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Garcia-Vilanova A, Allué-Guardia A, Chacon NM, Akhter A, Singh DK, Kaushal D, Restrepo BI, Schlesinger LS, Turner J, Weintraub ST, Torrelles JB. Proteomic analysis of lung responses to SARS-CoV-2 infection in aged non-human primates: clinical and research relevance. GeroScience 2024:10.1007/s11357-024-01264-3. [PMID: 38969861 DOI: 10.1007/s11357-024-01264-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/21/2024] [Indexed: 07/07/2024] Open
Abstract
With devastating health and socioeconomic impact worldwide, much work is left to understand the Coronavirus Disease 2019 (COVID-19), with emphasis in the severely affected elderly population. Here, we present a proteomics study of lung tissue obtained from aged vs. young rhesus macaques (Macaca mulatta) and olive baboons (Papio Anubis) infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Using age as a variable, we identified common proteomic profiles in the lungs of aged infected non-human primates (NHPs), including key regulators of immune function, as well as cell and tissue remodeling, and discuss the potential clinical relevance of such parameters. Further, we identified key differences in proteomic profiles between both NHP species, and compared those to what is known about SARS-CoV-2 in humans. Finally, we explored the translatability of these animal models in the context of aging and the human presentation of the COVID-19.
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Affiliation(s)
- Andreu Garcia-Vilanova
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA.
| | - Anna Allué-Guardia
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA.
- International Center for the Advancement of Research & Education (I•CARE), Texas Biomedical Research Institute, San Antonio, TX, USA.
| | - Nadine M Chacon
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
- Integrated Biomedical Sciences Program, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Anwari Akhter
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Dhiraj Kumar Singh
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Deepak Kaushal
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Blanca I Restrepo
- International Center for the Advancement of Research & Education (I•CARE), Texas Biomedical Research Institute, San Antonio, TX, USA
- University of Texas Health Science Center at Houston, School of Public Health, Brownsville Campus, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Larry S Schlesinger
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
- International Center for the Advancement of Research & Education (I•CARE), Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Joanne Turner
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
- International Center for the Advancement of Research & Education (I•CARE), Texas Biomedical Research Institute, San Antonio, TX, USA
- Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Jordi B Torrelles
- Population Health, Host Pathogen Interactions, and Disease Prevention and Intervention Programs, Texas Biomedical Research Institute, San Antonio, TX, USA.
- International Center for the Advancement of Research & Education (I•CARE), Texas Biomedical Research Institute, San Antonio, TX, USA.
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2
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Zhang J, Guo Y, Mak M, Tao Z. Translational medicine for acute lung injury. J Transl Med 2024; 22:25. [PMID: 38183140 PMCID: PMC10768317 DOI: 10.1186/s12967-023-04828-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 12/24/2023] [Indexed: 01/07/2024] Open
Abstract
Acute lung injury (ALI) is a complex disease with numerous causes. This review begins with a discussion of disease development from direct or indirect pulmonary insults, as well as varied pathogenesis. The heterogeneous nature of ALI is then elaborated upon, including its epidemiology, clinical manifestations, potential biomarkers, and genetic contributions. Although no medication is currently approved for this devastating illness, supportive care and pharmacological intervention for ALI treatment are summarized, followed by an assessment of the pathophysiological gap between human ALI and animal models. Lastly, current research progress on advanced nanomedicines for ALI therapeutics in preclinical and clinical settings is reviewed, demonstrating new opportunities towards developing an effective treatment for ALI.
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Affiliation(s)
- Jianguo Zhang
- Department of Emergency Medicine, The Affiliated Hospital, Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Yumeng Guo
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Michael Mak
- Department of Biomedical Engineering, School of Engineering and Applied Science, Yale University, New Haven, 06520, USA
| | - Zhimin Tao
- Department of Emergency Medicine, The Affiliated Hospital, Jiangsu University, Zhenjiang, 212001, Jiangsu, China.
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
- Department of Biomedical Engineering, School of Engineering and Applied Science, Yale University, New Haven, 06520, USA.
- Zhenjiang Key Laboratory of High Technology Research on Exosomes Foundation and Transformation Application, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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3
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El-Dehaibi F, Zamora R, Radder J, Yin J, Shah AM, Namas RA, Situ M, Zhao Y, Bain W, Morris A, McVerry BJ, Barclay DA, Billiar TR, Zhang Y, Kitsios GD, Vodovotz Y. A common single nucleotide polymorphism is associated with inflammation and critical illness outcomes. iScience 2023; 26:108333. [PMID: 38034362 PMCID: PMC10684809 DOI: 10.1016/j.isci.2023.108333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/25/2023] [Accepted: 10/22/2023] [Indexed: 12/02/2023] Open
Abstract
Acute inflammation is heterogeneous in critical illness and predictive of outcome. We hypothesized that genetic variability in novel, yet common, gene variants contributes to this heterogeneity and could stratify patient outcomes. We searched algorithmically for significant differences in systemic inflammatory mediators associated with any of 551,839 SNPs in one derivation (n = 380 patients with blunt trauma) and two validation (n = 75 trauma and n = 537 non-trauma patients) cohorts. This analysis identified rs10404939 in the LYPD4 gene. Trauma patients homozygous for the A allele (rs10404939AA; 27%) had different trajectories of systemic inflammation along with persistently elevated multiple organ dysfunction (MOD) indices vs. patients homozygous for the G allele (rs10404939GG; 26%). rs10404939AA homozygotes in the trauma validation cohort had elevated MOD indices, and non-trauma patients displayed more complex inflammatory networks and worse 90-day survival compared to rs10404939GG homozygotes. Thus, rs10404939 emerged as a common, broadly prognostic SNP in critical illness.
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Affiliation(s)
- Fayten El-Dehaibi
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ruben Zamora
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Josiah Radder
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jinling Yin
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ashti M. Shah
- Physician Scientist Training Program, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Rami A. Namas
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Michelle Situ
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yanwu Zhao
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - William Bain
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Bryan J. McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Derek A. Barclay
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Timothy R. Billiar
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Georgios D. Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yoram Vodovotz
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Center for Inflammation and Regeneration Modeling, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Center for Systems Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA
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4
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Suarez-Pajes E, Tosco-Herrera E, Ramirez-Falcon M, Gonzalez-Barbuzano S, Hernandez-Beeftink T, Guillen-Guio B, Villar J, Flores C. Genetic Determinants of the Acute Respiratory Distress Syndrome. J Clin Med 2023; 12:3713. [PMID: 37297908 PMCID: PMC10253474 DOI: 10.3390/jcm12113713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/18/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Acute respiratory distress syndrome (ARDS) is a life-threatening lung condition that arises from multiple causes, including sepsis, pneumonia, trauma, and severe coronavirus disease 2019 (COVID-19). Given the heterogeneity of causes and the lack of specific therapeutic options, it is crucial to understand the genetic and molecular mechanisms that underlie this condition. The identification of genetic risks and pharmacogenetic loci, which are involved in determining drug responses, could help enhance early patient diagnosis, assist in risk stratification of patients, and reveal novel targets for pharmacological interventions, including possibilities for drug repositioning. Here, we highlight the basis and importance of the most common genetic approaches to understanding the pathogenesis of ARDS and its critical triggers. We summarize the findings of screening common genetic variation via genome-wide association studies and analyses based on other approaches, such as polygenic risk scores, multi-trait analyses, or Mendelian randomization studies. We also provide an overview of results from rare genetic variation studies using Next-Generation Sequencing techniques and their links with inborn errors of immunity. Lastly, we discuss the genetic overlap between severe COVID-19 and ARDS by other causes.
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Affiliation(s)
- Eva Suarez-Pajes
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Eva Tosco-Herrera
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Melody Ramirez-Falcon
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Silvia Gonzalez-Barbuzano
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Tamara Hernandez-Beeftink
- Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester LE1 7RH, UK
| | - Beatriz Guillen-Guio
- Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester LE1 7RH, UK
| | - Jesús Villar
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Research Unit, Hospital Universitario de Gran Canaria Dr. Negrín, 35019 Las Palmas de Gran Canaria, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, 35450 Las Palmas de Gran Canaria, Spain
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5
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Whitney JE, Lee IH, Lee JW, Kong SW. Evolution of multiple omics approaches to define pathophysiology of pediatric acute respiratory distress syndrome. eLife 2022; 11:77405. [PMID: 35913450 PMCID: PMC9342956 DOI: 10.7554/elife.77405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 07/20/2022] [Indexed: 11/21/2022] Open
Abstract
Pediatric acute respiratory distress syndrome (PARDS), though both common and deadly in critically ill children, lacks targeted therapies. The development of effective pharmacotherapies has been limited, in part, by lack of clarity about the pathobiology of pediatric ARDS. Epithelial lung injury, vascular endothelial activation, and systemic immune activation are putative drivers of this complex disease process. Prior studies have used either hypothesis-driven (e.g., candidate genes and proteins, in vitro investigations) or unbiased (e.g., genome-wide association, transcriptomic, metabolomic) approaches to predict clinical outcomes and to define subphenotypes. Advances in multiple omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, have permitted more comprehensive investigation of PARDS pathobiology. However, omics studies have been limited in children compared to adults, and analyses across multiple tissue types are lacking. Here, we synthesized existing literature on the molecular mechanism of PARDS, summarized our interrogation of publicly available genomic databases to determine the association of candidate genes with PARDS phenotypes across multiple tissues and cell types, and integrated recent studies that used single-cell RNA sequencing (scRNA-seq). We conclude that novel profiling methods such as scRNA-seq, which permits more comprehensive, unbiased evaluation of pathophysiological mechanisms across tissue and cell types, should be employed to investigate the molecular mechanisms of PRDS toward the goal of identifying targeted therapies.
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Affiliation(s)
- Jane E Whitney
- Medical Critical Care, Pediatrics, Boston Children's Hospital, Boston, United States.,Department of Pediatrics, Harvard Medical School, Boston, United States
| | - In-Hee Lee
- Computational Health and Informatics Program, Boston Children's Hospital, Boston, United States
| | - Ji-Won Lee
- Department of Pharmacology, Faculty and Graduate School of Dental Medicine, Hokkaido University, Sapporo, Japan
| | - Sek Won Kong
- Department of Pediatrics, Harvard Medical School, Boston, United States.,Computational Health and Informatics Program, Boston Children's Hospital, Boston, United States
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6
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Battaglini D, Robba C, Pelosi P, Rocco PRM. Treatment for acute respiratory distress syndrome in adults: A narrative review of phase 2 and 3 trials. Expert Opin Emerg Drugs 2022; 27:187-209. [PMID: 35868654 DOI: 10.1080/14728214.2022.2105833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Ventilatory management and general supportive care of acute respiratory distress syndrome (ARDS) in the adult population have led to significant clinical improvements, but morbidity and mortality remain high. Pharmacologic strategies acting on the coagulation cascade, inflammation, oxidative stress, and endothelial cell injury have been targeted in the last decade for patients with ARDS, but only a few of these have shown potential benefits with a meaningful clinical response and improved patient outcomes. The lack of availability of specific pharmacologic treatments for ARDS can be attributed to its complex pathophysiology, different risk factors, huge heterogeneity, and difficult classification into specific biological phenotypes and genotypes. AREAS COVERED In this narrative review, we briefly discuss the relevance and current advances in pharmacologic treatments for ARDS in adults and the need for the development of new pharmacological strategies. EXPERT OPINION Identification of ARDS phenotypes, risk factors, heterogeneity, and pathophysiology may help to design clinical trials personalized according to ARDS-specific features, thus hopefully decreasing the rate of failed clinical pharmacologic trials. This concept is still under clinical investigation and needs further development.
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Affiliation(s)
- Denise Battaglini
- Dipartimento di Anestesia e Rianimazione, Policlinico San Martino, IRCCS per l'Oncologia e le Neuroscienze, Largo Rosanna Benzi, 10, 16132, Genoa, Italy
| | - Chiara Robba
- Dipartimento di Anestesia e Rianimazione, Policlinico San Martino, IRCCS per l'Oncologia e le Neuroscienze, Largo Rosanna Benzi, 10, 16132, Genoa, Italy.,Dipartimento di Scienze Chirurgiche e Diagnostiche Integrate, Università degli Studi di Genova, Largo Rosanna Benzi, 10, 16132, Genoa, Italy
| | - Paolo Pelosi
- Dipartimento di Anestesia e Rianimazione, Policlinico San Martino, IRCCS per l'Oncologia e le Neuroscienze, Largo Rosanna Benzi, 10, 16132, Genoa, Italy.,Dipartimento di Scienze Chirurgiche e Diagnostiche Integrate, Università degli Studi di Genova, Largo Rosanna Benzi, 10, 16132, Genoa, Italy
| | - Patricia R M Rocco
- Laboratory of Pulmonary Investigation, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Avenida Carlos Chagas Filho, 373, Bloco G1-014, Ilha do Fundão, Rio de Janeiro, RJ 21941-902, Brazil.,COVID-19 Virus Network from Ministry of Science, Technology, and Innovation, Brazilian Council for Scientific and Technological Development, and Foundation Carlos Chagas Filho Research Support of the State of Rio de Janeiro, Rio de Janeiro, Brazil
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7
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Keskinidou C, Vassiliou AG, Dimopoulou I, Kotanidou A, Orfanos SE. Mechanistic Understanding of Lung Inflammation: Recent Advances and Emerging Techniques. J Inflamm Res 2022; 15:3501-3546. [PMID: 35734098 PMCID: PMC9207257 DOI: 10.2147/jir.s282695] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/04/2022] [Indexed: 12/12/2022] Open
Abstract
Acute respiratory distress syndrome (ARDS) is a life-threatening lung injury characterized by an acute inflammatory response in the lung parenchyma. Hence, it is considered as the most appropriate clinical syndrome to study pathogenic mechanisms of lung inflammation. ARDS is associated with increased morbidity and mortality in the intensive care unit (ICU), while no effective pharmacological treatment exists. It is very important therefore to fully characterize the underlying pathobiology and the related mechanisms, in order to develop novel therapeutic approaches. In vivo and in vitro models are important pre-clinical tools in biological and medical research in the mechanistic and pathological understanding of the majority of diseases. In this review, we will present data from selected experimental models of lung injury/acute lung inflammation, which have been based on clinical disorders that can lead to the development of ARDS and related inflammatory lung processes in humans, including ventilation-induced lung injury (VILI), sepsis, ischemia/reperfusion, smoke, acid aspiration, radiation, transfusion-related acute lung injury (TRALI), influenza, Streptococcus (S.) pneumoniae and coronaviruses infection. Data from the corresponding clinical conditions will also be presented. The mechanisms related to lung inflammation that will be covered are oxidative stress, neutrophil extracellular traps, mitogen-activated protein kinase (MAPK) pathways, surfactant, and water and ion channels. Finally, we will present a brief overview of emerging techniques in the field of omics research that have been applied to ARDS research, encompassing genomics, transcriptomics, proteomics, and metabolomics, which may recognize factors to help stratify ICU patients at risk, predict their prognosis, and possibly, serve as more specific therapeutic targets.
