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Kgatle MM, Lawal IO, Mashabela G, Boshomane TMG, Koatale PC, Mahasha PW, Ndlovu H, Vorster M, Rodrigues HG, Zeevaart JR, Gordon S, Moura-Alves P, Sathekge MM. COVID-19 Is a Multi-Organ Aggressor: Epigenetic and Clinical Marks. Front Immunol 2021; 12:752380. [PMID: 34691068 PMCID: PMC8531724 DOI: 10.3389/fimmu.2021.752380] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/21/2021] [Indexed: 12/19/2022] Open
Abstract
The progression of coronavirus disease 2019 (COVID-19), resulting from a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, may be influenced by both genetic and environmental factors. Several viruses hijack the host genome machinery for their own advantage and survival, and similar phenomena might occur upon SARS-CoV-2 infection. Severe cases of COVID-19 may be driven by metabolic and epigenetic driven mechanisms, including DNA methylation and histone/chromatin alterations. These epigenetic phenomena may respond to enhanced viral replication and mediate persistent long-term infection and clinical phenotypes associated with severe COVID-19 cases and fatalities. Understanding the epigenetic events involved, and their clinical significance, may provide novel insights valuable for the therapeutic control and management of the COVID-19 pandemic. This review highlights different epigenetic marks potentially associated with COVID-19 development, clinical manifestation, and progression.
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Affiliation(s)
- Mankgopo Magdeline Kgatle
- Nuclear Medicine Research Infrastructure (NuMeRI), Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
| | - Ismaheel Opeyemi Lawal
- Nuclear Medicine Research Infrastructure (NuMeRI), Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, Steve Biko Academic Hospital, Pretoria, South Africa
| | - Gabriel Mashabela
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Tebatso Moshoeu Gillian Boshomane
- Nuclear Medicine Research Infrastructure (NuMeRI), Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, Steve Biko Academic Hospital, Pretoria, South Africa
- Nuclear and Oncology Division, AXIM Medical (Pty), Midrand
| | - Palesa Caroline Koatale
- Nuclear Medicine Research Infrastructure (NuMeRI), Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
| | - Phetole Walter Mahasha
- Precision Medicine and SAMRC Genomic Centre, Grants, Innovation, and Product Development (GIPD) Unit, South African Medical Research Council, Pretoria, South Africa
| | - Honest Ndlovu
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
| | - Mariza Vorster
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
| | - Hosana Gomes Rodrigues
- Laboratory of Nutrients and Tissue Repair, School of Applied Sciences, University of Campinas, Campinas, Brazil
| | - Jan Rijn Zeevaart
- Nuclear Medicine Research Infrastructure (NuMeRI), Steve Biko Academic Hospital, Pretoria, South Africa
- South African Nuclear Energy Corporation, Radiochemistry and NuMeRI PreClinical Imaging Facility, Mahikeng, South Africa
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan City, Taiwan
| | - Siamon Gordon
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan City, Taiwan
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Pedro Moura-Alves
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Mike Machaba Sathekge
- Nuclear Medicine Research Infrastructure (NuMeRI), Steve Biko Academic Hospital, Pretoria, South Africa
- Department of Nuclear Medicine, University of Pretoria & Steve Biko Academic Hospital, Pretoria, South Africa
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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2
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Balnis J, Adam AP, Chopra A, Chieng HC, Drake LA, Martino N, Bossardi Ramos R, Feustel PJ, Overmyer KA, Shishkova E, Coon JJ, Singer HA, Judson MA, Jaitovich A. Unique inflammatory profile is associated with higher SARS-CoV-2 acute respiratory distress syndrome (ARDS) mortality. Am J Physiol Regul Integr Comp Physiol 2021; 320:R250-R257. [PMID: 33434104 PMCID: PMC7938634 DOI: 10.1152/ajpregu.00324.2020] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/15/2020] [Accepted: 01/04/2021] [Indexed: 02/07/2023]
Abstract
The COVID19 pandemic has caused more than a million of deaths worldwide, primarily due to complications from COVID19-associated acute respiratory distress syndrome (ARDS). Controversy surrounds the circulating cytokine/chemokine profile of COVID19-associated ARDS, with some groups suggesting that it is similar to patients without COVID19 ARDS and others observing substantial differences. Moreover, although a hyperinflammatory phenotype associates with higher mortality in non-COVID19 ARDS, there is little information on the inflammatory landscape's association with mortality in patients with COVID19 ARDS. Even though the circulating leukocytes' transcriptomic signature has been associated with distinct phenotypes and outcomes in critical illness including ARDS, it is unclear whether the mortality-associated inflammatory mediators from patients with COVID19 are transcriptionally regulated in the leukocyte compartment. Here, we conducted a prospective cohort study of 41 mechanically ventilated patients with COVID19 infection using highly calibrated methods to define the levels of plasma cytokines/chemokines and their gene expressions in circulating leukocytes. Plasma IL1RA and IL8 were found positively associated with mortality, whereas RANTES and EGF negatively associated with that outcome. However, the leukocyte gene expression of these proteins had no statistically significant correlation with mortality. These data suggest a unique inflammatory signature associated with severe COVID19.
