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Chenoweth JG, Brandsma J, Striegel DA, Genzor P, Chiyka E, Blair PW, Krishnan S, Dogbe E, Boakye I, Fogel GB, Tsalik EL, Woods CW, Owusu-Ofori A, Oppong C, Oduro G, Vantha T, Letizia AG, Beckett CG, Schully KL, Clark DV. Sepsis endotypes identified by host gene expression across global cohorts. COMMUNICATIONS MEDICINE 2024; 4:120. [PMID: 38890515 PMCID: PMC11189468 DOI: 10.1038/s43856-024-00542-7] [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: 05/19/2023] [Accepted: 06/04/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Sepsis from infection is a global health priority and clinical trials have failed to deliver effective therapeutic interventions. To address complicating heterogeneity in sepsis pathobiology, and improve outcomes, promising precision medicine approaches are helping identify disease endotypes, however, they require a more complete definition of sepsis subgroups. METHODS Here, we use RNA sequencing from peripheral blood to interrogate the host response to sepsis from participants in a global observational study carried out in West Africa, Southeast Asia, and North America (N = 494). RESULTS We identify four sepsis subtypes differentiated by 28-day mortality. A low mortality immunocompetent group is specified by features that describe the adaptive immune system. In contrast, the three high mortality groups show elevated clinical severity consistent with multiple organ dysfunction. The immunosuppressed group members show signs of a dysfunctional immune response, the acute-inflammation group is set apart by molecular features of the innate immune response, while the immunometabolic group is characterized by metabolic pathways such as heme biosynthesis. CONCLUSIONS Our analysis reveals details of molecular endotypes in sepsis that support immunotherapeutic interventions and identifies biomarkers that predict outcomes in these groups.
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Affiliation(s)
- Josh G Chenoweth
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA.
| | - Joost Brandsma
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Deborah A Striegel
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Pavol Genzor
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Elizabeth Chiyka
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Paul W Blair
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Subramaniam Krishnan
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Elliot Dogbe
- Laboratory Services Directorate, KATH, Kumasi, Ghana
| | - Isaac Boakye
- Research and Development Unit, KATH, Kumasi, Ghana
| | | | - Ephraim L Tsalik
- Center for Infectious Disease Diagnostics and Innovation, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Danaher Diagnostics, Washington, DC., USA
| | - Christopher W Woods
- Center for Infectious Disease Diagnostics and Innovation, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Alex Owusu-Ofori
- Laboratory Services Directorate, KATH, Kumasi, Ghana
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Chris Oppong
- Accident and Emergency Department, KATH, Kumasi, Ghana
| | - George Oduro
- Accident and Emergency Department, KATH, Kumasi, Ghana
| | - Te Vantha
- Takeo Provincial Referral Hospital, Takeo, Cambodia
| | - Andrew G Letizia
- Naval Medical Research Unit EURAFCENT Ghana detachment, Accra, Ghana
| | - Charmagne G Beckett
- Naval Medical Research Command Infectious Diseases Directorate, Silver Spring, MD, USA
| | - Kevin L Schully
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Ft. Detrick, Maryland, MD, USA
| | - Danielle V Clark
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
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Chenoweth JG, Colantuoni C, Striegel DA, Genzor P, Brandsma J, Blair PW, Krishnan S, Chiyka E, Fazli M, Mehta R, Considine M, Cope L, Knight AC, Elayadi A, Fox A, Hertzano R, Letizia AG, Owusu-Ofori A, Boakye I, Aduboffour AA, Ansong D, Biney E, Oduro G, Schully KL, Clark DV. Gene expression signatures in blood from a West African sepsis cohort define host response phenotypes. Nat Commun 2024; 15:4606. [PMID: 38816375 PMCID: PMC11139862 DOI: 10.1038/s41467-024-48821-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 05/13/2024] [Indexed: 06/01/2024] Open
Abstract
Our limited understanding of the pathophysiological mechanisms that operate during sepsis is an obstacle to rational treatment and clinical trial design. There is a critical lack of data from low- and middle-income countries where the sepsis burden is increased which inhibits generalized strategies for therapeutic intervention. Here we perform RNA sequencing of whole blood to investigate longitudinal host response to sepsis in a Ghanaian cohort. Data dimensional reduction reveals dynamic gene expression patterns that describe cell type-specific molecular phenotypes including a dysregulated myeloid compartment shared between sepsis and COVID-19. The gene expression signatures reported here define a landscape of host response to sepsis that supports interventions via targeting immunophenotypes to improve outcomes.