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Affiliation(s)
- Chrysi Keskinidou
- First Department of Critical Care Medicine and Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, "Evangelismos" Hospital, Athens, Greece
| | - Alice G Vassiliou
- First Department of Critical Care Medicine and Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, "Evangelismos" Hospital, Athens, Greece
| | - Ioanna Dimopoulou
- First Department of Critical Care Medicine and Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, "Evangelismos" Hospital, Athens, Greece
| | - Anastasia Kotanidou
- First Department of Critical Care Medicine and Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, "Evangelismos" Hospital, Athens, Greece
| | - Stylianos E Orfanos
- First Department of Critical Care Medicine and Pulmonary Services, School of Medicine, National and Kapodistrian University of Athens, "Evangelismos" Hospital, Athens, Greece
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8
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Welker C, Huang J, Gil IJN, Ramakrishna H. 2021 Acute Respiratory Distress Syndrome Update, With Coronavirus Disease 2019 Focus. J Cardiothorac Vasc Anesth 2022; 36:1188-1195. [PMID: 33781671 PMCID: PMC7912364 DOI: 10.1053/j.jvca.2021.02.053] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 12/16/2022]
Abstract
Acute respiratory distress syndrome (ARDS) is a heterogeneous lung disease responsible for significant morbidity and mortality among critically ill patients, including those infected with severe acute respiratory syndrome coronavirus 2, the virus responsible for coronavirus disease 2019. Despite recent advances in pathophysiology, diagnostics, and therapeutics, ARDS is dangerously underdiagnosed, and supportive lung protective ventilation and prone positioning remain the mainstay interventions. Rescue therapies, including neuromuscular blockade and venovenous extracorporeal membrane oxygenation, remain a key component of clinical practice, although benefits are unclear. Even though coronavirus disease 2019 ARDS has some distinguishing features from traditional ARDS, including delayed onset, hyperinflammatory response, and pulmonary microthrombi, it clinically is similar to traditional ARDS and should be treated with established supportive therapies.
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Affiliation(s)
- Carson Welker
- Division of Critical Care Medicine, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN
| | - Jeffrey Huang
- Division of Critical Care Medicine, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN
| | - Iván J. Núñez Gil
- Department of Cardiology, Cardiovascular Institute, Hospital Clínico San Carlos, Madrid, Spain
| | - Harish Ramakrishna
- Division of Cardiovascular and Thoracic Anesthesiology, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN.
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9
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Zheng F, Pan Y, Yang Y, Zeng C, Fang X, Shu Q, Chen Q. Novel biomarkers for acute respiratory distress syndrome: genetics, epigenetics and transcriptomics. Biomark Med 2022; 16:217-231. [PMID: 35026957 DOI: 10.2217/bmm-2021-0749] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Acute respiratory distress syndrome (ARDS) can be induced by multiple clinical factors, including sepsis, acute pancreatitis, trauma, intestinal ischemia/reperfusion and burns. However, these factors alone may poorly explain the risk and outcomes of ARDS. Emerging evidence suggests that genomic-based or transcriptomic-based biomarkers may hold the promise to establish predictive or prognostic stratification methods for ARDS, and also to help in developing novel therapeutic targets for ARDS. Notably, genetic/epigenetic variations correlated with susceptibility and prognosis of ARDS and circulating microRNAs have emerged as potential biomarkers for diagnosis or prognosis of ARDS. Although limited by sample size, ethnicity and phenotypic heterogeneity, ongoing genetic/transcriptomic research contributes to the characterization of novel biomarkers and ultimately helps to develop innovative therapeutics for ARDS patients.
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Affiliation(s)
- Fei Zheng
- Department of Clinical Research Center, The Children's Hospital, School of Medicine, Zhejiang University, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Yihang Pan
- Department of Clinical Research Center, The Children's Hospital, School of Medicine, Zhejiang University, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Yang Yang
- Department of Intensive Care Medicine, The Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Congli Zeng
- Department of Anesthesia, Critical Care & Pain Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xiangming Fang
- Department of Anesthesiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Qiang Shu
- Department of Clinical Research Center, The Children's Hospital, School of Medicine, Zhejiang University, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Qixing Chen
- Department of Clinical Research Center, The Children's Hospital, School of Medicine, Zhejiang University, National Clinical Research Center for Child Health, Hangzhou, 310052, China
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10
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Beitler JR, Thompson BT, Baron RM, Bastarache JA, Denlinger LC, Esserman L, Gong MN, LaVange LM, Lewis RJ, Marshall JC, Martin TR, McAuley DF, Meyer NJ, Moss M, Reineck LA, Rubin E, Schmidt EP, Standiford TJ, Ware LB, Wong HR, Aggarwal NR, Calfee CS. Advancing precision medicine for acute respiratory distress syndrome. THE LANCET. RESPIRATORY MEDICINE 2022; 10:107-120. [PMID: 34310901 PMCID: PMC8302189 DOI: 10.1016/s2213-2600(21)00157-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 12/29/2022]
Abstract
Acute respiratory distress syndrome (ARDS) is a heterogeneous clinical syndrome. Understanding of the complex pathways involved in lung injury pathogenesis, resolution, and repair has grown considerably in recent decades. Nevertheless, to date, only therapies targeting ventilation-induced lung injury have consistently proven beneficial, and despite these gains, ARDS morbidity and mortality remain high. Many candidate therapies with promise in preclinical studies have been ineffective in human trials, probably at least in part due to clinical and biological heterogeneity that modifies treatment responsiveness in human ARDS. A precision medicine approach to ARDS seeks to better account for this heterogeneity by matching therapies to subgroups of patients that are anticipated to be most likely to benefit, which initially might be identified in part by assessing for heterogeneity of treatment effect in clinical trials. In October 2019, the US National Heart, Lung, and Blood Institute convened a workshop of multidisciplinary experts to explore research opportunities and challenges for accelerating precision medicine in ARDS. Topics of discussion included the rationale and challenges for a precision medicine approach in ARDS, the roles of preclinical ARDS models in precision medicine, essential features of cohort studies to advance precision medicine, and novel approaches to clinical trials to support development and validation of a precision medicine strategy. In this Position Paper, we summarise workshop discussions, recommendations, and unresolved questions for advancing precision medicine in ARDS. Although the workshop took place before the COVID-19 pandemic began, the pandemic has highlighted the urgent need for precision therapies for ARDS as the global scientific community grapples with many of the key concepts, innovations, and challenges discussed at this workshop.
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Affiliation(s)
- Jeremy R Beitler
- Center for Acute Respiratory Failure and Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University College of Physicians and Surgeons and New York-Presbyterian Hospital, New York, NY, USA
| | - B Taylor Thompson
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Rebecca M Baron
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Julie A Bastarache
- Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Loren C Denlinger
- Division of Allergy, Pulmonary and Critical Care Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Laura Esserman
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Michelle N Gong
- Division of Pulmonary and Critical Care Medicine, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, NY, USA
| | - Lisa M LaVange
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Roger J Lewis
- Department of Emergency Medicine, Harbor-UCLA Medical Center, Torrance, CA; Berry Consultants, LLC, Austin, TX; Department of Emergency Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - John C Marshall
- Departments of Surgery and Critical Care Medicine, University of Toronto, Toronto, Canada
| | - Thomas R Martin
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Daniel F McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast and Regional Intensive Care Unit, Royal Victoria Hospital, Belfast, Northern Ireland
| | - Nuala J Meyer
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marc Moss
- Division of Pulmonary Sciences and Critical Care, University of Colorado School of Medicine, Aurora, CO, USA
| | - Lora A Reineck
- Division of Lung Diseases, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | | | - Eric P Schmidt
- Division of Pulmonary Sciences and Critical Care, University of Colorado School of Medicine, Aurora, CO, USA
| | - Theodore J Standiford
- Division of Pulmonary & Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Lorraine B Ware
- Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Hector R Wong
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Neil R Aggarwal
- Division of Lung Diseases, National Heart, Lung, and Blood Institute, Bethesda, MD, USA.
| | - Carolyn S Calfee
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, and Department of Anesthesia, University of California San Francisco, San Francisco, CA, USA
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11
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Battaglini D, Al-Husinat L, Normando AG, Leme AP, Franchini K, Morales M, Pelosi P, Rocco PRM. Personalized medicine using omics approaches in acute respiratory distress syndrome to identify biological phenotypes. Respir Res 2022; 23:318. [PMCID: PMC9675217 DOI: 10.1186/s12931-022-02233-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/01/2022] [Indexed: 11/21/2022] Open
Abstract
In the last decade, research on acute respiratory distress syndrome (ARDS) has made considerable progress. However, ARDS remains a leading cause of mortality in the intensive care unit. ARDS presents distinct subphenotypes with different clinical and biological features. The pathophysiologic mechanisms of ARDS may contribute to the biological variability and partially explain why some pharmacologic therapies for ARDS have failed to improve patient outcomes. Therefore, identifying ARDS variability and heterogeneity might be a key strategy for finding effective treatments. Research involving studies on biomarkers and genomic, metabolomic, and proteomic technologies is increasing. These new approaches, which are dedicated to the identification and quantitative analysis of components from biological matrixes, may help differentiate between different types of damage and predict clinical outcome and risk. Omics technologies offer a new opportunity for the development of diagnostic tools and personalized therapy in ARDS. This narrative review assesses recent evidence regarding genomics, proteomics, and metabolomics in ARDS research.
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Affiliation(s)
- Denise Battaglini
- Anesthesia and Intensive Care, San Martino Policlinico Hospital, Instituto di Ricovero e Cura a Carattere Scientifico (IRCCS) for Oncology and Neuroscience, Genoa, Italy ,grid.5606.50000 0001 2151 3065Department of Surgical Science and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy ,grid.5841.80000 0004 1937 0247Department of Medicine, University of Barcelona, Barcelona, Spain
| | - Lou’i Al-Husinat
- grid.14440.350000 0004 0622 5497Department of Clinical Medical Sciences, Faculty of Medicine, Yarmouk University, P.O. Box 566, Irbid, 21163 Jordan
| | - Ana Gabriela Normando
- grid.452567.70000 0004 0445 0877Brazilian Biosciences National Laboratory, LNBio, Brazilian Center for Research in Energy and Materials, CNPEM, Campinas, Brazil
| | - Adriana Paes Leme
- grid.452567.70000 0004 0445 0877Brazilian Biosciences National Laboratory, LNBio, Brazilian Center for Research in Energy and Materials, CNPEM, Campinas, Brazil
| | - Kleber Franchini
- grid.452567.70000 0004 0445 0877Brazilian Biosciences National Laboratory, LNBio, Brazilian Center for Research in Energy and Materials, CNPEM, Campinas, Brazil
| | - Marcelo Morales
- grid.8536.80000 0001 2294 473XLaboratory of Cellular and Molecular Physiology, Carlos Chagas Filho Biophysics Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paolo Pelosi
- Anesthesia and Intensive Care, San Martino Policlinico Hospital, Instituto di Ricovero e Cura a Carattere Scientifico (IRCCS) for Oncology and Neuroscience, Genoa, Italy ,grid.5606.50000 0001 2151 3065Department of Surgical Science and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
| | - Patricia RM Rocco
- grid.8536.80000 0001 2294 473XLaboratory of Pulmonary Investigation, Carlos Chagas Filho Biophysics Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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12
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Nebulization of glutathione and N-Acetylcysteine as an adjuvant therapy for COVID-19 onset. ADVANCES IN REDOX RESEARCH : AN OFFICIAL JOURNAL OF THE SOCIETY FOR REDOX BIOLOGY AND MEDICINE AND THE SOCIETY FOR FREE RADICAL RESEARCH-EUROPE 2021; 3:100015. [PMID: 35425932 PMCID: PMC8349474 DOI: 10.1016/j.arres.2021.100015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/26/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022]
Abstract
Ever since its emergence, the highly transmissible and debilitating coronavirus disease spread at an incredibly fast rate, causing global devastation in a matter of months. SARS-CoV-2, the novel coronavirus responsible for COVID-19, infects hosts after binding to ACE2 receptors present on cells from many structures pertaining to the respiratory, cardiac, hematological, neurological, renal and gastrointestinal systems. COVID-19, however, appears to trigger a severe cytokine storm syndrome in pulmonary structures, resulting in oxidative stress, exacerbated inflammation and alveolar injury. Due to the recent nature of this disease no treatments have shown complete efficacy and safety. More recently, however, researchers have begun to direct some attention towards GSH and NAC. These natural antioxidants play an essential role in several biological processes in the body, especially the maintenance of the redox equilibrium. In fact, many diseases appear to be strongly related to severe oxidative stress and deficiency of endogenous GSH. The high ratios of ROS over GSH, in particular, appear to reflect severity of symptoms and prolonged hospitalization of COVID-19 patients. This imbalance interferes with the body's ability to detoxify the cellular microenvironment, fold proteins, replenish antioxidant levels, maintain healthy immune responses and even modulate apoptotic events. Oral administration of GSH and NAC is convenient and safe, but they are susceptible to degradation in the digestive tract. Considering this drawback, nebulization of GSH and NAC as an adjuvant therapy may therefore be a viable alternative for the management of the early stages of COVID-19.