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Affiliation(s)
- Joseph Balnis
- Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, New York
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Alejandro P Adam
- Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, New York
- Department of Ophthalmology, Albany Medical College, Albany, New York
| | - Amit Chopra
- Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, New York
| | - Hau C Chieng
- Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, New York
| | - Lisa A Drake
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Nina Martino
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Ramon Bossardi Ramos
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Paul J Feustel
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, New York
| | | | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Joshua J Coon
- Morgridge Institute for Research, Madison, Wisconsin
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Harold A Singer
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Marc A Judson
- Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, New York
| | - Ariel Jaitovich
- Division of Pulmonary and Critical Care Medicine, Albany Medical College, Albany, New York
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
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Chakravarty D, Nair SS, Hammouda N, Ratnani P, Gharib Y, Wagaskar V, Mohamed N, Lundon D, Dovey Z, Kyprianou N, Tewari AK. Sex differences in SARS-CoV-2 infection rates and the potential link to prostate cancer. Commun Biol 2020; 3:374. [PMID: 32641750 PMCID: PMC7343823 DOI: 10.1038/s42003-020-1088-9] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/17/2020] [Indexed: 01/08/2023] Open
Abstract
The recent outbreak of infections and the pandemic caused by SARS-CoV-2 represent one of the most severe threats to human health in more than a century. Emerging data from the United States and elsewhere suggest that the disease is more severe in men. Knowledge gained, and lessons learned, from studies of the biological interactions and molecular links that may explain the reasons for the greater severity of disease in men, and specifically in the age group at risk for prostate cancer, will lead to better management of COVID-19 in prostate cancer patients. Such information will be indispensable in the current and post-pandemic scenarios.
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Affiliation(s)
- Dimple Chakravarty
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Sujit S Nair
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Nada Hammouda
- Department of Emergency Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Parita Ratnani
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yasmine Gharib
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Vinayak Wagaskar
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nihal Mohamed
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dara Lundon
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zachary Dovey
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Natasha Kyprianou
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ashutosh K Tewari
- Department of Urology and The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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Lynn H, Sun X, Casanova N, Gonzales-Garay M, Bime C, Garcia JGN. Genomic and Genetic Approaches to Deciphering Acute Respiratory Distress Syndrome Risk and Mortality. Antioxid Redox Signal 2019; 31:1027-1052. [PMID: 31016989 PMCID: PMC6939590 DOI: 10.1089/ars.2018.7701] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Significance: Acute respiratory distress syndrome (ARDS) is a severe, highly heterogeneous critical illness with staggering mortality that is influenced by environmental factors, such as mechanical ventilation, and genetic factors. Significant unmet needs in ARDS are addressing the paucity of validated predictive biomarkers for ARDS risk and susceptibility that hamper the conduct of successful clinical trials in ARDS and the complete absence of novel disease-modifying therapeutic strategies. Recent Advances: The current ARDS definition relies on clinical characteristics that fail to capture the diversity of disease pathology, severity, and mortality risk. We undertook a comprehensive survey of the available ARDS literature to identify genes and genetic variants (candidate gene and limited genome-wide association study approaches) implicated in susceptibility to developing ARDS in hopes of uncovering novel biomarkers for ARDS risk and mortality and potentially novel therapeutic targets in ARDS. We further attempted to address the well-known health disparities that exist in susceptibility to and mortality from ARDS. Critical Issues: Bioinformatic analyses identified 201 ARDS candidate genes with pathway analysis indicating a strong predominance in key evolutionarily conserved inflammatory pathways, including reactive oxygen species, innate immunity-related inflammation, and endothelial vascular signaling pathways. Future Directions: Future studies employing a system biology approach that combines clinical characteristics, genomics, transcriptomics, and proteomics may allow for a better definition of biologically relevant pathways and genotype-phenotype connections and result in improved strategies for the sub-phenotyping of diverse ARDS patients via molecular signatures. These efforts should facilitate the potential for successful clinical trials in ARDS and yield a better fundamental understanding of ARDS pathobiology.
