1
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Zong W, Rahman T, Zhu L, Zeng X, Zhang Y, Zou J, Liu S, Ren Z, Li JJ, Sibille E, Lee AV, Oesterreich S, Ma T, Tseng GC. Transcriptomic congruence analysis for evaluating model organisms. Proc Natl Acad Sci U S A 2023; 120:e2202584120. [PMID: 36730203 PMCID: PMC9963430 DOI: 10.1073/pnas.2202584120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 11/17/2022] [Indexed: 02/03/2023] Open
Abstract
Model organisms are instrumental substitutes for human studies to expedite basic, translational, and clinical research. Despite their indispensable role in mechanistic investigation and drug development, molecular congruence of animal models to humans has long been questioned and debated. Little effort has been made for an objective quantification and mechanistic exploration of a model organism's resemblance to humans in terms of molecular response under disease or drug treatment. We hereby propose a framework, namely Congruence Analysis for Model Organisms (CAMO), for transcriptomic response analysis by developing threshold-free differential expression analysis, quantitative concordance/discordance scores incorporating data variabilities, pathway-centric downstream investigation, knowledge retrieval by text mining, and topological gene module detection for hypothesis generation. Instead of a genome-wide vague and dichotomous answer of "poorly" or "greatly" mimicking humans, CAMO assists researchers to numerically quantify congruence, to dissect true cross-species differences from unwanted biological or cohort variabilities, and to visually identify molecular mechanisms and pathway subnetworks that are best or least mimicked by model organisms, which altogether provides foundations for hypothesis generation and subsequent translational decisions.
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Affiliation(s)
- Wei Zong
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA15261
| | - Tanbin Rahman
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX77030
| | - Li Zhu
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA15261
| | - Xiangrui Zeng
- Martinos Center for Biomedical Imaging, Harvard Medical School, Boston, MA02129
| | - Yingjin Zhang
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA15261
| | - Jian Zou
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA15261
| | - Song Liu
- Department of Computer Science and Technology, Qilu University of Technology, Jinan, Shandong 250353, China
| | - Zhao Ren
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA15261
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, CA90095
| | - Etienne Sibille
- Campbell Family Mental Health Research Institute at the Centre for Addiction and Mental Health, Toronto, ONM5S 2S1, Canada
| | - Adrian V. Lee
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Medical Center Hillman Cancer Center University of Pittsburgh, Pittsburgh, PA15261
- Magee-Womens Research Institute, University of Pittsburgh Medical Center, Pittsburgh, PA15123
| | - Steffi Oesterreich
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Medical Center Hillman Cancer Center University of Pittsburgh, Pittsburgh, PA15261
- Magee-Womens Research Institute, University of Pittsburgh Medical Center, Pittsburgh, PA15123
| | - Tianzhou Ma
- Department of Epidemiology and Biostatistics, School of Public Health, University of Maryland, College Park, MD20742
| | - George C. Tseng
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA15261
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA15261
- Department of Computational and System, Biology, University of Pittsburgh, Pittsburgh, PA15261
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2
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Liu P, Fang M, Luo Y, Zheng F, Jin Y, Cheng F, Zhu H, Jin X. Rare Variants in Inborn Errors of Immunity Genes Associated With Covid-19 Severity. Front Cell Infect Microbiol 2022; 12:888582. [PMID: 35694544 PMCID: PMC9184678 DOI: 10.3389/fcimb.2022.888582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/21/2022] [Indexed: 01/08/2023] Open
Abstract
Host genetic factors have been shown to play an important role in SARS-CoV-2 infection and the course of Covid-19 disease. The genetic contributions of common variants influencing Covid-19 susceptibility and severity have been extensively studied in diverse populations. However, the studies of rare genetic defects arising from inborn errors of immunity (IEI) are relatively few, especially in the Chinese population. To fill this gap, we used a deeply sequenced dataset of nearly 500 patients, all of Chinese descent, to investigate putative functional rare variants. Specifically, we annotated rare variants in our call set and selected likely deleterious missense (LDM) and high-confidence predicted loss-of-function (HC-pLoF) variants. Further, we analyzed LDM and HC-pLoF variants between non-severe and severe Covid-19 patients by (a) performing gene- and pathway-level association analyses, (b) testing the number of mutations in previously reported genes mapped from LDM and HC-pLoF variants, and (c) uncovering candidate genes via protein-protein interaction (PPI) network analysis of Covid-19-related genes and genes defined from LDM and HC-pLoF variants. From our analyses, we found that (a) pathways Tuberculosis (hsa:05152), Primary Immunodeficiency (hsa:05340), and Influenza A (hsa:05164) showed significant enrichment in severe patients compared to the non-severe ones, (b) HC-pLoF mutations were enriched in Covid-19-related genes in severe patients, and (c) several candidate genes, such as IL12RB1, TBK1, TLR3, and IFNGR2, are uncovered by PPI network analysis and worth further investigation. These regions generally play an essential role in regulating antiviral innate immunity responses to foreign pathogens and in responding to many inflammatory diseases. We believe that our identified candidate genes/pathways can be potentially used as Covid-19 diagnostic markers and help distinguish patients at higher risk.