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13
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Giannini HM, Meyer NJ. Genetics of Acute Respiratory Distress Syndrome: Pathways to Precision. Crit Care Clin 2021; 37:817-834. [PMID: 34548135 DOI: 10.1016/j.ccc.2021.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Clinical risk factors alone fail to fully explain acute respiratory distress syndrome (ARDS) risk or ARDS death, suggesting that individual risk factors contribute. The goals of genomic ARDS studies include better mechanistic understanding, identifying dysregulated pathways that may be amenable to pharmacologic targeting, using genomic causal inference techniques to find measurable traits with meaning, and deconvoluting ARDS heterogeneity by proving reproducible subpopulations that may share a unique biology. This article discusses the latest advances in ARDS genomics, provides historical perspective, and highlights some of the ways that the coronavirus disease 2019 (COVID-19) pandemic is accelerating genomic ARDS research.
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Affiliation(s)
- Heather M Giannini
- University of Pennsylvania Perelman School of Medicine, 3400 Spruce Street, 5038 Gates Building, Philadelphia, PA 19104, USA
| | - Nuala J Meyer
- University of Pennsylvania Perelman School of Medicine, 3400 Spruce Street, 5038 Gates Building, Philadelphia, PA 19104, USA.
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14
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Hamadou WS, Mani R, Bouali N, Besbes S, Bourdon V, El Abed R, Ben Youssef Y, Mari V, Gesta P, Dreyfus H, Bonadona V, Dugast C, Zattara H, Faivre L, Noguchi T, Khélif A, Sobol H, Soua Z. Mutational analysis of apoptotic genes in familial aggregation of hematological malignancies. Bull Cancer 2021; 108:798-805. [PMID: 34140154 DOI: 10.1016/j.bulcan.2021.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 04/14/2021] [Accepted: 04/22/2021] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Apoptosis deregulation have been associated to tumorigenesis process and was highlighted as a prominent hallmark of cancer. Several mutations have been reported in several forms of Blood cancer. However, it has never been investigated in familial aggregations of hematological malignancies. METHODS In this study, we performed a mutational analysis by sequencing the entire coding regions in four key apoptotic genes FAS, FASLG, CASP8 and CASP10 in 92 independent families belonging to French and Tunisian populations and diagnosed with several forms of familial hematological malignancies. RESULTS We report 15 genetic variations among which 7 were previously reported in several form of cancers and have a potential effect on gene expression. Particularly, the CASP8 variants p.Asp302His and p.Lys337Lys were detected in 15% and 10% of our group of patients respectively and were previously reported in association to breast cancer and to breast cancer susceptibility. DISCUSSION In this study, we do not report the underlining deleterious mutations in familial hematological malignancies, but we describe some variants with potential risk of developing blood cancer. To gain further insights on the association between apoptosis pathway deregulation and familial hematological malignancies, more apoptotic genes should be investigated.
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Affiliation(s)
- Walid Sabri Hamadou
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia; Hail university, biology department, Hail, Saudi Arabia.
| | - Rahma Mani
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia
| | - Nouha Bouali
- Hail university, biology department, Hail, Saudi Arabia
| | - Sawsen Besbes
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia
| | - Violaine Bourdon
- Institut Paoli-Calmettes, département d'oncologie génétique, de prévention et dépistage, Marseille, France
| | - Rym El Abed
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia
| | - Yosra Ben Youssef
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia; CHU Farhat Hached, service d'hématologie clinique, Sousse, Tunisia
| | - Véronique Mari
- Centre de lutte contre le cancer, centre Antoine-Lacassagne, service d'oncologie génétique, Nice, France
| | - Paul Gesta
- Centre hospitalier, service d'oncologie génétique, Niort, France
| | | | - Valérie Bonadona
- Centre Léon-Bérard, unité de génétique épidémiologique, Lyon, France
| | | | - Hélène Zattara
- Hôpital de la Timone, département de génétique, Marseille, France
| | | | - Tetsuro Noguchi
- Institut Paoli-Calmettes, département d'oncologie génétique, de prévention et dépistage, Marseille, France
| | - Abderrahim Khélif
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia; CHU Farhat Hached, service d'hématologie clinique, Sousse, Tunisia
| | - Hagay Sobol
- Institut Paoli-Calmettes, département d'oncologie génétique, de prévention et dépistage, Marseille, France
| | - Zohra Soua
- Université de Sousse, faculté de médecine de Sousse, UR biologie moléculaire des leucémies et lymphomes, Sousse, Tunisia
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15
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Bossardi Ramos R, Adam AP. Molecular Mechanisms of Vascular Damage During Lung Injury. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1304:95-107. [PMID: 34019265 DOI: 10.1007/978-3-030-68748-9_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A variety of pulmonary and systemic insults promote an inflammatory response causing increased vascular permeability, leading to the development of acute lung injury (ALI), a condition necessitating hospitalization and intensive care, or the more severe acute respiratory distress syndrome (ARDS), a disease with a high mortality rate. Further, COVID-19 pandemic-associated ARDS is now a major cause of mortality worldwide. The pathogenesis of ALI is explained by injury to both the vascular endothelium and the alveolar epithelium. The disruption of the lung endothelial and epithelial barriers occurs in response to both systemic and local production of pro-inflammatory cytokines. Studies that evaluate the association of genetic polymorphisms with disease risk did not yield many potential therapeutic targets to treat and revert lung injury. This failure is probably due in part to the phenotypic complexity of ALI/ARDS, and genetic predisposition may be obscured by the multiple environmental and behavioral risk factors. In the last decade, new research has uncovered novel epigenetic mechanisms that control ALI/ARDS pathogenesis, including histone modifications and DNA methylation. Enzyme inhibitors such as DNMTi and HDACi may offer new alternative strategies to prevent or reverse the vascular damage that occurs during lung injury. This review will focus on the latest findings on the molecular mechanisms of vascular damage in ALI/ARDS, the genetic factors that might contribute to the susceptibility for developing this disease, and the epigenetic changes observed in humans, as well as in experimental models of ALI/ADRS.
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Affiliation(s)
- Ramon Bossardi Ramos
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA.
| | - Alejandro Pablo Adam
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA. .,Department of Ophthalmology, Albany Medical College, Albany, NY, USA.
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16
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Hess R, Henthorn P, Devoto M, Wang F, Feng R. An Exploratory Association Analysis of the Insulin Gene Region With Diabetes Mellitus in Two Dog Breeds. J Hered 2020; 110:793-800. [PMID: 31587057 PMCID: PMC6916661 DOI: 10.1093/jhered/esz059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/03/2019] [Indexed: 02/07/2023] Open
Abstract
Samoyeds and Australian Terriers are the 2 dog breeds at highest risk (>10-fold) for diabetes mellitus in the United States. It is unknown if the insulin (INS) gene is involved in the pathophysiology of diabetes in Samoyeds and Australian Terriers. It was hypothesized that the INS gene region provides a common genetic causality for diabetes in Samoyeds and Australian Terriers. We conducted a 2-stage genetic association study involving both breeds. In the discovery stage (Stage 1), Samoyeds with and without diabetes were compared in the frequencies of 447 tagging single-nucleotide polymorphisms (SNPs) within 2.5 megabases (Mb) up- and downstream of the INS gene on the Illumina CanineHD BeadChip. SNPs yielding a P-value < 0.005 were selected for further follow-up. In the validation stage (Stage 2), Australian Terriers with and without diabetes were compared in the SNPs genotyped by the Affymetrix GeneChip Canine Genome 2.0 Array and within 1 Mb up- and downstream of the selected SNPs from Stage 1. Two SNPs that were in high linkage disequilibrium (LD, r2 = 0.7) were selected from Stage 1. In Stage 2, among the 76 SNPs examined, 5 were significantly associated with diabetes after Bonferroni's correction for multiple comparisons. Three of these 5 SNPs were in complete LD (r2 = 1 for all associations) and the 2 remaining SNPs were in moderate LD (r2 = 0.4). In conclusion, an association between the INS gene region and diabetes was suggested in 2 dog breeds of different clades. This region could have importance in diabetes in other breeds or in canine diabetes at large.
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Affiliation(s)
- Rebecka Hess
- Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA
| | - Paula Henthorn
- Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA
| | - Marcella Devoto
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Translational and Precision Medicine, University of Rome Sapienza, Rome, Italy
| | - Fan Wang
- Department of Molecular Cardiology, Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | - Rui Feng
- Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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17
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Byrnes D, Masterson CH, Artigas A, Laffey JG. Mesenchymal Stem/Stromal Cells Therapy for Sepsis and Acute Respiratory Distress Syndrome. Semin Respir Crit Care Med 2020; 42:20-39. [PMID: 32767301 DOI: 10.1055/s-0040-1713422] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Sepsis and acute respiratory distress syndrome (ARDS) constitute devastating conditions with high morbidity and mortality. Sepsis results from abnormal host immune response, with evidence for both pro- and anti-inflammatory activation present from the earliest phases. The "proinflammatory" response predominates initially causing host injury, with later-phase sepsis characterized by immune cell hypofunction and opportunistic superinfection. ARDS is characterized by inflammation and disruption of the alveolar-capillary membrane leading to injury and lung dysfunction. Sepsis is the most common cause of ARDS. Approximately 20% of deaths worldwide in 2017 were due to sepsis, while ARDS occurs in over 10% of all intensive care unit patients and results in a mortality of 30 to 45%. Given the fact that sepsis and ARDS share some-but not all-underlying pathophysiologic injury mechanisms, the lack of specific therapies, and their frequent coexistence in the critically ill, it makes sense to consider therapies for both conditions together. In this article, we will focus on the therapeutic potential of mesenchymal stem/stromal cells (MSCs). MSCs are available from several tissues, including bone marrow, umbilical cord, and adipose tissue. Allogeneic administration is feasible, an important advantage for acute conditions like sepsis or ARDS. They possess diverse mechanisms of action of relevance to sepsis and ARDS, including direct and indirect antibacterial actions, potent effects on the innate and adaptive response, and pro-reparative effects. MSCs can be preactivated thereby potentiating their effects, while the use of their extracellular vesicles can avoid whole cell administration. While early-phase clinical trials suggest safety, considerable challenges exist in moving forward to phase III efficacy studies, and to implementation as a therapy should they prove effective.
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Affiliation(s)
- Declan Byrnes
- Department of Anaesthesia, School of Medicine, Clinical Sciences Institute, National University of Ireland, Galway, Ireland.,Regenerative Medicine Institute (REMEDI), CÚRAM Centre for Research in Medical Devices, National University of Ireland Galway, Galway, Ireland
| | - Claire H Masterson
- Department of Anaesthesia, School of Medicine, Clinical Sciences Institute, National University of Ireland, Galway, Ireland.,Regenerative Medicine Institute (REMEDI), CÚRAM Centre for Research in Medical Devices, National University of Ireland Galway, Galway, Ireland
| | - Antonio Artigas
- Critical Care Center, Corporació Sanitaria Parc Tauli, CIBER Enfermedades Respiratorias, Autonomous University of Barcelona, Sabadell, Spain
| | - John G Laffey
- Department of Anaesthesia, School of Medicine, Clinical Sciences Institute, National University of Ireland, Galway, Ireland.,Regenerative Medicine Institute (REMEDI), CÚRAM Centre for Research in Medical Devices, National University of Ireland Galway, Galway, Ireland.,Department of Anaesthesia, SAOLTA University Health Group, Galway University Hospitals, Galway, Ireland
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18
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Guillen-Guio B, Lorenzo-Salazar JM, Ma SF, Hou PC, Hernandez-Beeftink T, Corrales A, García-Laorden MI, Jou J, Espinosa E, Muriel A, Domínguez D, Lorente L, Martín MM, Rodríguez-Gallego C, Solé-Violán J, Ambrós A, Carriedo D, Blanco J, Añón JM, Reilly JP, Jones TK, Ittner CA, Feng R, Schöneweck F, Kiehntopf M, Noth I, Scholz M, Brunkhorst FM, Scherag A, Meyer NJ, Villar J, Flores C. Sepsis-associated acute respiratory distress syndrome in individuals of European ancestry: a genome-wide association study. THE LANCET RESPIRATORY MEDICINE 2020; 8:258-266. [PMID: 31982041 DOI: 10.1016/s2213-2600(19)30368-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/25/2019] [Accepted: 08/07/2019] [Indexed: 12/30/2022]
Abstract
BACKGROUND Acute respiratory distress syndrome (ARDS) is a lung inflammatory process caused mainly by sepsis. Most previous studies that identified genetic risks for ARDS focused on candidates with biological relevance. We aimed to identify novel genetic variants associated with ARDS susceptibility and to provide complementary functional evidence of their effect in gene regulation. METHODS We did a case-control genome-wide association study (GWAS) of 1935 European individuals, using patients with sepsis-associated ARDS as cases and patients with sepsis without ARDS as controls. The discovery stage included 672 patients admitted into a network of Spanish intensive care units between January, 2002, and January, 2017. The replication stage comprised 1345 individuals from two independent datasets from the MESSI cohort study (Sep 22, 2008-Nov 30, 2017; USA) and the VISEP (April 1, 2003-June 30, 2005) and MAXSEP (Oct 1, 2007-March 31, 2010) trials of the SepNet study (Germany). Results from discovery and replication stages were meta-analysed to identify association signals. We then used RNA sequencing data from lung biopsies, in-silico analyses, and luciferase reporter assays to assess the functionallity of associated variants. FINDINGS We identified a novel genome-wide significant association with sepsis-associated ARDS susceptibility (rs9508032, odds ratio [OR] 0·61, 95% CI 0·41-0·91, p=5·18 × 10-8) located within the Fms-related tyrosine kinase 1 (FLT1) gene, which encodes vascular endothelial growth factor receptor 1 (VEGFR-1). The region containing the sentinel variant and its best proxies acted as a silencer for the FLT1 promoter, and alleles with protective effects in ARDS further reduced promoter activity (p=0·0047). A literature mining of all previously described ARDS genes validated the association of vascular endothelial growth factor A (VEGFA; OR 0·55, 95% CI 0·41-0·73; p=4·69 × 10-5). INTERPRETATION A common variant within the FLT1 gene is associated with sepsis-associated ARDS. Our findings support a role for the vascular endothelial growth factor signalling pathway in ARDS pathogenesis and identify VEGFR-1 as a potential therapeutic target. FUNDING Instituto de Salud Carlos III, European Regional Development Funds, Instituto Tecnológico y de Energías Renovables.