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Affiliation(s)
- Josh G Chenoweth
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA.
| | - Carlo Colantuoni
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Deborah A Striegel
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Pavol Genzor
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Joost Brandsma
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Paul W Blair
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
- Department of Pathology, Uniformed Services University, Bethesda, MD, USA
| | - Subramaniam Krishnan
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Elizabeth Chiyka
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Mehran Fazli
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Rittal Mehta
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Michael Considine
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Leslie Cope
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Audrey C Knight
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Anissa Elayadi
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Anne Fox
- Naval Medical Research Unit EURAFCENT Ghana detachment, Accra, Ghana
| | - Ronna Hertzano
- Section on Omics and Translational Science of Hearing, Neurotology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Andrew G Letizia
- Naval Medical Research Unit EURAFCENT Ghana detachment, Accra, Ghana
| | - Alex Owusu-Ofori
- Laboratory Services Directorate, Komfo Anokye Teaching Hospital (KATH), Kumasi, Ghana
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Isaac Boakye
- Research and Development Unit, KATH, Kumasi, Ghana
| | - Albert A Aduboffour
- Laboratory Services Directorate, Komfo Anokye Teaching Hospital (KATH), Kumasi, Ghana
| | - Daniel Ansong
- Child Health Directorate, KATH, Kumasi, Ghana
- Department of Child Health, KNUST, Kumasi, Ghana
| | - Eno Biney
- Accident and Emergency Department, KATH, Kumasi, Ghana
| | - George Oduro
- Accident and Emergency Department, KATH, Kumasi, Ghana
| | - Kevin L Schully
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Command-Frederick, Ft. Detrick, MD, USA
| | - Danielle V Clark
- Austere environments Consortium for Enhanced Sepsis Outcomes (ACESO), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
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Bhavani SV, Robichaux C, Verhoef PA, Churpek MM, Coopersmith CM. Using Trajectories of Bedside Vital Signs to Identify COVID-19 Subphenotypes. Chest 2024; 165:529-539. [PMID: 37748574 PMCID: PMC10925543 DOI: 10.1016/j.chest.2023.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/23/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Trajectories of bedside vital signs have been used to identify sepsis subphenotypes with distinct outcomes and treatment responses. The objective of this study was to validate the vitals trajectory model in a multicenter cohort of patients hospitalized with COVID-19 and to evaluate the clinical characteristics and outcomes of the resulting subphenotypes. RESEARCH QUESTION Can the trajectory of routine bedside vital signs identify COVID-19 subphenotypes with distinct clinical characteristics and outcomes? STUDY DESIGN AND METHODS The study included adult patients admitted with COVID-19 to four academic hospitals in the Emory Healthcare system between March 1, 2020, and May 31, 2022. Using a validated group-based trajectory model, we classified patients into previously defined vital sign trajectories using oral temperature, heart rate, respiratory rate, and systolic and diastolic BP measured in the first 8 h of hospitalization. Clinical characteristics, biomarkers, and outcomes were compared between subphenotypes. Heterogeneity of treatment effect to tocilizumab was evaluated. RESULTS The 7,065 patients with hospitalized COVID-19 were classified into four subphenotypes: group A (n = 1,429, 20%)-high temperature, heart rate, respiratory rate, and hypotensive; group B (1,454, 21%)-high temperature, heart rate, respiratory rate, and hypertensive; group C (2,996, 42%)-low temperature, heart rate, respiratory rate, and normotensive; and group D (1,186, 17%)-low temperature, heart rate, respiratory rate, and hypotensive. Groups A and D had higher ORs of mechanical ventilation, vasopressors, and 30-day inpatient mortality (P < .001). On comparing patients receiving tocilizumab (n = 55) with those who met criteria for tocilizumab but were admitted before its use (n = 461), there was significant heterogeneity of treatment effect across subphenotypes in the association of tocilizumab with 30-day mortality (P = .001). INTERPRETATION By using bedside vital signs available in even low-resource settings, we found novel subphenotypes associated with distinct manifestations of COVID-19, which could lead to preemptive and targeted treatments.
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Affiliation(s)
| | - Chad Robichaux
- Department of Biomedical Informatics, Emory University, Atlanta, GA
| | - Philip A Verhoef
- Department of Medicine, University of Hawaii John A. Burns School of Medicine, Honolulu, HI; Hawaii Permanente Medical Group, Honolulu, HI
| | | | - Craig M Coopersmith
- Emory Critical Care Center, Atlanta, GA; Department of Surgery, Emory University, Atlanta, GA
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Zhang T, Wang S, Hua D, Shi X, Deng H, Jin S, Lv X. Identification of ZIP8-induced ferroptosis as a major type of cell death in monocytes under sepsis conditions. Redox Biol 2024; 69:102985. [PMID: 38103342 PMCID: PMC10764267 DOI: 10.1016/j.redox.2023.102985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 12/19/2023] Open
Abstract
Sepsis is a heterogenous syndrome with concurrent hyperinflammation and immune suppression. A prominent feature of immunosuppression during sepsis is the dysfunction and loss of monocytes; however, the major type of cell death contributing to this depletion, as well as its underlying molecular mechanisms, are yet to be identified. In this study, we confirmed the monocyte loss in septic patients based on a pooled gene expression data of periphery leukocytes. Using the collected reference gene sets from databases and published studies, we identified ferroptosis with a greater capacity to distinguish between sepsis and control samples than other cell death types. Further investigation on the molecular drivers, by a genetic algorithm-based feature selection and a weighted gene co-expression network analysis, revealed that zrt-/irt-like protein 8 (ZIP8), encoded by SLC39A8, was closely associated with ferroptosis of monocytes during sepsis. We validated the increase of ZIP8 of monocytes with in vivo and in vitro experiments. The in vitro studies also showed that downregulation of ZIP8 alleviated the lipopolysaccharide-induced lipid peroxidation, as well as restoring the reduction of GPX4, FTH1 and xCT. These findings suggest that ferroptosis might be a key factor in the loss of monocytes during sepsis, and that the heightened expression of ZIP8 may facilitate this progression.