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Affiliation(s)
- Panhong Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Beijing Genomeics Institute At Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Mingyan Fang
- Beijing Genomeics Institute At Shenzhen, BGI-Shenzhen, Shenzhen, China
- Beijing Genomeics Institute In Singapore, BGI-Singapore, Singapore, Singapore
| | - Yuxue Luo
- Beijing Genomeics Institute At Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Fang Zheng
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Jin
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fanjun Cheng
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huanhuan Zhu
- Beijing Genomeics Institute At Shenzhen, BGI-Shenzhen, Shenzhen, China
- *Correspondence: Xin Jin, ; Huanhuan Zhu,
| | - Xin Jin
- Beijing Genomeics Institute At Shenzhen, BGI-Shenzhen, Shenzhen, China
- Beijing Genomeics Institute In Singapore, BGI-Singapore, Singapore, Singapore
- School of Medicine, South China University of Technology, Guangzhou, China
- *Correspondence: Xin Jin, ; Huanhuan Zhu,
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3
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Gong KQ, Mikacenic C, Long ME, Frevert CW, Birkland TP, Charron J, Gharib SA, Manicone AM. MAP2K2 Delays Recovery in Murine Models of Acute Lung Injury and Associates with Acute Respiratory Distress Syndrome Outcome. Am J Respir Cell Mol Biol 2022; 66:555-563. [PMID: 35157553 PMCID: PMC9116357 DOI: 10.1165/rcmb.2021-0252oc] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 12/30/2021] [Indexed: 12/15/2022] Open
Abstract
Acute respiratory distress syndrome (ARDS) remains a significant problem in need of new pharmaceutical approaches to improve its resolution. Studies comparing gene expression signatures in rodents and humans with lung injury reveal conserved pathways, including MAPK (mitogen-activated protein kinase)/ERK (extracellular signal-related protein kinase) activation. In preclinical acute lung injury (ALI) models, inhibition of MAP2K1 (MAPK kinase 1)/MAP2K2 (MAPK kinase 2) improves measures of ALI. Myeloid cell deletion of MAP2K1 results in sustained MAP2K2 activation and nonresolving ALI, suggesting that MAP2K2 deactivation may be a key driver of ALI resolution. We used human genomic data from the iSPAAR (Identification of SNPs Predisposing to Altered Acute Lung Injury Risk) Consortium to assess genetic variants in MAP2K1 and MAP2K2 for association with mortality from ARDS. To determine the role of MAP2K2 in ALI recovery, we studied mice deficient in Map2k2 (Mek2-/-) and wild-type control mice in ALI models. We identified a MAP2K2 variant that was associated with death in ARDS and MAP2K2 expression. In Pseudomonas aeruginosa ALI, Mek2-/- mice had similar early alveolar neutrophilic recruitment but faster resolution of alveolar neutrophilia and vascular leak. Gene expression analysis revealed a role for MAP2K2 in promoting and sustaining select proinflammatory pathway activation in ALI. Bone marrow chimera studies indicate that leukocyte MAP2K2 is the key regulator of ALI duration. These studies implicate a role for MAP2K2 in ALI duration via transcriptional regulation of inflammatory programming with potential relevance to ARDS. Targeting leukocyte MAP2K2 may be an effective strategy to promote ALI resolution.