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Affiliation(s)
- Heather Lynn
- Department of Physiological Sciences and University of Arizona, Tucson, Arizona.,Department of Health Sciences, University of Arizona, Tucson, Arizona
| | - Xiaoguang Sun
- Department of Health Sciences, University of Arizona, Tucson, Arizona
| | - Nancy Casanova
- Department of Health Sciences, University of Arizona, Tucson, Arizona
| | | | - Christian Bime
- Department of Health Sciences, University of Arizona, Tucson, Arizona
| | - Joe G N Garcia
- Department of Health Sciences, University of Arizona, Tucson, Arizona
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Prows DR, Gibbons WJ, Smith JJ, Pilipenko V, Martin LJ. Age and Sex of Mice Markedly Affect Survival Times Associated with Hyperoxic Acute Lung Injury. PLoS One 2015; 10:e0130936. [PMID: 26103466 PMCID: PMC4478006 DOI: 10.1371/journal.pone.0130936] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 05/26/2015] [Indexed: 01/11/2023] Open
Abstract
Mortality associated with acute lung injury (ALI) remains substantial, with recent estimates of 35–45% similar to those obtained decades ago. Although evidence for sex-related differences in ALI mortality remains equivocal, death rates differ markedly for age, with more than 3-fold increased mortality in older versus younger patients. Strains of mice also show large differences in ALI mortality. To tease out genetic factors affecting mortality, we established a mouse model of differential hyperoxic ALI (HALI) survival. Separate genetic analyses of backcross and F2 populations generated from sensitive C57BL/6J (B) and resistant 129X1/SvJ (X1) progenitor strains identified two quantitative trait loci (QTLs; Shali1 and Shali2) with strong, equal but opposite, within-strain effects on survival. Congenic lines confirmed these opposing QTL effects, but also retained the low penetrance seen in the 6–12 week X1 control strain. Sorting mice into distinct age groups revealed that ‘age at exposure’ inversely correlated with survival time and explained reduced penetrance of the resistance trait. While B mice were already sensitive by 6 weeks old, X1 mice maintained significant resistance up to 3–4 weeks longer. Reanalysis of F2 data gave analogous age-related findings, and also supported sex-specific linkage for Shali1 and Shali2. Importantly, we have demonstrated in congenic mice that these age effects on survival correspond with B alleles for Shali1 (6-week old mice more sensitive) and Shali2 (10-week old mice more resistant) placed on the X1 background. Further studies revealed significant sex-specific survival differences in subcongenics for both QTLs. Accounting for age and sex markedly improved penetrance of both QTLs, thereby reducing trait variability, refining Shali1 to <8.5Mb, and supporting several sub-QTLs within the Shali2 interval. Together, these congenics will allow age- and sex-specific studies to interrogate myriad subphenotypes affected during ALI development and progression and identify intermediary injury biomarkers that can predict outcome.