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Affiliation(s)
- Beatriz Guillen-Guio
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Jose M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Shwu-Fan Ma
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Pei-Chi Hou
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Tamara Hernandez-Beeftink
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain; Research Unit, Hospital Universitario de Gran Canaria Dr Negrín, Las Palmas de Gran Canaria, Spain
| | - Almudena Corrales
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - M Isabel García-Laorden
- Research Unit, Hospital Universitario de Gran Canaria Dr Negrín, Las Palmas de Gran Canaria, Spain; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Jonathan Jou
- University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Elena Espinosa
- Department of Anesthesiology, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Arturo Muriel
- Intensive Care Unit, Hospital Universitario Rio Hortega, Valladolid, Spain
| | - David Domínguez
- Department of Anesthesiology, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Leonardo Lorente
- Intensive Care Unit, Hospital Universitario de Canarias, La Laguna, Tenerife, Spain
| | - María M Martín
- Intensive Care Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Carlos Rodríguez-Gallego
- Department of Immunology, Hospital Universitario de Gran Canaria Dr Negrín, Las Palmas de Gran Canaria, Spain
| | - Jordi Solé-Violán
- Intensive Care Unit, Hospital Universitario de Gran Canaria Dr Negrín, Las Palmas de Gran Canaria, Spain; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Alfonso Ambrós
- Intensive Care Unit, Hospital General de Ciudad Real, Ciudad Real, Spain
| | - Demetrio Carriedo
- Intensive Care Unit, Complejo Hospitalario Universitario de León, León, Spain
| | - Jesús Blanco
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Intensive Care Unit, Hospital Universitario Rio Hortega, Valladolid, Spain
| | - José M Añón
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Intensive Care Unit, Hospital Universitario La Paz, IdiPAZ, Madrid, Spain
| | - John P Reilly
- Division of Pulmonary, Allergy, and Critical Care Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Tiffanie K Jones
- Division of Pulmonary, Allergy, and Critical Care Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Caroline Ag Ittner
- Division of Pulmonary, Allergy, and Critical Care Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Rui Feng
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia PA, USA
| | - Franziska Schöneweck
- Integrated Research and Treatment Center, Jena University Hospital, Jena, Germany
| | - Michael Kiehntopf
- Center for Sepsis Control and Care, Institute of Clinical Chemistry and Laboratory Diagnostics, Jena University Hospital, Jena, Germany; Integrated Biobank Jena, Jena University Hospital, Jena, Germany
| | - Imre Noth
- Division of Pulmonary & Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Frank M Brunkhorst
- Center for Clinical Studies, Jena University Hospital, Jena, Germany; Paul-Martini-Clinical Sepsis Research Unit, Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany
| | - André Scherag
- Integrated Research and Treatment Center, Jena University Hospital, Jena, Germany; Institute of Medical Statistics, Computer and Data Sciences, Jena University Hospital, Jena, Germany
| | - Nuala J Meyer
- Division of Pulmonary, Allergy, and Critical Care Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Jesús Villar
- Research Unit, Hospital Universitario de Gran Canaria Dr Negrín, Las Palmas de Gran Canaria, Spain; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Keenan Research Center for Biomedical Sciences at the Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, Canada
| | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain; Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.
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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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21
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Gomez JL, Himes BE, Kaminski N. Precision Medicine in Critical Illness: Sepsis and Acute Respiratory Distress Syndrome. PRECISION IN PULMONARY, CRITICAL CARE, AND SLEEP MEDICINE 2019. [PMCID: PMC7120471 DOI: 10.1007/978-3-030-31507-8_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Sepsis and the acute respiratory distress syndrome (ARDS) each cause substantial morbidity and mortality. In contrast to other lung diseases, the entire course of disease in these syndromes is measured in days to weeks rather than months to years, which raises unique challenges in achieving precision medicine. We review advances in sepsis and ARDS resulting from omics studies, including those involving genome-wide association, gene expression, targeted proteomics, and metabolomics approaches. We focus on promising evidence of biological subtypes in both sepsis and ARDS that consistently display high risk for death. In sepsis, a gene expression signature with dysregulated adaptive immune signaling has evidence for a differential response to systemic steroid therapy, whereas in ARDS, a hyperinflammatory pattern identified in plasma using targeted proteomics responded more favorably to randomized interventions including high positive end-expiratory pressure, volume conservative fluid therapy, and simvastatin therapy. These early examples suggest heterogeneous biology that may be challenging to detect by clinical factors alone and speak to the promise of a precision approach that targets the right treatment at the right time to the right patient.
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Affiliation(s)
- Jose L. Gomez
- Assistant Professor Pulmonary, Critical Care and Sleep Medicine Section, Department of Medicine, Yale University School of Medicine, New Haven, CT USA
| | - Blanca E. Himes
- Assistant Professor of Informatics, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA USA
| | - Naftali Kaminski
- Boehringer-Ingelheim Endowed, Professor of Internal Medicine, Chief of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT USA
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22
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Kuldanek SA, Kelher M, Silliman CC. Risk factors, management and prevention of transfusion-related acute lung injury: a comprehensive update. Expert Rev Hematol 2019; 12:773-785. [PMID: 31282773 PMCID: PMC6715498 DOI: 10.1080/17474086.2019.1640599] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 07/03/2019] [Indexed: 12/13/2022]
Abstract
Introduction: Despite mitigation strategies that include the exclusion of females from plasma donation or the exclusion of females with a history of pregnancy or known anti-leukocyte antibody, transfusion-related acute lung injury (TRALI) remains a leading cause of transfusion-related morbidity and mortality. Areas covered: The definition of TRALI is discussed and re-aligned with the new Berlin Diagnostic Criteria for the acute respiratory distress syndrome (ARDS). The risk factors associated with TRALI are summarized as are the mitigation strategies to further reduce TRALI. The emerging basic research studies that may translate to clinical therapeutics for the prevention or treatment of TRALI are discussed. Expert opinion: At risk patients, including the genetic factors that may predispose patients to TRALI are summarized and discussed. The re-definition of TRALI employing the Berlin Criteria for ARDS will allow for increased recognition and improved research into pathophysiology and mitigation to reduce this fatal complication of hemotherapy.
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Affiliation(s)
- Susan A. Kuldanek
- The Division of Transfusion Medicine, School of Medicine University of Colorado Denver, Aurora, CO, USA
- Department of Pathology, School of Medicine University of Colorado Denver, Aurora, CO, USA
- Department of Pediatrics, School of Medicine University of Colorado Denver, Aurora, CO, USA
| | - Marguerite Kelher
- Department of Surgery, School of Medicine University of Colorado Denver, Aurora, CO, USA
| | - Christopher C. Silliman
- Department of Pediatrics, School of Medicine University of Colorado Denver, Aurora, CO, USA
- Department of Surgery, School of Medicine University of Colorado Denver, Aurora, CO, USA
- Vitalant Research Institute, Vitalant Mountain Division, Denver, CO, USA
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23
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Hernández-Beeftink T, Guillen-Guio B, Villar J, Flores C. Genomics and the Acute Respiratory Distress Syndrome: Current and Future Directions. Int J Mol Sci 2019; 20:E4004. [PMID: 31426444 PMCID: PMC6721149 DOI: 10.3390/ijms20164004] [Citation(s) in RCA: 19] [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] [Received: 07/17/2019] [Revised: 08/05/2019] [Accepted: 08/11/2019] [Indexed: 12/19/2022] Open
Abstract
The excessive hospital mortality associated with acute respiratory distress syndrome (ARDS) in adults mandates an urgent need for developing new therapies and tools for the early risk assessment of these patients. ARDS is a heterogeneous syndrome with multiple different pathogenetic processes contributing differently in different patients depending on clinical as well as genetic factors. Identifying genetic-based biomarkers holds the promise for establishing effective predictive and prognostic stratification methods and for targeting new therapies to improve ARDS outcomes. Here we provide an updated review of the available evidence supporting the presence of genetic factors that are predictive of ARDS development and of fatal outcomes in adult critically ill patients and that have been identified by applying different genomic and genetic approaches. We also introduce other incipient genomics approximations, such as admixture mapping, metagenomics and genome sequencing, among others, that will allow to boost this knowledge and likely reveal new genetic predictors of ARDS susceptibility and prognosis among critically ill patients.
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Affiliation(s)
- Tamara Hernández-Beeftink
- Research Unit, Hospital Universitario Dr. Negrín, Las Palmas de Gran Canaria 35010, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife 38010, Spain
| | - Beatriz Guillen-Guio
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife 38010, Spain
| | - Jesús Villar
- Research Unit, Hospital Universitario Dr. Negrín, Las Palmas de Gran Canaria 35010, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife 38010, Spain.
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid 28029, Spain.
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife 38600, Spain.
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Santa Cruz de Tenerife 38200, Spain.
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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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25
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Duan X, Gan J, Peng DY, Bao Q, Xiao L, Wei L, Wu J. Identification and functional analysis of microRNAs in rats following focal cerebral ischemia injury. Mol Med Rep 2019; 19:4175-4184. [PMID: 30896823 PMCID: PMC6471137 DOI: 10.3892/mmr.2019.10073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 02/22/2019] [Indexed: 01/08/2023] Open
Abstract
MicroRNA sequencing (miRNA‑seq) was performed in the present study to investigate miRNA expression profiles in infarcted brain areas following focal cerebral ischemia induced by middle cerebral artery occlusion in rats. In total, 20 miRNAs were identified to be upregulated and 17 to be downregulated in the infarct area. The expression levels of six differentially expressed miRNAs (DEmiRs), miR‑211‑5p, miR‑183‑5p, miR‑10b‑3p, miR‑182, miR‑217‑5p and miR‑96‑5p, were examined by reverse transcription‑quantitative polymerase chain reaction. Subsequently, a miRNA‑mRNA network was constructed. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed to investigate the functions of the mRNAs targeted by these DEmiRs. The present study aimed to investigate the association between miRNAs and cerebral ischemia to provide potential insight into the molecular mechanisms underlying ischemic stroke.
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Affiliation(s)
- Xianchun Duan
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui 230012, P.R. China
| | - Jianghua Gan
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui 230012, P.R. China
| | - Dai-Yin Peng
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui 230012, P.R. China
| | - Qiuyu Bao
- School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, P.R. China
| | - Ling Xiao
- School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, P.R. China
| | - Liangbing Wei
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui 230012, P.R. China
| | - Jian Wu
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui 230012, P.R. China
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26
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Lin S, Yue X, Wu H, Han TL, Zhu J, Wang C, Lei M, Zhang M, Liu Q, Xu F. Explore potential plasma biomarkers of acute respiratory distress syndrome (ARDS) using GC-MS metabolomics analysis. Clin Biochem 2019; 66:49-56. [PMID: 30779905 DOI: 10.1016/j.clinbiochem.2019.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/06/2019] [Accepted: 02/15/2019] [Indexed: 12/16/2022]
Abstract
OBJECTIVES The aim of this study was to analyse the metabolomics of patients with acute respiratory distress syndrome (ARDS) for the identification of metabolic markers with potential diagnostic and prognostic value. METHODS The enrolled subjects included adult patients with ARDS that met the Berlin definition and healthy controls matched based on age, gender, and body mass index (BMI). Plasma samples were collected from 37 patients with ARDS and 28 healthy controls. The plasma metabolites were detected with gas chromatography-mass spectrometry (GC-MS), and the relevant metabolic pathways were predicted using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. RESULTS A total of 222 metabolites were identified in our study, of which 128 were significantly altered in patients with ARDS compared with healthy controls. Phenylalanine, aspartic acid, and carbamic acid levels were significantly different between all groups of patients with ARDS classified from mild to severe. Furthermore, four metabolites, ornithine, caprylic acid, azetidine, and iminodiacetic acid, could serve as biomarkers to potentially predict the severity of ARDS. We discovered 92 pathways that were significantly different between ARDS and control groups, including 57 pathways linked to metabolism. CONCLUSIONS Plasma metabolomics may improve our understanding of ARDS biology. Specific products related to hypoxia may serve as early biomarkers for ARDS prediction, while the metabolites with significant correlations with partial pressure of arterial oxygen (PaO2)/percentage of inspired oxygen (FiO2) may play a role in determining ARDS severity. This study suggests that metabolomic analysis in patients at risk of ARDS or those with early ARDS may provide new insight into disease pathogenesis or prognosis.
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Affiliation(s)
- Shihui Lin
- The Chongqing Key Laboratory of Translation Medicine in Major Metabolic Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Departmen of Emergency and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, China
| | - Xi Yue
- Departmen of Emergency and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, China
| | - Hua Wu
- Stanford University, Center for Cognitive and Neurobiological Imaging, Palo Alto, CA, USA
| | - Ting-Li Han
- China-Canada-New Zealand Jointed International Mass Spectrometry Center of Maternal-Fetal Medicine, Chongqing Medical University, China; University of Auckland, Liggins Institute, Auckland, NZ, New Zealand
| | - Jing Zhu
- Departmen of Emergency and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, China
| | - Chuanjiang Wang
- Departmen of Emergency and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, China
| | - Ming Lei
- Departmen of Emergency and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, China
| | - Mu Zhang
- Departmen of Emergency and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, China
| | - Qiong Liu
- Departmen of Emergency and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, China
| | - Fang Xu
- Departmen of Emergency and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, China.
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Abstract
Acute respiratory distress syndrome (ARDS) is a syndrome of acute respiratory failure caused by noncardiogenic pulmonary edema. Despite five decades of basic and clinical research, there is still no effective pharmacotherapy for this condition and the treatment remains primarily supportive. It is critical to study the molecular and physiologic mechanisms that cause ARDS to improve our understanding of this syndrome and reduce mortality. The goal of this review is to describe our current understanding of the pathogenesis and pathophysiology of ARDS. First, we will describe how pulmonary edema fluid accumulates in ARDS due to lung inflammation and increased alveolar endothelial and epithelial permeabilities. Next, we will review how pulmonary edema fluid is normally cleared in the uninjured lung, and describe how these pathways are disrupted in ARDS. Finally, we will explain how clinical trials and preclinical studies of novel therapeutic agents have further refined our understanding of this condition, highlighting, in particular, the study of mesenchymal stromal cells in the treatment of ARDS.