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Affiliation(s)
- Ke-Qin Gong
- Division of Pulmonary, Critical Care and Sleep Medicine, and
| | - Carmen Mikacenic
- Division of Pulmonary, Critical Care and Sleep Medicine, and
- Benaroya Research Institute, Seattle, Washington
| | - Matthew E. Long
- Division of Pulmonary, Critical Care and Sleep Medicine, and
- Division of Pulmonary, Critical Care and Sleep Medicine, the Ohio State University Wexner Medical Center, Columbus, Ohio; and
| | - Charles W. Frevert
- Division of Pulmonary, Critical Care and Sleep Medicine, and
- Department of Comparative Medicine, University of Washington, Seattle, Washington
| | | | - Jean Charron
- Oncology Division, Quebec University Hospital Center–Laval University Research Center, Laval University Research Center and Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Quebec City, Quebec, Canada
| | - Sina A. Gharib
- Division of Pulmonary, Critical Care and Sleep Medicine, and
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4
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Su K, Wang J, Lv Y, Tian M, Zhao YY, Minshall RD, Hu G. YAP expression in endothelial cells prevents ventilator-induced lung injury. Am J Physiol Lung Cell Mol Physiol 2021; 320:L568-L582. [PMID: 33565367 DOI: 10.1152/ajplung.00472.2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Ventilator-induced lung injury is associated with an increase in mortality in patients with respiratory dysfunction, although mechanical ventilation is an essential intervention implemented in the intensive care unit. Intrinsic molecular mechanisms for minimizing lung inflammatory injury during mechanical ventilation remain poorly defined. We hypothesize that Yes-associated protein (YAP) expression in endothelial cells protects the lung against ventilator-induced injury. Wild-type and endothelial-specific YAP-deficient mice were subjected to a low (7 mL/kg) or high (21 mL/kg) tidal volume (VT) ventilation for 4 h. Infiltration of inflammatory cells into the lung, vascular permeability, lung histopathology, and the levels of inflammatory cytokines were measured. Here, we showed that mechanical ventilation with high VT upregulated YAP protein expression in pulmonary endothelial cells. Endothelial-specific YAP knockout mice following high VT ventilation exhibited increased neutrophil counts and protein content in bronchoalveolar lavage fluid, Evans blue leakage, and histological lung injury compared with wild-type littermate controls. Deletion of YAP in endothelial cells exaggerated vascular endothelial (VE)-cadherin phosphorylation, downregulation of vascular endothelial protein tyrosine phosphatase (VE-PTP), and dissociation of VE-cadherin and catenins following mechanical ventilation. Importantly, exogenous expression of wild-type VE-PTP in the pulmonary vasculature rescued YAP ablation-induced increases in neutrophil counts and protein content in bronchoalveolar lavage fluid, vascular leakage, and histological lung injury as well as VE-cadherin phosphorylation and dissociation from catenins following ventilation. These data demonstrate that YAP expression in endothelial cells suppresses lung inflammatory response and edema formation by modulating VE-PTP-mediated VE-cadherin phosphorylation and thus plays a protective role in ventilator-induced lung injury.
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Affiliation(s)
- Kai Su
- Department of Anesthesiology, University of Illinois College of Medicine, Chicago, Illinois.,Department of Anesthesiology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Jianguo Wang
- Department of Anesthesiology, University of Illinois College of Medicine, Chicago, Illinois.,Department of Anesthesiology, Affiliated Hospital of Jining Medical University, Shandong, China
| | - Yang Lv
- Department of Anesthesiology, University of Illinois College of Medicine, Chicago, Illinois
| | - Ming Tian
- Department of Anesthesiology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - You-Yang Zhao
- Program for Lung and Vascular Biology, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois.,Division of Critical Care, Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Richard D Minshall
- Department of Anesthesiology, University of Illinois College of Medicine, Chicago, Illinois.,Department of Pharmacology, University of Illinois College of Medicine, Chicago, Illinois
| | - Guochang Hu
- Department of Anesthesiology, University of Illinois College of Medicine, Chicago, Illinois.,Department of Pharmacology, University of Illinois College of Medicine, Chicago, Illinois
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5
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Zhu CH, Yu J, Wang BQ, Nie Y, Wang L, Shan SQ. Dexmedetomidine reduces ventilator-induced lung injury via ERK1/2 pathway activation. Mol Med Rep 2020; 22:5378-5384. [PMID: 33173983 PMCID: PMC7647005 DOI: 10.3892/mmr.2020.11612] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 09/15/2020] [Indexed: 02/07/2023] Open
Abstract
Mechanical ventilation (MV) can contribute to ventilator-induced lung injury (VILI); dexmedetomidine (Dex) treatment attenuates MV-related pulmonary inflammation, but the mechanisms remain unclear. Therefore, the present study aimed to explore the protective effect and the possible molecular mechanisms of Dex in a VILI rodent model. Adult male Sprague-Dawley rats were randomly assigned to one of seven groups (n=24 rats/group). Rats were euthanized after 4 h of continuous MV, and pathological changes, lung wet/dry (W/D) weight ratio, the levels of inflammatory cytokines (IL-1β, TNF-α and IL-6) in the bronchoalveolar lavage fluid (BALF), and the expression levels of Bcl-2 homologous antagonist/killer (Bak), Bcl-2, pro-caspase-3, cleaved caspase-3 and the phosphorylation of ERK1/2 in the lung tissues were measured. Propidium iodide uptake and TUNEL staining were used to detect epithelial cell death. The Dex pretreatment group exhibited fewer pathological changes, lower W/D ratios and lower expression levels of inflammatory cytokines in BALF compared with the VILI group. Dex significantly attenuated the ratio of Bak/Bcl-2, cleaved caspase-3 expression levels and epithelial cell death, and increased the expression of phosphorylated ERK1/2. The protective effects of Dex could be partially reversed by PD98059, which is a mitogen-activated protein kinase (upstream of ERK1/2) inhibitor. Overall, dexmedetomidine was found to reduce the inflammatory response and epithelial cell death caused by VILI, via the activation of the ERK1/2 signaling pathway.