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Affiliation(s)
- Daniel R. Prows
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- * E-mail:
| | - William J. Gibbons
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Jessica J. Smith
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Valentina Pilipenko
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Lisa J. Martin
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Biostatistics & Epidemiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
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Luo L, Deng J, Wang DX, He J, Deng W. Regulation of epithelial sodium channel expression by oestradiol and progestogen in alveolar epithelial cells. Respir Physiol Neurobiol 2015; 216:52-62. [PMID: 26051998 DOI: 10.1016/j.resp.2015.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 05/15/2015] [Accepted: 06/01/2015] [Indexed: 01/11/2023]
Abstract
Oestrogen (E) and progestogen (P) exert regulatory effects on the epithelial Na(+) channel (ENaC) in the kidneys and the colon. However, the effects of E and P on the ENaC and on alveolar fluid clearance (AFC) remain unclear, and the mechanisms of action of these hormones are unknown. In this study, we showed that E and/or P administration increased AFC by more than 25% and increased the expression of the α and γ subunits of ENaC by approximately 35% in rats subjected to oleic acid-induced acute lung injury (ALI). A similar effect was observed in the dexamethasone-treated group. Furthermore, E and/or P treatment inhibited 11β-hydroxysteroid dehydrogenase (HSD) type 2 (11β-HSD2) activity, increased corticosterone expression and decreased the serum adrenocorticotrophic hormone (ACTH) levels. These effects were similar to those observed following treatment with carbenoxolone (CBX), a nonspecific HSD inhibitor. Further investigation showed that CBX further significantly increased AFC and α-ENaC expression after treatment with a low dose of E and/or P. In vitro, E or P alone inhibited 11β-HSD2 activity in a dose-dependent manner and increased α-ENaC expression by at least 50%, and E combined with P increased α-ENaC expression by more than 80%. Thus, E and P may augment the expression of α-ENaC, enhance AFC, attenuate pulmonary oedema by inhibiting 11β-HSD2 activity, and increase the active glucocorticoid levels in vivo and in vitro.
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Affiliation(s)
- Ling Luo
- Department of Respiratory Medicine, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jia Deng
- First Department of Internal Medicine, Traditional Chinese Medical Hospital of Jiangbei District, Chongqing, China
| | - Dao-xin Wang
- Department of Respiratory Medicine, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Jing He
- Department of Respiratory Medicine, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wang Deng
- Department of Respiratory Medicine, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Meyer NJ. Beyond single-nucleotide polymorphisms: genetics, genomics, and other 'omic approaches to acute respiratory distress syndrome. Clin Chest Med 2014; 35:673-84. [PMID: 25453417 DOI: 10.1016/j.ccm.2014.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This article summarizes the contributions of high-throughput genomic, proteomic, metabolomic, and gene expression investigations to the understanding of inherited or acquired risk for acute respiratory distress syndrome (ARDS). Although not yet widely applied to a complex trait like ARDS, these techniques are now routinely used to study a variety of disease states. Omic applications hold great promise for identifying novel factors that may contribute to ARDS pathophysiology or may be appropriate for further development as biomarkers or surrogates in clinical studies. Opportunities and challenges of different techniques are discussed, and examples of successful applications in non-ARDS fields are used to illustrate the potential use of each technique.
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Affiliation(s)
- Nuala J Meyer
- Pulmonary, Allergy, and Critical Care Medicine, University of Pennsylvania, Perelman School of Medicine, 3600 Spruce Street, 5039 Maloney Building, Philadelphia, PA 19104, USA.
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O'Mahony DS, Glavan BJ, Holden TD, Fong C, Black RA, Rona G, Tejera P, Christiani DC, Wurfel MM. Inflammation and immune-related candidate gene associations with acute lung injury susceptibility and severity: a validation study. PLoS One 2012; 7:e51104. [PMID: 23251429 PMCID: PMC3522667 DOI: 10.1371/journal.pone.0051104] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Accepted: 10/31/2012] [Indexed: 02/06/2023] Open
Abstract
Introduction Common variants in genes related to inflammation, innate immunity, epithelial cell function, and angiogenesis have been reported to be associated with risks for Acute Lung Injury (ALI) and related outcomes. We tested whether previously-reported associations can be validated in an independent cohort at risk for ALI. Methods We identified 37 genetic variants in 27 genes previously associated with ALI and related outcomes. We prepared allelic discrimination assays for 12 SNPs from 11 genes with MAF>0.05 and genotyped these SNPs in Caucasian subjects from a cohort of critically ill patients meeting criteria for the systemic inflammatory response syndrome (SIRS) followed for development of ALI, duration of mechanical ventilation, and in-hospital death. We tested for associations using additive and recessive genetic models. Results Among Caucasian subjects with SIRS (n = 750), we identified a nominal association between rs2069832 in IL6 and ALI susceptibility (ORadj 1.61; 95% confidence interval [CI], 1.04–2.48, P = 0.03). In a sensitivity analysis limiting ALI cases to those who qualified for the Acute Respiratory Distress Syndrome (ARDS), rs61330082 in NAMPT was nominally associated with risk for ARDS. In terms of ALI outcomes, SNPs in MBL2 (rs1800450) and IL8 (rs4073) were nominally associated with fewer ventilator-free days (VFDs), and SNPs in NFE2L2 (rs6721961) and NAMPT (rs61330082) were nominally associated with 28-day mortality. The directions of effect for these nominal associations were in the same direction as previously reported but none of the associations survived correction for multiple hypothesis testing. Conclusion Although our primary analyses failed to statistically validate prior associations, our results provide some support for associations between SNPs in IL6 and NAMPT and risk for development of lung injury and for SNPs in IL8, MBL2, NFE2L2 and NAMPT with severity in ALI outcomes. These associations provide further evidence that genetic factors in genes related to immunity and inflammation contribute to ALI pathogenesis.
