH中功能性基因类别的改变包括炎症，细胞粘附，运动性，细胞骨架和凋亡。特定的基因和规范途径与几种先前提出的机制重叠，并提出了新的治疗靶标，例如AP1信号传导（J AM College Cardiol Abstract 2014；准备中的手稿）。 BMPR2沉默的肺动脉内皮细胞（PAEC）的全球表达分析，这是遗传性肺动脉高压（PAH）的体外模型，揭示了RAS/RAF/RAF/ERK/AP1信号的激活。针对此途径可能有助于对PAH的治疗（J Am College Cardiol Abstract 2014；准备中的手稿）。 在一个敲低实验中，发现在脉管系统中高度表达的孤儿核受体COUP-TFII广泛调节对TNF诱发的炎症的内皮反应（American Thoracic Society Abstract 2011）。在以内皮炎症为特征的条件下，政变-TFII可能是有用的治疗靶标（美国胸腔社会摘要2011；手稿准备）。