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Affiliation(s)
- Laura A. Huppert
- Department of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Michael A. Matthay
- Departments of Medicine and Anesthesia, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA USA
| | - Lorraine B. Ware
- Department of Medicine, Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, TN USA
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28
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Spadaro S, Park M, Turrini C, Tunstall T, Thwaites R, Mauri T, Ragazzi R, Ruggeri P, Hansel TT, Caramori G, Volta CA. Biomarkers for Acute Respiratory Distress syndrome and prospects for personalised medicine. JOURNAL OF INFLAMMATION-LONDON 2019; 16:1. [PMID: 30675131 PMCID: PMC6332898 DOI: 10.1186/s12950-018-0202-y] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 11/22/2018] [Indexed: 12/11/2022]
Abstract
Acute lung injury (ALI) affects over 10% of patients hospitalised in critical care, with acute respiratory distress syndrome (ARDS) being the most severe form of ALI and having a mortality rate in the region of 40%. There has been slow but incremental progress in identification of biomarkers that contribute to the pathophysiology of ARDS, have utility in diagnosis and monitoring, and that are potential therapeutic targets (Calfee CS, Delucchi K, Parsons PE, Thompson BT, Ware LB, Matthay MA, Thompson T, Ware LB, Matthay MA, Lancet Respir Med 2014, 2:611–-620). However, a major issue is that ARDS is such a heterogeneous, multi-factorial, end-stage condition that the strategies for “lumping and splitting” are critical (Prescott HC, Calfee CS, Thompson BT, Angus DC, Liu VX, Am J Respir Crit Care Med 2016, 194:147–-155). Nevertheless, sequencing of the human genome, the availability of improved methods for analysis of transcription to mRNA (gene expression), and development of sensitive immunoassays has allowed the application of network biology to ARDS, with these biomarkers offering potential for personalised or precision medicine (Sweeney TE, Khatri P, Toward precision medicine Crit Care Med; 2017 45:934-939). Biomarker panels have potential applications in molecular phenotyping for identifying patients at risk of developing ARDS, diagnosis of ARDS, risk stratification and monitoring. Two subphenotypes of ARDS have been identified on the basis of blood biomarkers: hypo-inflammatory and hyper-inflammatory. The hyper-inflammatory subphenotype is associated with shock, metabolic acidosis and worst clinical outcomes. Biomarkers of particular interest have included interleukins (IL-6 and IL-8), interferon gamma (IFN-γ), surfactant proteins (SPD and SPB), von Willebrand factor antigen, angiopoietin 1/2 and plasminogen activator inhibitor-1 (PAI-1). In terms of gene expression (mRNA) in blood there have been found to be increases in neutrophil-related genes in sepsis-induced and influenza-induced ARDS, but whole blood expression does not give a robust diagnostic test for ARDS. Despite improvements in management of ARDS on the critical care unit, this complex disease continues to be a major life-threatening event. Clinical trials of β2-agonists, statins, surfactants and keratinocyte growth factor (KGF) have been disappointing. In addition, monoclonal antibodies (anti-TNF) and TNFR fusion protein have also been unconvincing. However, there have been major advances in methods of mechanical ventilation, a neuromuscular blocker (cisatracurium besilate) has shown some benefit, and stem cell therapy is being developed. In the future, by understanding the role of biomarkers in the pathophysiology of ARDS and lung injury, it is hoped that this will provide rational therapeutic targets and ultimately improve clinical care (Seymour CW, Gomez H, Chang CH, Clermont G, Kellum JA, Kennedy J, Yende S, Angus DC, Crit Care 2017, 21:257).
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Affiliation(s)
- Savino Spadaro
- 1Department of Morphology, Surgery and Experimental Medicine, Intensive Care Section, University of Ferrara, 44121 Ferrara, Italy
| | - Mirae Park
- 2Faculty of Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Cecilia Turrini
- 1Department of Morphology, Surgery and Experimental Medicine, Intensive Care Section, University of Ferrara, 44121 Ferrara, Italy
| | - Tanushree Tunstall
- 2Faculty of Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Ryan Thwaites
- 2Faculty of Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Tommaso Mauri
- 3Department of Anesthesia, Critical Care and Emergency, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Riccardo Ragazzi
- 1Department of Morphology, Surgery and Experimental Medicine, Intensive Care Section, University of Ferrara, 44121 Ferrara, Italy
| | - Paolo Ruggeri
- 4Unità Operativa Complessa di Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy
| | - Trevor T Hansel
- 2Faculty of Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Gaetano Caramori
- 4Unità Operativa Complessa di Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy
| | - Carlo Alberto Volta
- 1Department of Morphology, Surgery and Experimental Medicine, Intensive Care Section, University of Ferrara, 44121 Ferrara, Italy
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High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report. Ann Am Thorac Soc 2019; 16:1-16. [PMID: 30592451 PMCID: PMC6812157 DOI: 10.1513/annalsats.201810-716ws] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
High-throughput, "next-generation" sequencing methods are now being broadly applied across all fields of biomedical research, including respiratory disease, critical care, and sleep medicine. Although there are numerous review articles and best practice guidelines related to sequencing methods and data analysis, there are fewer resources summarizing issues related to study design and interpretation, especially as applied to common, complex, nonmalignant diseases. To address these gaps, a single-day workshop was held at the American Thoracic Society meeting in May 2017, led by the American Thoracic Society Section on Genetics and Genomics. The aim of this workshop was to review the design, analysis, interpretation, and functional follow-up of high-throughput sequencing studies in respiratory, critical care, and sleep medicine research. This workshop brought together experts in multiple fields, including genetic epidemiology, biobanking, bioinformatics, and research ethics, along with physician-scientists with expertise in a range of relevant diseases. The workshop focused on application of DNA and RNA sequencing research in common chronic diseases and did not cover sequencing studies in lung cancer, monogenic diseases (e.g., cystic fibrosis), or microbiome sequencing. Participants reviewed and discussed study design, data analysis and presentation, interpretation, functional follow-up, and reporting of results. This report summarizes the main conclusions of the workshop, specifically addressing the application of these methods in respiratory, critical care, and sleep medicine research. This workshop report may serve as a resource for our research community as well as for journal editors and reviewers of sequencing-based manuscript submissions in our research field.
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Lin Z, Thorenoor N, Wu R, DiAngelo SL, Ye M, Thomas NJ, Liao X, Lin TR, Warren S, Floros J. Genetic Association of Pulmonary Surfactant Protein Genes, SFTPA1, SFTPA2, SFTPB, SFTPC, and SFTPD With Cystic Fibrosis. Front Immunol 2018; 9:2256. [PMID: 30333828 PMCID: PMC6175982 DOI: 10.3389/fimmu.2018.02256] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 09/11/2018] [Indexed: 01/03/2023] Open
Abstract
Surfactant proteins (SP) are involved in surfactant function and innate immunity in the human lung. Both lung function and innate immunity are altered in CF, and altered SP levels and genetic association are observed in Cystic Fibrosis (CF). We hypothesized that single nucleotide polymorphisms (SNPs) within the SP genes associate with CF or severity subgroups, either through single SNP or via SNP-SNP interactions between two SNPs of a given gene (intragenic) and/or between two genes (intergenic). We genotyped a total of 17 SP SNPs from 72 case-trio pedigree (SFTPA1 (5), SFTPA2 (4), SFTPB (4), SFTPC (2), and SFTPD (2)), and identified SP SNP associations by applying quantitative genetic principles. The results showed (a) Two SNPs, SFTPB rs7316 (p = 0.0083) and SFTPC rs1124 (p = 0.0154), each associated with CF. (b) Three intragenic SNP-SNP interactions, SFTPB (rs2077079, rs3024798), and SFTPA1 (rs1136451, rs1059057 and rs4253527), associated with CF. (c) A total of 34 intergenic SNP-SNP interactions among the 4 SP genes to be associated with CF. (d) No SNP-SNP interaction was observed between SFTPA1 or SFTPA2 and SFTPD. (e) Equal number of SNP-SNP interactions were observed between SFTPB and SFTPA1/SFTPA2 (n = 7) and SP-B and SFTPD (n = 7). (f) SFTPC exhibited significant SNP-SNP interactions with SFTPA1/SFTPA2 (n = 11), SFTPB (n = 4) and SFTPD (n = 3). (g) A single SFTPB SNP was associated with mild CF after Bonferroni correction, and several intergenic interactions that are associated (p < 0.01) with either mild or moderate/severe CF were observed. These collectively indicate that complex SNP-SNP interactions of the SP genes may contribute to the pulmonary disease in CF patients. We speculate that SPs may serve as modifiers for the varied progression of pulmonary disease in CF and/or its severity.
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Affiliation(s)
- Zhenwu Lin
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Nithyananda Thorenoor
- Department of Pediatrics, Center for Host Defense, Inflammation, and Lung Disease (CHILD) Research, Pennsylvania State University, Hershey, PA, United States
| | - Rongling Wu
- Public Health Science, College of Medicine, Pennsylvania State University, Hershey, PA, United States
| | - Susan L DiAngelo
- Department of Pediatrics, Center for Host Defense, Inflammation, and Lung Disease (CHILD) Research, Pennsylvania State University, Hershey, PA, United States
| | - Meixia Ye
- Public Health Science, College of Medicine, Pennsylvania State University, Hershey, PA, United States.,Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Neal J Thomas
- Department of Pediatrics, Center for Host Defense, Inflammation, and Lung Disease (CHILD) Research, Pennsylvania State University, Hershey, PA, United States
| | - Xiaojie Liao
- Department of Pediatrics, Center for Host Defense, Inflammation, and Lung Disease (CHILD) Research, Pennsylvania State University, Hershey, PA, United States
| | - Tony R Lin
- Department of Pediatrics, Center for Host Defense, Inflammation, and Lung Disease (CHILD) Research, Pennsylvania State University, Hershey, PA, United States
| | - Stuart Warren
- Department of Pediatrics, Center for Host Defense, Inflammation, and Lung Disease (CHILD) Research, Pennsylvania State University, Hershey, PA, United States
| | - Joanna Floros
- Department of Pediatrics, Center for Host Defense, Inflammation, and Lung Disease (CHILD) Research, Pennsylvania State University, Hershey, PA, United States.,Obstetrics and Gynecology, Pennsylvania State University College of Medicine, Hershey, PA, United States
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31
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Hernandez-Pacheco N, Guillen-Guio B, Acosta-Herrera M, Pino-Yanes M, Corrales A, Ambrós A, Nogales L, Muriel A, González-Higueras E, Diaz-Dominguez FJ, Zavala E, Belda J, Ma SF, Villar J, Flores C. A vascular endothelial growth factor receptor gene variant is associated with susceptibility to acute respiratory distress syndrome. Intensive Care Med Exp 2018; 6:16. [PMID: 29987654 PMCID: PMC6037659 DOI: 10.1186/s40635-018-0181-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/20/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The acute respiratory distress syndrome (ARDS) is one of the main causes of mortality in adults admitted to intensive care units. Previous studies have demonstrated the existence of genetic variants involved in the susceptibility and outcomes of this syndrome. We aimed to identify novel genes implicated in sepsis-induced ARDS susceptibility. METHODS We first performed a prioritization of candidate genes by integrating our own genomic data from a transcriptomic study in an animal model of ARDS and from the only published genome-wide association study of ARDS study in humans. Then, we selected single nucleotide polymorphisms (SNPs) from prioritized genes to conduct a case-control discovery association study in patients with sepsis-induced ARDS (n = 225) and population-based controls (n = 899). Finally, we validated our findings in an independent sample of 661 sepsis-induced ARDS cases and 234 at-risk controls. RESULTS Three candidate genes were prioritized: dynein cytoplasmic-2 heavy chain-1, fms-related tyrosine kinase 1 (FLT1), and integrin alpha-1. Of those, a SNP from FLT1 gene (rs9513106) was associated with ARDS in the discovery study, with an odds ratio (OR) for the C allele of 0.76, 95% confidence interval (CI) 0.58-0.98 (p = 0.037). This result was replicated in an independent study (OR = 0.78, 95% CI = 0.62-0.98, p = 0.039), showing consistent direction of effects in a meta-analysis (OR = 0.77, 95% CI = 0.65-0.92, p = 0.003). CONCLUSIONS We identified FLT1 as a novel ARDS susceptibility gene and demonstrated that integration of genomic data can be a valid procedure to identify novel susceptibility genes. These results contribute to previous firm associations and functional evidences implicating FLT1 gene in other complex traits that are mechanistically linked, through the key role of endothelium, to the pathophysiology of ARDS.
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Affiliation(s)
- Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Beatriz Guillen-Guio
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Marialbert Acosta-Herrera
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Dr. Negrin, Las Palmas de Gran Canaria, Spain
- Instituto de Parasitología y Biomedicina López-Neyra, IPBLN-CSIC, P.T.S, Granada, Spain
| | - Maria Pino-Yanes
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Tenerife Spain
| | - Almudena Corrales
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Alfonso Ambrós
- Intensive Care Unit, Hospital General de Ciudad Real, Ciudad Real, Spain
| | - Leonor Nogales
- Intensive Care Unit, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | - Arturo Muriel
- Intensive Care Unit, Hospital Universitario Rio Hortega, Valladolid, Spain
| | | | | | - Elizabeth Zavala
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Intensive Care Unit, Hospital Clinic Barcelona, Barcelona, Spain
| | - Javier Belda
- Department of Anesthesiology, Hospital Clínico Universitario, Universidad de Valencia, Valencia, Spain
| | - Shwu-Fan Ma
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, USA
| | - Jesús Villar
- Research Unit, Hospital Universitario Dr. Negrin, Las Palmas de Gran Canaria, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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Hussain M, Xu C, Ahmad M, Majeed A, Lu M, Wu X, Tang L, Wu X. Acute Respiratory Distress Syndrome: Bench-to-Bedside Approaches to Improve Drug Development. Clin Pharmacol Ther 2018; 104:484-494. [PMID: 29484641 PMCID: PMC7162218 DOI: 10.1002/cpt.1034] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 01/11/2018] [Accepted: 01/21/2018] [Indexed: 12/20/2022]
Abstract
Despite 50 years of extensive research, no definite drug is currently available to treat acute respiratory distress syndrome (ARDS), and the supportive therapies remain the mainstay of treatment. To improve drug development for ARDS, researchers need to deeply analyze the “omics” approaches, reevaluate the suitable therapeutic targets, resolve the problems of inadequate animal modeling, develop the strategies to reduce the heterogeneity, and reconsider new therapeutic and analytical approaches for better designs of clinical trials.