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Affiliation(s)
- D. Shane O'Mahony
- Division of Pulmonary and Critical Care Medicine, Harborview Medical Center, University of Washington, Seattle, Washington, United States of America
| | - Bradford J. Glavan
- Division of Pulmonary and Critical Care Medicine, Harborview Medical Center, University of Washington, Seattle, Washington, United States of America
| | - Tarah D. Holden
- Division of Pulmonary and Critical Care Medicine, Harborview Medical Center, University of Washington, Seattle, Washington, United States of America
| | - Christie Fong
- Division of Pulmonary and Critical Care Medicine, Harborview Medical Center, University of Washington, Seattle, Washington, United States of America
| | - R. Anthony Black
- Institute of Translational Health Sciences (ITHS), University of Washington, Seattle, Washington, United States of America
| | - Gail Rona
- Division of Pulmonary and Critical Care Medicine, Harborview Medical Center, University of Washington, Seattle, Washington, United States of America
| | - Paula Tejera
- Harvard School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - David C. Christiani
- Harvard School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Mark M. Wurfel
- Division of Pulmonary and Critical Care Medicine, Harborview Medical Center, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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Meyer NJ, Daye ZJ, Rushefski M, Aplenc R, Lanken PN, Shashaty MGS, Christie JD, Feng R. SNP-set analysis replicates acute lung injury genetic risk factors. BMC MEDICAL GENETICS 2012; 13:52. [PMID: 22742663 PMCID: PMC3512475 DOI: 10.1186/1471-2350-13-52] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 06/18/2012] [Indexed: 12/19/2022]
Abstract
BACKGROUND We used a gene - based replication strategy to test the reproducibility of prior acute lung injury (ALI) candidate gene associations. METHODS We phenotyped 474 patients from a prospective severe trauma cohort study for ALI. Genomic DNA from subjects' blood was genotyped using the IBC chip, a multiplex single nucleotide polymorphism (SNP) array. Results were filtered for 25 candidate genes selected using prespecified literature search criteria and present on the IBC platform. For each gene, we grouped SNPs according to haplotype blocks and tested the joint effect of all SNPs on susceptibility to ALI using the SNP-set kernel association test. Results were compared to single SNP analysis of the candidate SNPs. Analyses were separate for genetically determined ancestry (African or European). RESULTS We identified 4 genes in African ancestry and 2 in European ancestry trauma subjects which replicated their associations with ALI. Ours is the first replication of IL6, IL10, IRAK3, and VEGFA associations in non-European populations with ALI. Only one gene - VEGFA - demonstrated association with ALI in both ancestries, with distinct haplotype blocks in each ancestry driving the association. We also report the association between trauma-associated ALI and NFKBIA in European ancestry subjects. CONCLUSIONS Prior ALI genetic associations are reproducible and replicate in a trauma cohort. Kernel - based SNP-set analysis is a more powerful method to detect ALI association than single SNP analysis, and thus may be more useful for replication testing. Further, gene-based replication can extend candidate gene associations to diverse ethnicities.
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Affiliation(s)
- Nuala J Meyer
- Department of Medicine: Pulmonary, Allergy, and Critical Care Division, Perelman School of Medicine University of Pennsylvania, 3600 Spruce Street, 874 Maloney, Philadelphia, PA 19104, USA.