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Affiliation(s)
- Chun-Hua Zhu
- Department of Anesthesiology, Cangzhou Central Hospital, Cangzhou, Hebei 061000, P.R. China
| | - Jian Yu
- Department of Anesthesiology, Cangzhou Central Hospital, Cangzhou, Hebei 061000, P.R. China
| | - Ben-Qing Wang
- Department of Anesthesiology, Cangzhou Central Hospital, Cangzhou, Hebei 061000, P.R. China
| | - Yu Nie
- Department of Anesthesiology, Cangzhou Central Hospital, Cangzhou, Hebei 061000, P.R. China
| | - Lei Wang
- Department of Anesthesiology, Cangzhou Central Hospital, Cangzhou, Hebei 061000, P.R. China
| | - Shi-Qiang Shan
- Department of Anesthesiology, Cangzhou Central Hospital, Cangzhou, Hebei 061000, P.R. China
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6
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Tovar A, Smith GJ, Thomas JM, Crouse WL, Harkema JR, Kelada SNP. Transcriptional Profiling of the Murine Airway Response to Acute Ozone Exposure. Toxicol Sci 2020; 173:114-130. [PMID: 31626304 PMCID: PMC6944221 DOI: 10.1093/toxsci/kfz219] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Ambient ozone (O3) exposure has serious consequences on respiratory health, including airway inflammation and injury. Decades of research have yielded thorough descriptions of these outcomes; however, less is known about the molecular processes that drive them. The aim of this study was to further describe the cellular and molecular responses to O3 exposure in murine airways, with a particular focus on transcriptional responses in 2 critical pulmonary tissue compartments: conducting airways (CA) and airway macrophages (AM). After exposing adult, female C57BL/6J mice to filtered air, 1 or 2 ppm O3, we assessed hallmark responses including airway inflammation (cell counts and cytokine secretion) and injury (epithelial permeability), followed by gene expression profiling of CA and AM by RNA-seq. As expected, we observed concentration-dependent increases in airway inflammation and injury. Conducting airways and AM both exhibited changes in gene expression to both 1 and 2 ppm O3 that were largely compartment-specific. In CA, genes associated with epithelial barrier function, detoxification processes, and cellular proliferation were altered, while O3 affected genes involved in innate immune signaling, cytokine production, and extracellular matrix remodeling in AM. Further, CA and AM also exhibited notable differences in concentration-response expression patterns for large numbers of genes. Overall, our study has described transcriptional responses to acute O3 exposure, revealing both shared and unique gene expression patterns across multiple concentrations of O3 and in 2 important O3-responsive tissues. These profiles provide broad mechanistic insight into pulmonary O3 toxicity, and reveal a variety of targets for focused follow-up studies.
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Affiliation(s)
- Adelaide Tovar
- Department of Genetics
- Curriculum in Genetics & Molecular Biology
| | - Gregory J Smith
- Department of Genetics
- Curriculum in Toxicology & Environmental Medicine
| | | | - Wesley L Crouse
- Department of Genetics
- Curriculum in Bioinformatics & Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Jack R Harkema
- Department of Pathology & Diagnostic Investigation and Institute for Integrated Toxicology, Michigan State University, East Lansing, Michigan 48824
| | - Samir N P Kelada
- Department of Genetics
- Curriculum in Genetics & Molecular Biology
- Curriculum in Toxicology & Environmental Medicine
- Curriculum in Bioinformatics & Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
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7
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Long ME, Gong KQ, Eddy WE, Volk JS, Morrell ED, Mikacenic C, West TE, Skerrett SJ, Charron J, Liles WC, Manicone AM. MEK1 regulates pulmonary macrophage inflammatory responses and resolution of acute lung injury. JCI Insight 2019; 4:132377. [PMID: 31801908 PMCID: PMC6962022 DOI: 10.1172/jci.insight.132377] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/16/2019] [Indexed: 12/13/2022] Open
Abstract
The MEK1/2-ERK1/2 pathway has been implicated in regulating the inflammatory response to lung injury and infection, and pharmacologic MEK1/2 inhibitor compounds are reported to reduce detrimental inflammation in multiple animal models of disease, in part through modulation of leukocyte responses. However, the specific contribution of myeloid MEK1 in regulating acute lung injury (ALI) and its resolution remain unknown. Here, the role of myeloid Mek1 was investigated in a murine model of LPS-induced ALI (LPS-ALI) by genetic deletion using the Cre-floxed system (LysMCre × Mekfl), and human alveolar macrophages from healthy volunteers and patients with acute respiratory distress syndrome (ARDS) were obtained to assess activation of the MEK1/2-ERK1/2 pathway. Myeloid Mek1 deletion results in a failure to resolve LPS-ALI, and alveolar macrophages lacking MEK1 had increased activation of MEK2 and the downstream target ERK1/2 on day 4 of LPS-ALI. The clinical significance of these findings is supported by increased activation of the MEK1/2-ERK1/2 pathway in alveolar macrophages from patients with ARDS compared with alveolar macrophages from healthy volunteers. This study reveals a critical role for myeloid MEK1 in promoting resolution of LPS-ALI and controlling the duration of macrophage proinflammatory responses.