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Affiliation(s)
- Musaddique Hussain
- Department of Pharmacology, Hangzhou City, 310058, China.,The Key Respiratory Drug Research Laboratory of China Food and Drug Administration, School of Medicine, Zhejiang University, Hangzhou City, 310058, China
| | - Chengyun Xu
- Department of Pharmacology, Hangzhou City, 310058, China.,The Key Respiratory Drug Research Laboratory of China Food and Drug Administration, School of Medicine, Zhejiang University, Hangzhou City, 310058, China
| | - Mashaal Ahmad
- Department of Pharmacology, Hangzhou City, 310058, China.,The Key Respiratory Drug Research Laboratory of China Food and Drug Administration, School of Medicine, Zhejiang University, Hangzhou City, 310058, China
| | - Abdul Majeed
- Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Meiping Lu
- Department of Respiratory Medicine, the Affiliated Children Hospital, School of Medicine, Zhejiang University, Hangzhou City, 310006, China
| | - Xiling Wu
- Department of Respiratory Medicine, the Affiliated Children Hospital, School of Medicine, Zhejiang University, Hangzhou City, 310006, China
| | - Lanfang Tang
- Department of Respiratory Medicine, the Affiliated Children Hospital, School of Medicine, Zhejiang University, Hangzhou City, 310006, China
| | - Ximei Wu
- Department of Pharmacology, Hangzhou City, 310058, China.,The Key Respiratory Drug Research Laboratory of China Food and Drug Administration, School of Medicine, Zhejiang University, Hangzhou City, 310058, China
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Reilly JP, Christie JD, Meyer NJ. Fifty Years of Research in ARDS. Genomic Contributions and Opportunities. Am J Respir Crit Care Med 2017; 196:1113-1121. [PMID: 28481621 PMCID: PMC5694838 DOI: 10.1164/rccm.201702-0405cp] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/05/2017] [Indexed: 02/06/2023] Open
Abstract
Clinical factors alone poorly explain acute respiratory distress syndrome (ARDS) risk and ARDS outcome. In the search for individual factors that may influence ARDS risk, the past 20 years have witnessed the identification of numerous genes and genetic variants that are associated with ARDS. The field of ARDS genomics has cycled from candidate gene association studies to bias-free approaches that identify new candidates, and increasing effort is made to understand the functional consequences that may underlie significant associations. More recently, methodologies of causal inference are being applied to maximize the information gained from genetic associations. Although challenges of sample size, both recognized and unrecognized phenotypic heterogeneity, and the paucity of early ARDS lung tissue limit some applications of the rapidly evolving field of genomic investigation, ongoing genetic research offers unique contributions to elucidating ARDS pathogenesis and the paradigm of precision ARDS medicine.
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Affiliation(s)
- John P. Reilly
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pennsylvania Perelman School of Medicine
- Center for Translational Lung Biology, and
| | - Jason D. Christie
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pennsylvania Perelman School of Medicine
- Center for Translational Lung Biology, and
- Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Nuala J. Meyer
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pennsylvania Perelman School of Medicine
- Center for Translational Lung Biology, and
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34
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Affiliation(s)
- B Taylor Thompson
- From the Division of Pulmonary and Critical Care, Department of Medicine, Massachusetts General Hospital, and Harvard Medical School - both in Boston (B.T.T.); Centre for Inflammation and Tissue Repair, the Division of Medicine, University College London, London (R.C.C.); and the Divisions of Nephrology and Critical Care Medicine, University of California San Francisco, San Francisco (K.D.L.)
| | - Rachel C Chambers
- From the Division of Pulmonary and Critical Care, Department of Medicine, Massachusetts General Hospital, and Harvard Medical School - both in Boston (B.T.T.); Centre for Inflammation and Tissue Repair, the Division of Medicine, University College London, London (R.C.C.); and the Divisions of Nephrology and Critical Care Medicine, University of California San Francisco, San Francisco (K.D.L.)
| | - Kathleen D Liu
- From the Division of Pulmonary and Critical Care, Department of Medicine, Massachusetts General Hospital, and Harvard Medical School - both in Boston (B.T.T.); Centre for Inflammation and Tissue Repair, the Division of Medicine, University College London, London (R.C.C.); and the Divisions of Nephrology and Critical Care Medicine, University of California San Francisco, San Francisco (K.D.L.)
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35
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Meyer NJ, Calfee CS. Novel translational approaches to the search for precision therapies for acute respiratory distress syndrome. THE LANCET. RESPIRATORY MEDICINE 2017; 5:512-523. [PMID: 28664850 PMCID: PMC7103930 DOI: 10.1016/s2213-2600(17)30187-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 03/30/2017] [Accepted: 04/06/2017] [Indexed: 02/07/2023]
Abstract
In the 50 years since acute respiratory distress syndrome (ARDS) was first described, substantial progress has been made in identifying the risk factors for and the pathogenic contributors to the syndrome and in characterising the protein expression patterns in plasma and bronchoalveolar lavage fluid from patients with ARDS. Despite this effort, however, pharmacological options for ARDS remain scarce. Frequently cited reasons for this absence of specific drug therapies include the heterogeneity of patients with ARDS, the potential for a differential response to drugs, and the possibility that the wrong targets have been studied. Advances in applied biomolecular technology and bioinformatics have enabled breakthroughs for other complex traits, such as cardiovascular disease or asthma, particularly when a precision medicine paradigm, wherein a biomarker or gene expression pattern indicates a patient's likelihood of responding to a treatment, has been pursued. In this Review, we consider the biological and analytical techniques that could facilitate a precision medicine approach for ARDS.
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Affiliation(s)
- Nuala J Meyer
- Division of Pulmonary, Allergy, and Critical Care Medicine and Center for Translational Lung Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Carolyn S Calfee
- Department of Medicine and Department of Anesthesia, University of California, San Francisco, CA, USA.
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36
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Maslove DM, Lamontagne F, Marshall JC, Heyland DK. A path to precision in the ICU. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2017; 21:79. [PMID: 28366166 PMCID: PMC5376689 DOI: 10.1186/s13054-017-1653-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Precision medicine is increasingly touted as a groundbreaking new paradigm in biomedicine. In the ICU, the complexity and ambiguity of critical illness syndromes have been identified as fundamental justifications for the adoption of a precision approach to research and practice. Inherently protean diseases states such as sepsis and acute respiratory distress syndrome have manifestations that are physiologically and anatomically diffuse, and that fluctuate over short periods of time. This leads to considerable heterogeneity among patients, and conditions in which a “one size fits all” approach to therapy can lead to widely divergent results. Current ICU therapy can thus be seen as imprecise, with the potential to realize substantial gains from the adoption of precision medicine approaches. A number of challenges still face the development and adoption of precision critical care, a transition that may occur incrementally rather than wholesale. This article describes a few concrete approaches to addressing these challenges. First, novel clinical trial designs, including registry randomized controlled trials and platform trials, suggest ways in which conventional trials can be adapted to better accommodate the physiologic heterogeneity of critical illness. Second, beyond the “omics” technologies already synonymous with precision medicine, the data-rich environment of the ICU can generate complex physiologic signatures that could fuel precision-minded research and practice. Third, the role of computing infrastructure and modern informatics methods will be central to the pursuit of precision medicine in the ICU, necessitating close collaboration with data scientists. As work toward precision critical care continues, small proof-of-concept studies may prove useful in highlighting the potential of this approach.
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Affiliation(s)
- David M Maslove
- Department of Critical Care Medicine, Queen's University, Kingston, ON, Canada. .,Department of Medicine, Queen's University, Kingston, ON, Canada. .,Department of Critical Care Medicine, Kingston General Hospital, Davies 2, 76 Stuart St., Kingston, Ontario, K7L 2V7, Canada.
| | - Francois Lamontagne
- Department of Medicine, Université de Sherbrooke, Sherbrooke, QC, Canada.,Centre de Recherche du CHU de Sherbrooke, Sherbrooke, QC, Canada.,Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada
| | - John C Marshall
- Department of Surgery, University of Toronto, Toronto, ON, Canada.,Interdepartmental Division of Critical Care, University of Toronto, Toronto, ON, Canada.,St. Michael's Hospital, Toronto, ON, Canada
| | - Daren K Heyland
- Department of Critical Care Medicine, Queen's University, Kingston, ON, Canada.,Clinical Evaluation Research Unit, Kingston General Hospital, Kingston, ON, Canada
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37
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Xu W, Song Y. Biomarkers for patients with trauma associated acute respiratory distress syndrome. Mil Med Res 2017; 4:25. [PMID: 28824814 PMCID: PMC5558771 DOI: 10.1186/s40779-017-0134-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 08/03/2017] [Indexed: 12/21/2022] Open
Abstract
Trauma is a major factor that contributes to the risk for acute respiratory distress syndrome (ARDS). Biomarkers that predict the risk, diagnosis, treatment response and prognosis of ARDS after trauma have been widely investigated. In addition to their applications in clinical diagnosis and treatment, these biomarkers provide important insights into our understanding of the pathogenesis of ARDS. This review begins with a brief introduction regarding the incidence and pathogenesis of trauma-associated ARDS. Then, we focus on reviewing the clinical trials that have been designed to investigate the value of biomarkers in ARDS after trauma. Biomarkers with a confirmed value in ARDS have been organized on the basis of key pathogenic processes that are central to ARDS and are described in detail. Among these, angiopoietin 2 (Ang-2), L-selectin, Clara cell protein 16 (CC16), soluable receptor for advanced glycation end products (sRAGE), Surfactant protein D (SP-D), histones, mtDNAs and some biomarker panels had a certain association with the diagnosis and prognosis of trauma-related ARDS. Further investigations are needed regarding the design of trials, the best sampling approaches and the optimal combinations of the biomarker panels.
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Affiliation(s)
- Wujian Xu
- Department of Respiratory Medicine, Jinling Hospital, 305 Zhongshan Road, Nanjing, 210002 China.,Nanjing University Institute of Respiratory Medicine, Nanjing, 210002 China
| | - Yong Song
- Department of Respiratory Medicine, Jinling Hospital, 305 Zhongshan Road, Nanjing, 210002 China.,Nanjing University Institute of Respiratory Medicine, Nanjing, 210002 China
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38
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Cantu E, Suzuki Y, Diamond JM, Ellis J, Tiwari J, Beduhn B, Nellen JR, Shah R, Meyer NJ, Lederer DJ, Kawut SM, Palmer SM, Snyder LD, Hartwig MG, Lama VN, Bhorade S, Crespo M, Demissie E, Wille K, Orens J, Shah PD, Weinacker A, Weill D, Wilkes D, Roe D, Ware LB, Wang F, Feng R, Christie JD. Protein Quantitative Trait Loci Analysis Identifies Genetic Variation in the Innate Immune Regulator TOLLIP in Post-Lung Transplant Primary Graft Dysfunction Risk. Am J Transplant 2016; 16:833-40. [PMID: 26663441 PMCID: PMC4767612 DOI: 10.1111/ajt.13525] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 09/02/2015] [Accepted: 09/03/2015] [Indexed: 01/25/2023]
Abstract
The authors previously identified plasma plasminogen activator inhibitor-1 (PAI-1) level as a quantitative lung injury biomarker in primary graft dysfunction (PGD). They hypothesized that plasma levels of PAI-1 used as a quantitative trait could facilitate discovery of genetic loci important in PGD pathogenesis. A two-stage cohort study was performed. In stage 1, they tested associations of loci with PAI-1 plasma level using linear modeling. Genotyping was performed using the Illumina CVD Bead Chip v2. Loci meeting a p < 5 × 10(-4) cutoff were carried forward and tested in stage 2 for association with PGD. Two hundred ninety-seven enrollees were evaluated in stage 1. Six loci, associated with PAI-1, were carried forward to stage 2 and evaluated in 728 patients. rs3168046 (Toll interacting protein [TOLLIP]) was significantly associated with PGD (p = 0.006). The increased risk of PGD for carrying at least one copy of this variant was 11.7% (95% confidence interval 4.9-18.5%). The false-positive rate for individuals with this genotype who did not have PGD was 6.1%. Variants in the TOLLIP gene are associated with higher circulating PAI-1 plasma levels and validate for association with clinical PGD. A protein quantitative trait analysis for PGD risk prioritizes genetic variations in TOLLIP and supports a role for Toll-like receptors in PGD pathogenesis.