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Cmet S, Fabris C, Fattovich G, Falleti E, Bitetto D, Cussigh A, Fontanini E, Fornasiere E, Pirisi M, Toniutto P. Carriage of the EGF rs4444903 A>G functional polymorphism associates with disease progression in chronic HBV infection. Clin Exp Immunol 2012; 167:296-302. [PMID: 22236006 DOI: 10.1111/j.1365-2249.2011.04497.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Because epidermal growth factor (EGF) up-regulation is characteristic of the cirrhotic liver, we hypothesised that the EGF rs4444903 A > G functional polymorphism might be associated with a worse disease course in patients with chronic HBV infection. To verify this hypothesis, 170 HBV-positive patients (125 males) with a median age of 52 years were studied. Sixty-two of these patients were followed longitudinally for a median time of 21 years. Genotyping for the EGF rs4444903 A > G polymorphism was performed by the polymerase chain reaction-based restriction fragment length polymorphism assay. In the cross-sectional study, the EGF rs4444903 A > G polymorphism genotypic frequencies significantly differed between transplant patients (A/A = 20·4%, A/G = 52·3%, G/G = 27·3%) and HBsAg+ carriers (active and inactive: A/A = 35·7%, A/G = 47·6%, G/G = 16·7%, P = 0·036 for the linear trend). In the longitudinal study, the EGF rs4444903 A > G polymorphism was found to be an independent predictor of cirrhosis development (O.R. 7·73, 95% C.I. 1·21-49·5, P = 0·007). Three groups of patients were identified: A/A female homozygotes (n = 9), A/A male homozygotes (n = 13) and carriers of the G allele of either gender (n = 40). Cirrhosis did not occur among A/A females (n = 0/9), seldom occurred among A/A males (n = 2/13) and reached the highest frequency among G/* patients (n = 13/40, P = 0·026). In conclusion, the EGF rs4444903 A > G polymorphism appears to be associated with an unfavourable disease course of chronic HBV infection and cirrhosis development. This effect might be modulated, at least in part, by the gender of the patient.
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Affiliation(s)
- S Cmet
- Laboratory Medicine, Department of Medical Sciences, Clinical and Experimental, University of Udine, Udine, Italy
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Burnham EL, McCord JM, Bose S, Brown LAS, House R, Moss M, Gaydos J. Protandim does not influence alveolar epithelial permeability or intrapulmonary oxidative stress in human subjects with alcohol use disorders. Am J Physiol Lung Cell Mol Physiol 2012; 302:L688-99. [PMID: 22268125 DOI: 10.1152/ajplung.00171.2011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Alcohol use disorders (AUDs), including alcohol abuse and dependence, have been linked to the development of acute lung injury (ALI). Prior clinical investigations suggested an association between AUDs and abnormal alveolar epithelial permeability mediated through pulmonary oxidative stress that may partially explain this relationship. We sought to determine if correcting pulmonary oxidative stress in the setting of AUDs would normalize alveolar epithelial permeability in a double-blinded, randomized, placebo-controlled trial of Protandim, a nutraceutical reported to enhance antioxidant activity. We randomized 30 otherwise healthy AUD subjects to receive directly observed inpatient oral therapy with either Protandim (1,350 mg/day) or placebo. Subjects underwent bronchoalveolar lavage (BAL) and blood sampling before study drug administration and after 7 days of therapy; all AUD subjects completed the study protocol without adverse events. BAL total protein was measured at each timepoint as an indicator of alveolar epithelial permeability. In subjects with AUDs, before study drug initiation, BAL total protein values were not significantly higher than in 11 concurrently enrolled controls (P = 0.07). Over the 7-day study period, AUD subjects did not exhibit a significant change in BAL total protein, regardless of their randomization to Protandim {n = 14, -2% [intraquartile range (IQR), -56-146%]} or to placebo [n = 16, 77% (IQR -20-290%); P = 0.19]. Additionally, among those with AUDs, no significant changes in BAL oxidative stress indexes, epithelial growth factor, fibroblast growth factor, interleukin-1β, or interleukin-10 were observed regardless of drug type received. Plasma thiobarbituric acid reactive substances, a marker of lipid peroxidation, decreased significantly over time among AUD subjects randomized to placebo (P < 0.01). These results suggest that Protandim for 7 days in individuals with AUDs who are newly abstinent does not alter alveolar epithelial permeability. However, our work demonstrates the feasibility of safely conducting clinical trials that include serial bronchoscopies in a vulnerable population at risk for acute lung injury.