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Affiliation(s)
- Matthew E. Long
- Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Ke-Qin Gong
- Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - William E. Eddy
- Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Joseph S. Volk
- Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Eric D. Morrell
- Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Carmen Mikacenic
- Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - T. Eoin West
- Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Shawn J. Skerrett
- Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jean Charron
- CHU de Québec-Université Laval Research Center (Oncology division), Université Laval Cancer Research Center and Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Quebec, Canada
| | - W. Conrad Liles
- Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Anne M. Manicone
- Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
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8
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Viola H, Chang J, Grunwell JR, Hecker L, Tirouvanziam R, Grotberg JB, Takayama S. Microphysiological systems modeling acute respiratory distress syndrome that capture mechanical force-induced injury-inflammation-repair. APL Bioeng 2019; 3:041503. [PMID: 31768486 PMCID: PMC6874511 DOI: 10.1063/1.5111549] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 11/08/2019] [Indexed: 12/14/2022] Open
Abstract
Complex in vitro models of the tissue microenvironment, termed microphysiological systems, have enormous potential to transform the process of discovering drugs and disease mechanisms. Such a paradigm shift is urgently needed in acute respiratory distress syndrome (ARDS), an acute lung condition with no successful therapies and a 40% mortality rate. Here, we consider how microphysiological systems could improve understanding of biological mechanisms driving ARDS and ultimately improve the success of therapies in clinical trials. We first discuss how microphysiological systems could explain the biological mechanisms underlying the segregation of ARDS patients into two clinically distinct phenotypes. Then, we contend that ARDS-mimetic microphysiological systems should recapitulate three critical aspects of the distal airway microenvironment, namely, mechanical force, inflammation, and fibrosis, and we review models that incorporate each of these aspects. Finally, we recognize the substantial challenges associated with combining inflammation, fibrosis, and/or mechanical force in microphysiological systems. Nevertheless, complex in vitro models are a novel paradigm for studying ARDS, and they could ultimately improve patient care.
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Affiliation(s)
| | - Jonathan Chang
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory School of Medicine, Atlanta, Georgia 30332, USA
| | - Jocelyn R. Grunwell
- Department of Pediatrics, Division of Critical Care Medicine, Children's Healthcare of Atlanta at Egleston, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Louise Hecker
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, University of Arizona, Tucson, Arizona 85724, USA and Southern Arizona Veterans Affairs Health Care System, Tucson, Arizona 85723, USA
| | - Rabindra Tirouvanziam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, USA and Center for CF and Airways Disease Research, Children's Healthcare of Atlanta, Atlanta, Georgia 30322, USA
| | - James B. Grotberg
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
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9
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Gratz D, Hund TJ, Falvo MJ, Wold LE. Reverse Translation: Using Computational Modeling to Enhance Translational Research. Circ Res 2019; 122:1496-1498. [PMID: 29798899 DOI: 10.1161/circresaha.118.313003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Daniel Gratz
- From the Dorothy M. Davis Heart and Lung Research Institute (D.G., T.J.H., L.E.W.).,The Ohio State University Wexner Medical Center, Columbus; Department of Biomedical Engineering, College of Engineering (D.G., T.J.H.)
| | - Thomas J Hund
- From the Dorothy M. Davis Heart and Lung Research Institute (D.G., T.J.H., L.E.W.).,Department of Internal Medicine (T.J.H.).,The Ohio State University Wexner Medical Center, Columbus; Department of Biomedical Engineering, College of Engineering (D.G., T.J.H.)
| | - Michael J Falvo
- The Ohio State University, Columbus; War Related Illness and Injury Study Center, Department of Veterans Affairs, New Jersey Health Care System, East Orange (M.J.F.).,Rutgers Biomedical and Health Sciences, New Jersey Medical School, Newark (M.J.F.)
| | - Loren E Wold
- From the Dorothy M. Davis Heart and Lung Research Institute (D.G., T.J.H., L.E.W.) .,College of Nursing (L.E.W.).,Department of Physiology and Cell Biology (L.E.W.)