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Affiliation(s)
- Edward Cantu
- Division of Cardiovascular Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Yoshikazu Suzuki
- Division of Cardiovascular Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Joshua M. Diamond
- Pulmonary, Allergy, and Critical Care Division, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - John Ellis
- Division of Cardiovascular Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Jaya Tiwari
- Division of Cardiovascular Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Ben Beduhn
- Division of Cardiovascular Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - James R. Nellen
- Division of Cardiovascular Surgery, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Rupal Shah
- Pulmonary, Allergy, and Critical Care Division, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Nuala J. Meyer
- Pulmonary, Allergy, and Critical Care Division, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - David J. Lederer
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University College of Physicians and Surgeons, New York, New York
| | - Steven M. Kawut
- Pulmonary, Allergy, and Critical Care Division, University of Pennsylvania School of Medicine, Philadelphia, PA,Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, PA,Penn Cardiovascular Institute, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Scott M. Palmer
- Division of Pulmonary, Allergy, and Critical Care Medicine, Duke University, Durham, North Carolina
| | - Laurie D. Snyder
- Division of Pulmonary, Allergy, and Critical Care Medicine, Duke University, Durham, North Carolina
| | - Matthew G. Hartwig
- Division of Cardiothoracic Surgery, Duke University, Durham, North Carolina
| | - Vibha N. Lama
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan
| | - Sangeeta Bhorade
- Division of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois
| | - Maria Crespo
- Division of Pulmonary, Allergy, and Critical Care, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ejigayehu Demissie
- Pulmonary, Allergy, and Critical Care Division, University of Pennsylvania School of Medicine, Philadelphia, PA,Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Keith Wille
- Division of Pulmonary and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jonathan Orens
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Johns Hopkins University Hospital, Baltimore, Maryland
| | - Pali D. Shah
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Johns Hopkins University Hospital, Baltimore, Maryland
| | - Ann Weinacker
- Division of Pulmonary and Critical Care Medicine, Stanford University, Palo Alto, California
| | - David Weill
- Division of Pulmonary and Critical Care Medicine, Stanford University, Palo Alto, California
| | - David Wilkes
- Division of Pulmonary, Allergy, Critical Care, and Occupational Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - David Roe
- Division of Pulmonary, Allergy, Critical Care, and Occupational Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Lorraine B. Ware
- Departments of Medicine and Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee
| | - Fan Wang
- Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Rui Feng
- Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Jason D. Christie
- Pulmonary, Allergy, and Critical Care Division, University of Pennsylvania School of Medicine, Philadelphia, PA,Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, PA
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Acosta-Herrera M, Lorenzo-Diaz F, Pino-Yanes M, Corrales A, Valladares F, Klassert TE, Valladares B, Slevogt H, Ma SF, Villar J, Flores C. Lung Transcriptomics during Protective Ventilatory Support in Sepsis-Induced Acute Lung Injury. PLoS One 2015; 10:e0132296. [PMID: 26147972 PMCID: PMC4492998 DOI: 10.1371/journal.pone.0132296] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/11/2015] [Indexed: 01/17/2023] Open
Abstract
Acute lung injury (ALI) is a severe inflammatory process of the lung. The only proven life-saving support is mechanical ventilation (MV) using low tidal volumes (LVT) plus moderate to high levels of positive end-expiratory pressure (PEEP). However, it is currently unknown how they exert the protective effects. To identify the molecular mechanisms modulated by protective MV, this study reports transcriptomic analyses based on microarray and microRNA sequencing in lung tissues from a clinically relevant animal model of sepsis-induced ALI. Sepsis was induced by cecal ligation and puncture (CLP) in male Sprague-Dawley rats. At 24 hours post-CLP, septic animals were randomized to three ventilatory strategies: spontaneous breathing, LVT (6 ml/kg) plus 10 cmH2O PEEP and high tidal volume (HVT, 20 ml/kg) plus 2 cmH2O PEEP. Healthy, non-septic, non-ventilated animals served as controls. After 4 hours of ventilation, lung samples were obtained for histological examination and gene expression analysis using microarray and microRNA sequencing. Validations were assessed using parallel analyses on existing publicly available genome-wide association study findings and transcriptomic human data. The catalogue of deregulated processes differed among experimental groups. The 'response to microorganisms' was the most prominent biological process in septic, non-ventilated and in HVT animals. Unexpectedly, the 'neuron projection morphogenesis' process was one of the most significantly deregulated in LVT. Further support for the key role of the latter process was obtained by microRNA studies, as four species targeting many of its genes (Mir-27a, Mir-103, Mir-17-5p and Mir-130a) were found deregulated. Additional analyses revealed 'VEGF signaling' as a central underlying response mechanism to all the septic groups (spontaneously breathing or mechanically ventilated). Based on this data, we conclude that a co-deregulation of 'VEGF signaling' along with 'neuron projection morphogenesis', which have been never anticipated in ALI pathogenesis, promotes lung-protective effects of LVT with high levels of PEEP.
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Affiliation(s)
- Marialbert Acosta-Herrera
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Fabian Lorenzo-Diaz
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Maria Pino-Yanes
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Almudena Corrales
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Francisco Valladares
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Department of Anatomy, Pathology and Histology, University of La Laguna, Santa Cruz de Tenerife, Spain
| | | | - Basilio Valladares
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Hortense Slevogt
- Septomics Research Centre, Jena University Hospital, Jena, Germany
| | - Shwu-Fan Ma
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Jesus Villar
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario Dr. Negrin, Las Palmas de Gran Canaria, Spain
- Keenan Research Center for Biomedical Science at the Li KaShing Knowledge Institute, St. Michael´s Hospital, Toronto, Canada
| | - Carlos Flores
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
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40
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Comorbidities and assessment of severity of pediatric acute respiratory distress syndrome: proceedings from the Pediatric Acute Lung Injury Consensus Conference. Pediatr Crit Care Med 2015; 16:S41-50. [PMID: 26035363 DOI: 10.1097/pcc.0000000000000430] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVES To determine the impact of patient-specific and disease-related characteristics on the severity of illness and on outcome in pediatric patients with acute respiratory distress syndrome with the intent of guiding current medical practice and identifying important areas for future research. DESIGN Electronic searches of PubMed, EMBASE, Web of Science, Cochrane, and Scopus were conducted. References were reviewed for relevance and features included in the following section. SETTINGS Not applicable. SUBJECTS PICU patients with evidence of acute lung injury, acute hypoxemic respiratory failure, and acute respiratory distress syndrome. INTERVENTIONS Not applicable. MEASUREMENTS AND MAIN RESULTS The comorbidities associated with outcome in pediatric acute respiratory distress syndrome can be divided into 1) patient-specific factors and 2) factors inherent to the disease process. The primary comorbidity associated with poor outcome is preexisting congenital or acquired immunodeficiency. Severity of disease is often described by factors identifiable at admission to the ICU. Many measures that are predictive are influenced by the underlying disease process itself, but may also be influenced by nutritional status, chronic comorbidities, or underlying genetic predisposition. Of the measures available at the bedside, both PaO2/FIO2 ratio and oxygenation index are fairly consistent and robust predictors of disease severity and outcomes. Multiple organ system dysfunction is the single most important independent clinical risk factor for mortality in children at the onset of acute respiratory distress syndrome. CONCLUSIONS The assessment of oxygenation and ventilation indices simultaneously with genetic and biomarker measurements holds the most promise for improved risk stratification for pediatric acute respiratory distress syndrome patients in the very near future. The next phases of pediatric acute respiratory distress syndrome pathophysiology and outcomes research will be enhanced if 1) age group differences are examined, 2) standardized datasets with adequately explicit definitions are used, 3) data are obtained at standardized times after pediatric acute respiratory distress syndrome onset, and 4) nonpulmonary organ failure scores are created and implemented.
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Wei Y, Wang Z, Su L, Chen F, Tejera P, Bajwa EK, Wurfel MM, Lin X, Christiani DC. Platelet count mediates the contribution of a genetic variant in LRRC16A to ARDS risk. Chest 2015; 147:607-617. [PMID: 25254322 DOI: 10.1378/chest.14-1246] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Platelets are believed to be critical in pulmonary-origin ARDS as mediators of endothelial damage through their interactions with fibrinogen and multiple signal transduction pathways. A prior meta-analysis identified five loci for platelet count (PLT): BAD, LRRC16A, CD36, JMJD1C, and SLMO2. This study aims to validate the quantitative trait loci (QTLs) of PLT within BAD, LRRC16A, CD36, JMJD1C, and SLMO2 among critically ill patients and to investigate the associations of these QTLs with ARDS risk that may be mediated through PLT. METHODS ARDS cases and at-risk control subjects were recruited from the intensive care unit of the Massachusetts General Hospital. Exome-wide genotyping data of 629 ARDS cases and 1,026 at-risk control subjects and genome-wide gene expression profiles of 18 at-risk control subjects were generated for analysis. RESULTS Single-nucleotide polymorphism (SNP) rs7766874 within LRRC16A was a significant locus for PLT among at-risk control subjects (β = -13.00; 95% CI, -23.22 to -2.77; P = .013). This association was validated using LRRC16A gene expression data from at-risk control subjects (β = 77.03 per 1 SD increase of log2-transformed expression; 95% CI, 27.26-126.80; P = .005). Further, rs7766874 was associated with ARDS risk conditioned on PLT (OR = 0.68; 95% CI, 0.51-0.90; P = .007), interacting with PLT (OR = 1.15 per effect allele per 100 × 103/μL of PLT; 95% CI, 1.03-1.30; P = .015), and mediated through PLT (indirect OR = 1.045; 95% CI, 1.007-1.085; P = .021). CONCLUSIONS Our findings support the role of LRRC16A in platelet formation and suggest the importance of LRRC16A in ARDS pathophysiology by interacting with, and being mediated through, platelets.
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Affiliation(s)
- Yongyue Wei
- Department of Environmental Health, Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhaoxi Wang
- Department of Environmental Health, Harvard School of Public Health, Boston, MA
| | - Li Su
- Department of Environmental Health, Harvard School of Public Health, Boston, MA
| | - Feng Chen
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Paula Tejera
- Department of Environmental Health, Harvard School of Public Health, Boston, MA
| | - Ednan K Bajwa
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Mark M Wurfel
- Division of Pulmonary and Critical Care Medicine, University of Washington, Harborview Medical Center, Seattle, WA
| | - Xihong Lin
- Department of Biostatistics, Harvard School of Public Health, Boston, MA
| | - David C Christiani
- Department of Environmental Health, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA.
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Erranz MB, Wilhelm BJ, Riquelme VR, Cruces RP. [Genetic predisposition and Pediatric Acute Respiratory Distress Syndrome: New tools for genetic study]. REVISTA CHILENA DE PEDIATRIA 2015; 86:73-79. [PMID: 26235685 DOI: 10.1016/j.rchipe.2015.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/02/2015] [Indexed: 06/04/2023]
Abstract
Acute respiratory distress syndrome (ARDS) is the most severe form of respiratory failure. Theoretically, any acute lung condition can lead to ARDS, but only a small percentage of individuals actually develop the disease. On this basis, genetic factors have been implicated in the risk of developing ARDS. Based on the pathophysiology of this disease, many candidate genes have been evaluated as potential modifiers in patient, as well as in animal models, of ARDS. Recent experimental data and clinical studies suggest that variations of genes involved in key processes of tissue, cellular and molecular lung damage may influence susceptibility and prognosis of ARDS. However, the pathogenesis of pediatric ARDS is complex, and therefore, it can be expected that many genes might contribute. Genetic variations such as single nucleotide polymorphisms and copy-number variations are likely associated with susceptibility to ARDS in children with primary lung injury. Genome-wide association (GWA) studies can objectively examine these variations, and help identify important new genes and pathogenetic pathways for future analysis. This approach might also have diagnostic and therapeutic implications, such as predicting patient risk or developing a personalized therapeutic approach to this serious syndrome.
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Affiliation(s)
- M Benjamín Erranz
- Centro de Medicina Regenerativa, Facultad de Medicina Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - B Jan Wilhelm
- Departamento de Pediatría, Facultad de Medicina Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - V Raquel Riquelme
- Unidad de Paciente Crítico Pediátrica, Hospital El Carmen de Maipú, Santiago, Chile
| | - R Pablo Cruces
- Unidad de Paciente Crítico Pediátrica, Hospital El Carmen de Maipú, Santiago, Chile; Centro de Investigación de Medicina Veterinaria, Escuela de Medicina Veterinaria, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Santiago, Chile.
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Rautanen A, Mills TC, Gordon AC, Hutton P, Steffens M, Nuamah R, Chiche JD, Parks T, Chapman SJ, Davenport EE, Elliott KS, Bion J, Lichtner P, Meitinger T, Wienker TF, Caulfield MJ, Mein C, Bloos F, Bobek I, Cotogni P, Sramek V, Sarapuu S, Kobilay M, Ranieri VM, Rello J, Sirgo G, Weiss YG, Russwurm S, Schneider EM, Reinhart K, Holloway PAH, Knight JC, Garrard CS, Russell JA, Walley KR, Stüber F, Hill AVS, Hinds CJ. Genome-wide association study of survival from sepsis due to pneumonia: an observational cohort study. THE LANCET. RESPIRATORY MEDICINE 2015; 3:53-60. [PMID: 25533491 PMCID: PMC4314768 DOI: 10.1016/s2213-2600(14)70290-5] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Sepsis continues to be a major cause of death, disability, and health-care expenditure worldwide. Despite evidence suggesting that host genetics can influence sepsis outcomes, no specific loci have yet been convincingly replicated. The aim of this study was to identify genetic variants that influence sepsis survival. METHODS We did a genome-wide association study in three independent cohorts of white adult patients admitted to intensive care units with sepsis, severe sepsis, or septic shock (as defined by the International Consensus Criteria) due to pneumonia or intra-abdominal infection (cohorts 1-3, n=2534 patients). The primary outcome was 28 day survival. Results for the cohort of patients with sepsis due to pneumonia were combined in a meta-analysis of 1553 patients from all three cohorts, of whom 359 died within 28 days of admission to the intensive-care unit. The most significantly associated single nucleotide polymorphisms (SNPs) were genotyped in a further 538 white patients with sepsis due to pneumonia (cohort 4), of whom 106 died. FINDINGS In the genome-wide meta-analysis of three independent pneumonia cohorts (cohorts 1-3), common variants in the FER gene were strongly associated with survival (p=9·7 × 10(-8)). Further genotyping of the top associated SNP (rs4957796) in the additional cohort (cohort 4) resulted in a combined p value of 5·6 × 10(-8) (odds ratio 0·56, 95% CI 0·45-0·69). In a time-to-event analysis, each allele reduced the mortality over 28 days by 44% (hazard ratio for death 0·56, 95% CI 0·45-0·69; likelihood ratio test p=3·4 × 10(-9), after adjustment for age and stratification by cohort). Mortality was 9·5% in patients carrying the CC genotype, 15·2% in those carrying the TC genotype, and 25·3% in those carrying the TT genotype. No significant genetic associations were identified when patients with sepsis due to pneumonia and intra-abdominal infection were combined. INTERPRETATION We have identified common variants in the FER gene that associate with a reduced risk of death from sepsis due to pneumonia. The FER gene and associated molecular pathways are potential novel targets for therapy or prevention and candidates for the development of biomarkers for risk stratification. FUNDING European Commission and the Wellcome Trust.