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Affiliation(s)
- Ellen L Burnham
- Division of Pulmonary Sciences and Critical Care Medicine, Univ. of Colorado School of Medicine, Aurora, CO 80045, USA.
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12
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Garcia JGN. Focusing on the flood: targeting functional polymorphisms in ALI permeability pathways. Am J Respir Crit Care Med 2011; 183:1287-9. [PMID: 21596828 DOI: 10.1164/rccm.201104-0623ed] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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13
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An NFKB1 promoter insertion/deletion polymorphism influences risk and outcome in acute respiratory distress syndrome among Caucasians. PLoS One 2011; 6:e19469. [PMID: 21573030 PMCID: PMC3090449 DOI: 10.1371/journal.pone.0019469] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 03/30/2011] [Indexed: 12/26/2022] Open
Abstract
Background Nuclear factor-κB (NF-κB) is required for transcription of many pro-inflammatory genes and has been implicated in the pathogenesis of acute respiratory distress syndrome (ARDS). We hypothesized that a known functional polymorphism in the promoter of the NFKB1 gene may affect susceptibility to and outcome from ARDS. Methods A case control study was conducted among a cohort of patients admitted to the intensive care unit (ICU) with risk factors for the development of ARDS. 379 patients with ARDS and 793 at-risk controls were studied. Patients were followed for 60 days with development of ARDS as a primary outcome; ARDS-related mortality and organ dysfunction were secondary outcomes. Results Patients homozygous for the 4 base pair deletion in the promoter of NFKB1 (del/del) did not have an increased odds ratio (OR) of developing ARDS in unadjusted analysis but were more likely to develop ARDS in the presence of a significant interaction between the del/del genotype and age (OR 5.21, 95% CI 1.35–20.0). In multivariate analysis, patients with ARDS and the del/del genotype also had increased 60 day mortality (HR 1.54, 95% CI 1.01–2.36) and more severe daily organ dysfunction (P<.001) when compared to ARDS patients with other genotypes. Conclusion The del/del genotype is associated with an age-dependent increase in odds of developing ARDS. Patients with the del/del genotype and ARDS also have increased hazard of 60 day mortality and more organ failure.
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Cardinal-Fernández P, Nin N, Lorente JA. [Acute lung injury and acute respiratory distress syndrome: a genomic perspective]. Med Intensiva 2011; 35:361-72. [PMID: 21429625 DOI: 10.1016/j.medin.2011.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 12/20/2010] [Accepted: 02/02/2011] [Indexed: 11/16/2022]
Abstract
Genomics have allowed important advances in the knowledge of the etiology and pathogenesis of complex disease entities such as acute lung injury (ALI) and acute respiratory distress syndrome (ARDS). Genomic medicine aims to personalize and optimize diagnosis, prognosis and treatment by determining the influence of genetic polymorphisms in specific diseases. The scientific community must cope with the important challenge of securing rapid transfer of knowledge to clinical practice, in order to prevent patients from becoming exposed to unnecessary risks. In the present article we describe the main concepts of genomic medicine pertaining to ALI/ARDS, and its currently recognized clinical applications.
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Affiliation(s)
- P Cardinal-Fernández
- Unidad de Cuidados Intensivos, CASMU-IAMPP-Hospital Central de las Fuerzas Armadas, Montevideo, Uruguay.