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10
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Rogers AJ. Genome-Wide Association Study in Acute Respiratory Distress Syndrome. Finding the Needle in the Haystack to Advance Our Understanding of Acute Respiratory Distress Syndrome. Am J Respir Crit Care Med 2019; 197:1373-1374. [PMID: 29438627 DOI: 10.1164/rccm.201801-0098ed] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Angela J Rogers
- 1 Department of Medicine Stanford University Stanford, California
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11
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Talikka M, Belcastro V, Gubian S, Martin F, Peitsch MC, Hoeng J. Systems toxicology meta-analysis—From aerosol exposure to nanotoxicology. CURRENT OPINION IN TOXICOLOGY 2019. [DOI: 10.1016/j.cotox.2019.03.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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12
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Mumby S, Chung KF, Adcock IM. Transcriptional Effects of Ozone and Impact on Airway Inflammation. Front Immunol 2019; 10:1610. [PMID: 31354743 PMCID: PMC6635463 DOI: 10.3389/fimmu.2019.01610] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/27/2019] [Indexed: 12/24/2022] Open
Abstract
Epidemiological and challenge studies in healthy subjects and in individuals with asthma highlight the health impact of environmental ozone even at levels considered safe. Acute ozone exposure in man results in sputum neutrophilia in 30% of subjects particularly young children, females, and those with ongoing cardiopulmonary disease. This may be associated with systemic inflammation although not in all cases. Chronic exposure amplifies these effects and can result in the formation of asthma-like symptoms and immunopathology. Asthmatic patients who respond to ozone (responders) induce a greater number of genes in bronchoalveolar (BAL) macrophages than healthy responders with up-regulation of inflammatory and immune pathways under the control of cytokines and chemokines and the enhanced expression of remodeling and repair programmes including those associated with protease imbalances and cell-cell adhesion. These pathways are under the control of several key transcription regulatory factors including nuclear factor (NF)-κB, anti-oxidant factors such as nuclear factor (erythroid-derived 2)-like 2 NRF2, the p38 mitogen activated protein kinase (MAPK), and priming of the immune system by up-regulating toll-like receptor (TLR) expression. Murine and cellular models of acute and chronic ozone exposure recapitulate the inflammatory effects seen in humans and enable the elucidation of key transcriptional pathways. These studies emphasize the importance of distinct transcriptional networks in driving the detrimental effects of ozone. Studies indicate the critical role of mediators including IL-1, IL-17, and IL-33 in driving ozone effects on airway inflammation, remodeling and hyperresponsiveness. Transcription analysis and proof of mechanisms studies will enable the development of drugs to ameliorate the effects of ozone exposure in susceptible individuals.
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Affiliation(s)
- Sharon Mumby
- Respiratory Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Kian Fan Chung
- Respiratory Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Ian M Adcock
- Respiratory Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom
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13
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Hoegl S, Burns N, Angulo M, Francis D, Osborne CM, Mills TW, Blackburn MR, Eltzschig HK, Vohwinkel CU. Capturing the multifactorial nature of ARDS - "Two-hit" approach to model murine acute lung injury. Physiol Rep 2019; 6:e13648. [PMID: 29595879 PMCID: PMC5875538 DOI: 10.14814/phy2.13648] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 02/12/2018] [Accepted: 02/14/2018] [Indexed: 02/06/2023] Open
Abstract
Severe acute respiratory distress syndrome (ARDS) presents typically with an initializing event, followed by the need for mechanical ventilation. Most animal models of ALI are limited by the fact that they focus on a singular cause of acute lung injury (ALI) and therefore fail to mimic the complex, multifactorial pathobiology of ARDS. To better capture this scenario, we provide a comprehensive characterization of models of ALI combining two injuries: intra tracheal (i.t.) instillation of LPS or hypochloric acid (HCl) followed by ventilator‐induced lung injury (VILI). We hypothesized, that mice pretreated with LPS or HCl prior to VILI and thus receiving a (“two‐hit injury”) will sustain a superadditive lung injury when compared to VILI. Mice were allocated to following treatment groups: control with i.t. NaCl, ventilation with low peak inspiratory pressure (PIP), i.t. HCl, i.t. LPS, VILI (high PIP), HCl i.t. followed by VILI and LPS i.t. followed by VILI. Severity of injury was determined by protein content and MPO activity in bronchoalveolar lavage (BAL), the expression of inflammatory cytokines and histopathology. Mice subjected to VILI after HCl or LPS instillation displayed augmented lung injury, compared to singular lung injury. However, mice that received i.t. LPS prior to VILI showed significantly increased inflammatory lung injury compared to animals that underwent i.t. HCl followed by VILI. The two‐hit lung injury models described, resulting in additive but differential acute lung injury recaptures the clinical relevant multifactorial etiology of ALI and could be a valuable tool in translational research.