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Affiliation(s)
- Anna Rautanen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Tara C Mills
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | - Michael Steffens
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE) of the University of Bonn, Bonn, Germany
| | - Rosamond Nuamah
- William Harvey Research Institute, Barts and The London School of Medicine Queen Mary University of London, London, UK
| | | | - Tom Parks
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stephen J Chapman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Emma E Davenport
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Julian Bion
- School of Clinical and Experimental Medicine, University of Birmingham, Birmingham, UK
| | - Peter Lichtner
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Technische Universität München, Institute of Human Genetics, Munich, Germany
| | - Thomas F Wienker
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE) of the University of Bonn, Bonn, Germany
| | - Mark J Caulfield
- William Harvey Research Institute, Barts and The London School of Medicine Queen Mary University of London, London, UK
| | - Charles Mein
- William Harvey Research Institute, Barts and The London School of Medicine Queen Mary University of London, London, UK
| | - Frank Bloos
- Jena University Hospital and Center for Sepsis Control and Care, Jena, Germany
| | - Ilona Bobek
- National Health Service Centre, Budapest, Hungary
| | | | | | | | | | | | - Jordi Rello
- CIBERES, Vall d'Hebron Institute of Research, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Gonzalo Sirgo
- Joan XXIII University Hospital, Pere Virgili Health Institute, University Rovirai Virgili, Tarragona, Spain
| | | | | | - E Marion Schneider
- Section of Experimental Anesthesiology, University Hospital, Ulm, Germany
| | - Konrad Reinhart
- Jena University Hospital and Center for Sepsis Control and Care, Jena, Germany
| | | | - Julian C Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | | | - Frank Stüber
- Department of Anaesthesiology and Pain Medicine, Bern University Hospital, and University of Bern, Switzerland
| | - Adrian V S Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Charles J Hinds
- William Harvey Research Institute, Barts and The London School of Medicine Queen Mary University of London, London, UK
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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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Wang H, Yang L, Deng J, Wang B, Yang X, Yang R, Cheng M, Fang W, Qiu F, Zhang X, Ji W, Ran P, Zhou Y, Lu J. Genetic variant in the 3'-untranslated region of VEGFR1 gene influences chronic obstructive pulmonary disease and lung cancer development in Chinese population. Mutagenesis 2014; 29:311-7. [PMID: 24891316 DOI: 10.1093/mutage/geu020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Lung inflammation and epithelial to mesenchymal transition (EMT) are two pathogenic features for the two contextual diseases: chronic obstructive pulmonary disease (COPD) and lung cancer. VEGFR1 (or FLT1) plays a certain role in promoting tumour growth, inflammation and EMT. To simultaneously test the association between the single nucleotide polymorphisms (SNPs) in VEGFR1 and risk of COPD and lung cancer would reveal genetic mechanisms shared by these two diseases and joint aetiology. We conducted a two-population hospital-based case-control study. Three potential functional SNPs (rs664393, rs7326277 and rs9554314) were genotyped in southern Chinese and validated in eastern Chinese to explore their associations with COPD risk in 1511 COPD patients and 1677 normal lung function controls, and with lung cancer risk in 1559 lung cancer cases and 1679 cancer-free controls. We also detected the function of the promising SNP. Individuals carrying the rs7326277C (CT+CC) variant genotypes of VEGFR1 had a significant decrease in risk of both COPD (OR = 0.78; 95% CI = 0.68-0.90) and lung cancer (OR = 0.79; 95% CI = 0.64-0.98), compared with those carrying the rs7326277TT genotype. Functional assays further showed that the rs7326277C genotypes had lower transcriptional activity and caused decreased VEGFR expression, compared with the rs7326277TT genotype. However, no significant association was observed for the other two SNPs (rs664393 and rs9554314) and either COPD or lung cancer risk. Our data suggested that the rs7326277C variant of VEGFR1 could reduce both COPD and lung cancer risk by lowering VEGFR1 mRNA expression; the SNP might be a common susceptible locus for both COPD and lung cancer.
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Affiliation(s)
- Hui Wang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Guangzhou 510182, Guangdong, China, School of Public Health, Guangdong Key Laboratory of Molecular Epidemiology, Guangdong Pharmaceutical University, Guangzhou 510310, Guangdong, China
| | - Lei Yang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Guangzhou 510182, Guangdong, China
| | - Jieqiong Deng
- Soochow University Laboratory of Cancer Molecular Genetics, Medical College of Soochow University, Suzhou 215123, China and
| | - Bo Wang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Guangzhou 510182, Guangdong, China
| | - Xiaorong Yang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Guangzhou 510182, Guangdong, China
| | - Rongrong Yang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Guangzhou 510182, Guangdong, China
| | - Mei Cheng
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Guangzhou 510182, Guangdong, China
| | - Wenxiang Fang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Guangzhou 510182, Guangdong, China
| | - Fuman Qiu
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Guangzhou 510182, Guangdong, China
| | - Xin Zhang
- Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital, The State Key Lab of Respiratory Disease, Guangzhou Medical University, Guangzhou 510120, Guangdong, China
| | - Weidong Ji
- Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital, The State Key Lab of Respiratory Disease, Guangzhou Medical University, Guangzhou 510120, Guangdong, China
| | - Pixin Ran
- Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital, The State Key Lab of Respiratory Disease, Guangzhou Medical University, Guangzhou 510120, Guangdong, China
| | - Yifeng Zhou
- Soochow University Laboratory of Cancer Molecular Genetics, Medical College of Soochow University, Suzhou 215123, China and
| | - Jiachun Lu
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Guangzhou 510182, Guangdong, China,
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Rogers AJ, Matthay MA. Applying metabolomics to uncover novel biology in ARDS. Am J Physiol Lung Cell Mol Physiol 2014; 306:L957-61. [PMID: 24727586 PMCID: PMC4042190 DOI: 10.1152/ajplung.00376.2013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 04/10/2014] [Indexed: 11/22/2022] Open
Abstract
A better understanding of the pathogenesis and the resolution of the acute respiratory distress syndrome (ARDS) is needed. Although some progress has been made with the use of protein biomarkers and candidate gene studies in understanding the pathobiology of ARDS, we propose that new studies that measure the chemical breakdown products of cellular metabolism (metabolomics) may provide new insights into ARDS, in part because metabolomics targets a later point in the genomics cascade than is possible with studies of DNA, RNA, and protein biomarkers. Technological advances have made large-scale metabolomic profiling increasingly feasible. Metabolomic approaches have already achieved novel insights in nonpulmonary diseases such as diabetes mellitus and malignancy, as well as in sepsis, a major risk factor for developing ARDS. Metabolomic profiling is a promising approach to identify novel pathways in both patients at risk for developing ARDS as well as in the early phase of established ARDS.
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Affiliation(s)
- Angela J Rogers
- Division of Pulmonary and Critical Care Medicine, Stanford University, Stanford, California; and
| | - Michael A Matthay
- Department of Medicine and Anesthesia, University of California, San Francisco, California
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Diamond JM, Akimova T, Kazi A, Shah RJ, Cantu E, Feng R, Levine MH, Kawut SM, Meyer NJ, Lee JC, Hancock WW, Aplenc R, Ware LB, Palmer SM, Bhorade S, Lama VN, Weinacker A, Orens J, Wille K, Crespo M, Lederer DJ, Arcasoy S, Demissie E, Christie JD. Genetic variation in the prostaglandin E2 pathway is associated with primary graft dysfunction. Am J Respir Crit Care Med 2014; 189:567-75. [PMID: 24467603 DOI: 10.1164/rccm.201307-1283oc] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
RATIONALE Biologic pathways with significant genetic conservation across human populations have been implicated in the pathogenesis of primary graft dysfunction (PGD). The evaluation of the role of recipient genetic variation in PGD has thus far been limited to single, candidate gene analyses. OBJECTIVES We sought to identify genetic variants in lung transplant recipients that are responsible for increased risk of PGD using a two-phase large-scale genotyping approach. METHODS Phase 1 was a large-scale candidate gene association study of the multicenter, prospective Lung Transplant Outcomes Group cohort. Phase 2 included functional evaluation of selected variants and a bioinformatics screening of variants identified in phase 1. MEASUREMENTS AND MAIN RESULTS After genetic data quality control, 680 lung transplant recipients were included in the analysis. In phase 1, a total of 17 variants were significantly associated with PGD, four of which were in the prostaglandin E2 family of genes. Among these were a coding variant in the gene encoding prostaglandin E2 synthase (PTGES2; P = 9.3 × 10(-5)) resulting in an arginine to histidine substitution at amino acid position 298, and three variants in a block containing the 5' promoter and first intron of the PTGER4 gene (encoding prostaglandin E2 receptor subtype 4; all P < 5 × 10(-5)). Functional evaluation in regulatory T cells identified that rs4434423A in the PTGER4 gene was associated with differential suppressive function of regulatory T cells. CONCLUSIONS Further research aimed at replication and additional functional insight into the role played by genetic variation in prostaglandin E2 synthetic and signaling pathways in PGD is warranted.
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Acosta-Herrera M, Pino-Yanes M, Perez-Mendez L, Villar J, Flores C. Assessing the quality of studies supporting genetic susceptibility and outcomes of ARDS. Front Genet 2014; 5:20. [PMID: 24567738 PMCID: PMC3915143 DOI: 10.3389/fgene.2014.00020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 01/21/2014] [Indexed: 12/12/2022] Open
Abstract
The acute respiratory distress syndrome (ARDS) is a severe inflammatory disease manifested as a result of pulmonary and systemic responses to several insults. It is now well accepted that genetic variation influences these responses. However, little is known about the genes that are responsible for patient susceptibility and outcome of ARDS. Methodological flaws are still abundant among genetic association studies with ARDS and here, we aimed to highlight the quality criteria where the standards have not been reached, to expose the associated genes to facilitate replication attempts, and to provide quick-reference guidance for future studies. We conducted a PubMed search from January 2008 to September 2012 for original articles. Studies were considered if a statistically significant association was declared with either susceptibility or outcomes of all-cause ARDS. Fourteen criteria were used for evaluation and results were compared to those from a previous quality assessment report. Significant improvements affecting study design and statistical analysis were detected. However, major issues such as adjustments for the underlying population stratification and replication studies remain poorly addressed.
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Affiliation(s)
- Marialbert Acosta-Herrera
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III Madrid, Spain ; Research Unit, Hospital Universitario N.S. de Candelaria Santa Cruz de Tenerife, Spain ; Research Unit, Hospital Universitario Dr. Negrin Las Palmas de Gran Canaria, Spain
| | - Maria Pino-Yanes
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III Madrid, Spain ; Research Unit, Hospital Universitario N.S. de Candelaria Santa Cruz de Tenerife, Spain ; Department of Medicine, University of California San Francisco, CA, USA
| | - Lina Perez-Mendez
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III Madrid, Spain ; Research Unit, Hospital Universitario N.S. de Candelaria Santa Cruz de Tenerife, Spain
| | - Jesús Villar
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III Madrid, Spain ; Research Unit, Hospital Universitario Dr. Negrin Las Palmas de Gran Canaria, Spain ; Keenan Research Center at the Li Ka Shing Knowledge Institute, St. Michael's Hospital Toronto, ON, Canada
| | - Carlos Flores
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III Madrid, Spain ; Research Unit, Hospital Universitario N.S. de Candelaria Santa Cruz de Tenerife, Spain ; Applied Genomics Group (G2A), Genetics Laboratory, Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna Santa Cruz de Tenerife, Spain
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Leikauf GD, Concel VJ, Bein K, Liu P, Berndt A, Martin TM, Ganguly K, Jang AS, Brant KA, Dopico RA, Upadhyay S, Cario C, Di YPP, Vuga LJ, Kostem E, Eskin E, You M, Kaminski N, Prows DR, Knoell DL, Fabisiak JP. Functional genomic assessment of phosgene-induced acute lung injury in mice. Am J Respir Cell Mol Biol 2013; 49:368-83. [PMID: 23590305 DOI: 10.1165/rcmb.2012-0337oc] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
In this study, a genetically diverse panel of 43 mouse strains was exposed to phosgene and genome-wide association mapping performed using a high-density single nucleotide polymorphism (SNP) assembly. Transcriptomic analysis was also used to improve the genetic resolution in the identification of genetic determinants of phosgene-induced acute lung injury (ALI). We prioritized the identified genes based on whether the encoded protein was previously associated with lung injury or contained a nonsynonymous SNP within a functional domain. Candidates were selected that contained a promoter SNP that could alter a putative transcription factor binding site and had variable expression by transcriptomic analyses. The latter two criteria also required that ≥10% of mice carried the minor allele and that this allele could account for ≥10% of the phenotypic difference noted between the strains at the phenotypic extremes. This integrative, functional approach revealed 14 candidate genes that included Atp1a1, Alox5, Galnt11, Hrh1, Mbd4, Phactr2, Plxnd1, Ptprt, Reln, and Zfand4, which had significant SNP associations, and Itga9, Man1a2, Mapk14, and Vwf, which had suggestive SNP associations. Of the genes with significant SNP associations, Atp1a1, Alox5, Plxnd1, Ptprt, and Zfand4 could be associated with ALI in several ways. Using a competitive electrophoretic mobility shift analysis, Atp1a1 promoter (rs215053185) oligonucleotide containing the minor G allele formed a major distinct faster-migrating complex. In addition, a gene with a suggestive SNP association, Itga9, is linked to transforming growth factor β1 signaling, which previously has been associated with the susceptibility to ALI in mice.
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Affiliation(s)
- George D Leikauf
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, PA 15219, USA.
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Ho Jang G, Christie JD, Feng R. A method for calling copy number polymorphism using haplotypes. Front Genet 2013; 4:165. [PMID: 24069028 PMCID: PMC3780619 DOI: 10.3389/fgene.2013.00165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 08/07/2013] [Indexed: 12/15/2022] Open
Abstract
Single nucleotide polymorphism (SNP) and copy number variation (CNV) are both widespread characteristic of the human genome, but are often called separately on common genotyping platforms. To capture integrated SNP and CNV information, methods have been developed for calling allelic specific copy numbers or so called copy number polymorphism (CNP), using limited inter-marker correlation. In this paper, we proposed a haplotype-based maximum likelihood method to call CNP, which takes advantage of the valuable multi-locus linkage disequilibrium (LD) information in the population. We also developed a computationally efficient algorithm to estimate haplotype frequencies and optimize individual CNP calls iteratively, even at presence of missing data. Through simulations, we demonstrated our model is more sensitive and accurate in detecting various CNV regions, compared with commonly-used CNV calling methods including PennCNV, another hidden Markov model (HMM) using CNP, a scan statistic, segCNV, and cnvHap. Our method often performs better in the regions with higher LD, in longer CNV regions, and in common CNV than the opposite. We implemented our method on the genotypes of 90 HapMap CEU samples and 23 patients with acute lung injury (ALI). For each ALI patient the genotyping was performed twice. The CNPs from our method show good consistency and accuracy comparable to others.
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Affiliation(s)
- Gun Ho Jang
- Department of Biostatistics and Epidemiology, Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania Philadelphia, PA, USA
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