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Meyer NJ, Li M, Feng R, Bradfield J, Gallop R, Bellamy S, Fuchs BD, Lanken PN, Albelda SM, Rushefski M, Aplenc R, Abramova H, Atochina-Vasserman EN, Beers MF, Calfee CS, Cohen MJ, Pittet JF, Christiani DC, O'Keefe GE, Ware LB, May AK, Wurfel MM, Hakonarson H, Christie JD. ANGPT2 genetic variant is associated with trauma-associated acute lung injury and altered plasma angiopoietin-2 isoform ratio. Am J Respir Crit Care Med 2011; 183:1344-53. [PMID: 21257790 DOI: 10.1164/rccm.201005-0701oc] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
RATIONALE Acute lung injury (ALI) acts as a complex genetic trait, yet its genetic risk factors remain incompletely understood. Large-scale genotyping has not previously been reported for ALI. OBJECTIVES To identify ALI risk variants after major trauma using a large-scale candidate gene approach. METHODS We performed a two-stage genetic association study. We derived findings in an African American cohort (n = 222) using a cardiopulmonary disease-centric 50K single nucleotide polymorphism (SNP) array. Genotype and haplotype distributions were compared between subjects with ALI and without ALI, with adjustment for clinical factors. Top performing SNPs (P < 10(-4)) were tested in a multicenter European American trauma-associated ALI case-control population (n = 600 ALI; n = 2,266 population-based control subjects) for replication. The ALI-associated genomic region was sequenced, analyzed for in silico prediction of function, and plasma was assayed by ELISA and immunoblot. MEASUREMENTS AND MAIN RESULTS Five SNPs demonstrated a significant association with ALI after adjustment for covariates in Stage I. Two SNPs in ANGPT2 (rs1868554 and rs2442598) replicated their significant association with ALI in Stage II. rs1868554 was robust to multiple comparison correction: odds ratio 1.22 (1.06-1.40), P = 0.0047. Resequencing identified predicted novel splice sites in linkage disequilibrium with rs1868554, and immunoblots showed higher proportion of variant angiopoietin-2 (ANG2) isoform associated with rs1868554T (0.81 vs. 0.48; P = 0.038). CONCLUSIONS An ANGPT2 region is associated with both ALI and variation in plasma angiopoietin-2 isoforms. Characterization of the variant isoform and its genetic regulation may yield important insights about ALI pathogenesis and susceptibility.
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Affiliation(s)
- Nuala J Meyer
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
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Bastarache JA, Ong T, Matthay MA, Ware LB. Alveolar fluid clearance is faster in women with acute lung injury compared to men. J Crit Care 2010; 26:249-56. [PMID: 20688464 DOI: 10.1016/j.jcrc.2010.06.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 05/28/2010] [Accepted: 06/14/2010] [Indexed: 01/11/2023]
Abstract
PURPOSE Studies suggest that there is a sex difference in the development and outcomes of acute lung injury (ALI). Few studies have directly addressed the association of sex and alveolar fluid clearance (AFC), a process that is critical to ALI resolution. MATERIALS AND METHODS To test the hypothesis that female sex is associated with an increased AFC rate, we measured AFC rates in 150 mechanically ventilated patients with acute pulmonary edema and a pulmonary edema fluid-to-plasma protein ratio (EF/PL) diagnostic of low permeability (EF/PL <0.65, n = 69) or high permeability (EF/PL ≥0.65, n = 81) edema. We measured protein concentration in serial samples of undiluted EF collected within 6 hours of intubation and calculated net rate of AFC. In addition, plasma levels of receptor for advanced glycation end products were measured as a surrogate marker for alveolar epithelial injury. RESULTS In patients with ALI, women had higher rates of net AFC at 4 hours compared to men (11.9% per hour vs 4.3% per hour, P = .017) and more women had maximal rates of AFC. There were no differences in circulating levels of receptor for advanced glycation end products between men and women. CONCLUSIONS These findings may have significant implications for future ALI studies and potential therapies.
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Affiliation(s)
- Julie A Bastarache
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232-2650, USA.
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Reddy AJ, Kleeberger SR. Genetic polymorphisms associated with acute lung injury. Pharmacogenomics 2009; 10:1527-39. [PMID: 19761373 DOI: 10.2217/pgs.09.89] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Acute lung injury and acute respiratory distress syndrome are the result of intense inflammation in the lungs leading to respiratory failure. The causes of acute lung injury/acute respiratory distress syndrome are numerous (e.g., pneumonia, sepsis and trauma) but the reasons why certain individuals develop lung injury in response to these stimuli and others do not are not well understood. There is ample evidence in the literature that gene-host and gene-environment interactions may play a large role in the morbidity and mortality associated with this syndrome. In this review, we initially discuss methods for identification of candidate acute lung injury/acute respiratory distress syndrome susceptibility genes using a number of model systems including in vitro cell systems and inbred mice. We then describe examples of polymorphisms in genes that have been associated with the pathogenesis of acute lung injury/acute respiratory distress syndrome in human case-control studies. Systematic bench to bedside approaches to understand the genetic contribution to acute lung injury/acute respiratory distress syndrome have provided important insight to this complex disease and continuation of these investigations could lead to the development of novel prevention or intervention strategies.
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Affiliation(s)
- Anita J Reddy
- Respiratory Institute, Cleveland Clinic Health System, OH, USA
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