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Affiliation(s)
- Sandra Hoegl
- Organ Protection Program, School of Medicine, Department of Anesthesiology, University of Colorado, Aurora, Colorado.,Developmental Lung Biology, Cardio Vascular Pulmonary Research Laboratories, Division of Pulmonary Sciences and Critical Care Medicine, Division of Pediatric Critical Care, Departments of Medicine and Pediatrics, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Nana Burns
- Feinberg School of Medicine, Division of Pulmonary and Critical Care, Northwestern University, Chicago, Illinois
| | - Martín Angulo
- Department of Respiratory Therapy, Colorado Children's Hospital, Aurora, Colorado
| | - Daniel Francis
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center Houston, Houston, Texas
| | - Christopher M Osborne
- Feinberg School of Medicine, Division of Pulmonary and Critical Care, Northwestern University, Chicago, Illinois
| | - Tingting W Mills
- Department of Anesthesiology, University Hospital of Ludwig-Maximilians-University, Munich, Germany
| | - Michael R Blackburn
- Department of Anesthesiology, University Hospital of Ludwig-Maximilians-University, Munich, Germany
| | - Holger K Eltzschig
- Organ Protection Program, School of Medicine, Department of Anesthesiology, University of Colorado, Aurora, Colorado
| | - Christine U Vohwinkel
- Organ Protection Program, School of Medicine, Department of Anesthesiology, University of Colorado, Aurora, Colorado.,Feinberg School of Medicine, Division of Pulmonary and Critical Care, Northwestern University, Chicago, Illinois
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14
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Abstract
PURPOSE OF REVIEW ARDS is a severe pulmonary disease characterized by inflammation. However, inflammation-directed therapies have yet failed to improve the outcome in ARDS patients. One of the reasons may be the underestimated complexity of inflammation. Here, we summarize recent insights into the complex interrelations between inflammatory circuits. RECENT FINDINGS Gene expression analysis from animal models or from patients with ARDS, sepsis or trauma show an enormous number of differentially expressed genes with highly significant overlaps between the various conditions. These similarities, however, should not obscure the complexity of inflammation. We suggest to consider inflammation in ARDS as a system controlled by scale-free networks of genome-wide molecular interaction with hubs (e.g. NFκB, C/EBPβ, ATF3), exhibiting nonlinear emergence and the ability to adapt, meaning for instance that mild and life-threatening inflammation in ARDS are distinct processes. In order to comprehend this complex system, it seems necessary to combine model-driven simulations, data-driven modelling and hypothesis-driven experimental studies. Recent experimental studies have illustrated how several regulatory circuits interact during pulmonary inflammation, including the resolution of inflammation, the inflammasome, autophagy and apoptosis. SUMMARY We suggest that therapeutic interventions in ARDS should be based on a systems approach to inflammation.
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15
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Moore BB. Groundhog Day for Rodent Models of Acute Lung Injury: Clear Relevance or Renewed Debate? Am J Respir Cell Mol Biol 2018; 57:141-142. [PMID: 28762770 DOI: 10.1165/rcmb.2017-0119ed] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Bethany B Moore
- 1 Department of Internal Medicine University of Michigan Ann Arbor, Michigan
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16
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Abdulnour REE, Howrylak JA, Tavares AH, Douda DN, Henkels KM, Miller TE, Fredenburgh LE, Baron RM, Gomez-Cambronero J, Levy BD. Phospholipase D isoforms differentially regulate leukocyte responses to acute lung injury. J Leukoc Biol 2018; 103:919-932. [PMID: 29437245 DOI: 10.1002/jlb.3a0617-252rr] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 01/03/2018] [Accepted: 01/10/2018] [Indexed: 12/30/2022] Open
Abstract
Phospholipase D (PLD) plays important roles in cellular responses to tissue injury that are critical to acute inflammatory diseases, such as the acute respiratory distress syndrome (ARDS). We investigated the expression of PLD isoforms and related phospholipid phosphatases in patients with ARDS, and their roles in a murine model of self-limited acute lung injury (ALI). Gene expression microarray analysis on whole blood obtained from patients that met clinical criteria for ARDS and clinically matched controls (non-ARDS) demonstrated that PLD1 gene expression was increased in patients with ARDS relative to non-ARDS and correlated with survival. In contrast, PLD2 expression was associated with mortality. In a murine model of self-resolving ALI, lung Pld1 expression increased and Pld2 expression decreased 24 h after intrabronchial acid. Total lung PLD activity was increased 24 h after injury. Pld1-/- mice demonstrated impaired alveolar barrier function and increased tissue injury relative to WT and Pld2-/- , whereas Pld2-/- mice demonstrated increased recruitment of neutrophils and macrophages, and decreased tissue injury. Isoform-specific PLD inhibitors mirrored the results with isoform-specific Pld-KO mice. PLD1 gene expression knockdown in human leukocytes was associated with decreased phagocytosis by neutrophils, whereas reactive oxygen species production and phagocytosis decreased in M2-macrophages. PLD2 gene expression knockdown increased neutrophil and M2-macrophage transmigration, and increased M2-macrophage phagocytosis. These results uncovered selective regulation of PLD isoforms after ALI, and opposing effects of selective isoform knockdown on host responses and tissue injury. These findings support therapeutic strategies targeting specific PLD isoforms for the treatment of ARDS.
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Affiliation(s)
- Raja-Elie E Abdulnour
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Judie A Howrylak
- Division of Pulmonary Allergy and Critical Care Medicine, Penn State Hershey Medical Center, Hershey, Pennsylvania, USA
| | - Alexander H Tavares
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - David N Douda
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Karen M Henkels
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio, USA
| | - Taylor E Miller
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio, USA
| | - Laura E Fredenburgh
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Rebecca M Baron
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Julian Gomez-Cambronero
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, Ohio, USA.,Center for Experimental Therapeutics and Reperfusion Injury, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Bruce D Levy
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Center for Experimental Therapeutics and Reperfusion Injury, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Sweeney TE, Thomas NJ, Howrylak JA, Wong HR, Rogers AJ, Khatri P. Multicohort Analysis of Whole-Blood Gene Expression Data Does Not Form a Robust Diagnostic for Acute Respiratory Distress Syndrome. Crit Care Med 2018; 46:244-251. [PMID: 29337789 PMCID: PMC5774019 DOI: 10.1097/ccm.0000000000002839] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
OBJECTIVES To identify a novel, generalizable diagnostic for acute respiratory distress syndrome using whole-blood gene expression arrays from multiple acute respiratory distress syndrome cohorts of varying etiologies. DATA SOURCES We performed a systematic search for human whole-blood gene expression arrays of acute respiratory distress syndrome in National Institutes of Health Gene Expression Omnibus and ArrayExpress. We also included the Glue Grant gene expression cohorts. STUDY SELECTION We included investigator-defined acute respiratory distress syndrome within 48 hours of diagnosis and compared these with relevant critically ill controls. DATA EXTRACTION We used multicohort analysis of gene expression to identify genes significantly associated with acute respiratory distress syndrome, both with and without adjustment for clinical severity score. We performed gene ontology enrichment using Database for Annotation, Visualization and Integrated Discovery and cell type enrichment tests for both immune cells and pneumocyte gene expression. Finally, we selected a gene set optimized for diagnostic power across the datasets and used leave-one-dataset-out cross validation to assess robustness of the model. DATA SYNTHESIS We identified datasets from three adult cohorts with sepsis, one pediatric cohort with acute respiratory failure, and two datasets of adult patients with trauma and burns, for a total of 148 acute respiratory distress syndrome cases and 268 critically ill controls. We identified 30 genes that were significantly associated with acute respiratory distress syndrome (false discovery rate < 20% and effect size >1.3), many of which had been previously associated with sepsis. When metaregression was used to adjust for clinical severity scores, none of these genes remained significant. Cell type enrichment was notable for bands and neutrophils, suggesting that the gene expression signature is one of acute inflammation rather than lung injury per se. Finally, an attempt to develop a generalizable diagnostic gene set for acute respiratory distress syndrome showed a mean area under the receiver-operating characteristic curve of only 0.63 on leave-one-dataset-out cross validation. CONCLUSIONS The whole-blood gene expression signature across a wide clinical spectrum of acute respiratory distress syndrome is likely confounded by systemic inflammation, limiting the utility of whole-blood gene expression studies for uncovering a generalizable diagnostic gene signature.
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Affiliation(s)
- Timothy E Sweeney
- Stanford Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA
- Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA
| | - Neal J Thomas
- Division of Pediatric Critical Care Medicine, Penn State Hershey Children's Hospital, Hershey, PA
| | - Judie A Howrylak
- Division of Pulmonary and Critical Care Medicine, Penn State Milton S. Hershey Medical Center, Hershey, PA
| | - Hector R Wong
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Angela J Rogers
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Stanford University School of Medicine, Stanford, CA
| | - Purvesh Khatri
- Stanford Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA
- Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA
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18
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Gregory DJ, Kramnik I, Kobzik L. Protection of macrophages from intracellular pathogens by miR-182-5p mimic-a gene expression meta-analysis approach. FEBS J 2017; 285:244-260. [PMID: 29197182 DOI: 10.1111/febs.14348] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 09/29/2017] [Accepted: 11/28/2017] [Indexed: 12/25/2022]
Abstract
The goals of this study were to (a) define which host genes are of particular importance during the interactions between macrophages and intracellular pathogens, and (b) use this knowledge to gain fresh, experimental understanding of how macrophage activities may be manipulated during host defense. We designed an in silico method for meta-analysis of microarray gene expression data, and used this to combine data from 16 different studies of cells in the monocyte-macrophage lineage infected with seven different pathogens. Three thousand four hundred ninety-eight genes were identified, which we call the macrophage intracellular pathogen response (macIPR) gene set. As expected, the macIPR gene set showed a strong bias toward genes previously associated with the immune response. Predicted target sites for miR-182-5p (miR-182) were strongly over-represented among macIPR genes, indicating an unexpected role for miR-182-regulatable genes during intracellular pathogenesis. We therefore transfected primary human alveolar macrophage-like monocyte-derived macrophages from multiple different donors with synthetic miR-182, and found that miR-182 overexpression (a) increases proinflammatory gene induction during infection with Francisella tularensis live vaccine strain (LVS), (b) primes macrophages for increased autophagy, and (c) enhances macrophage control of both gram negative F. tularensisLVS and gram positive Bacillus anthracisANR-1 spores. These data therefore suggest a new application for miR-182 in promoting resistance to intracellular pathogens.
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Affiliation(s)
- David J Gregory
- Molecular and Physiological Sciences Program, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Igor Kramnik
- Pulmonary Center, Department of Medicine, National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, MA, USA
| | - Lester Kobzik
- Molecular and Physiological Sciences Program, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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