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Affiliation(s)
- Tong Zhang
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Sheng Wang
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Dongsheng Hua
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Xuan Shi
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Huimin Deng
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Shuqing Jin
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200092, China.
| | - Xin Lv
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200092, China.
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5
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Beltrán-García J, Casabó-Vallés G, Osca-Verdegal R, Navarrete-López P, Rodriguez-Gimillo M, Nacher-Sendra E, Ferrando-Sánchez C, García-López E, Pallardó FV, Carbonell N, Mena-Mollá S, García-Giménez JL. Alterations in leukocyte DNA methylome are associated to immunosuppression in severe clinical phenotypes of septic patients. Front Immunol 2024; 14:1333705. [PMID: 38235139 PMCID: PMC10791922 DOI: 10.3389/fimmu.2023.1333705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024] Open
Abstract
Introduction Sepsis patients experience a complex interplay of host pro- and anti-inflammatory processes which compromise the clinical outcome. Despite considering the latest clinical and scientific research, our comprehension of the immunosuppressive events in septic episodes remains incomplete. Additionally, a lack of data exists regarding the role of epigenetics in modulating immunosuppression, subsequently impacting patient survival. Methods To advance the current understanding of the mechanisms underlying immunosuppression, in this study we explored the dynamics of DNA methylation using the Infinium Methylation EPIC v1.0 BeadChip Kit in leukocytes from patients suffering from sepsis, septic shock, and critically ill patients as controls, within the first 24 h after admission in the Intensive Care Unit of a tertiary hospital. Results and discussion Employing two distinct analysis approaches (DMRcate and mCSEA) in comparing septic shock and critically ill patients, we identified 1,256 differentially methylated regions (DMRs) intricately linked to critical immune system pathways. The examination of the top 100 differentially methylated positions (DMPs) between septic shock and critically ill patients facilitated a clear demarcation among the three patient groups. Notably, the top 6,657 DMPs exhibited associations with organ dysfunction and lactate levels. Among the individual genes displaying significant differential methylation, IL10, TREM1, IL1B, and TNFAIP8 emerged with the most pronounced methylation alterations across the diverse patient groups when subjected to DNA bisulfite pyrosequencing analysis. These findings underscore the dynamic nature of DNA methylation profiles, highlighting the most pronounced alterations in patients with septic shock, and revealing their close association with the disease.
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Affiliation(s)
- Jesús Beltrán-García
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Carlos III Health Institute, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
- Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Germán Casabó-Vallés
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
- EpiDisease S. L. (Spin-Off CIBER-ISCIII), Parc Científic de la Universitat de València, Valencia, Spain
| | - Rebeca Osca-Verdegal
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Carlos III Health Institute, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
- Salk Institute for Biological Studies, San Diego, CA, United States
| | - Paula Navarrete-López
- Department of Animal Reproduction, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)-Centro Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - María Rodriguez-Gimillo
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Intensive Care Unit, Hospital Clínico Universitario de Valencia (HCUV), Valencia, Spain
| | - Elena Nacher-Sendra
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Carolina Ferrando-Sánchez
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Intensive Care Unit, Hospital Clínico Universitario de Valencia (HCUV), Valencia, Spain
| | - Eva García-López
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Carlos III Health Institute, Valencia, Spain
- EpiDisease S. L. (Spin-Off CIBER-ISCIII), Parc Científic de la Universitat de València, Valencia, Spain
| | - Federico V Pallardó
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Carlos III Health Institute, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Nieves Carbonell
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Intensive Care Unit, Hospital Clínico Universitario de Valencia (HCUV), Valencia, Spain
| | - Salvador Mena-Mollá
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - José Luis García-Giménez
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Carlos III Health Institute, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
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Liang P, Wu Y, Qu S, Younis M, Wang W, Wu Z, Huang X. Exploring the biomarkers and potential therapeutic drugs for sepsis via integrated bioinformatic analysis. BMC Infect Dis 2024; 24:32. [PMID: 38166628 PMCID: PMC10763157 DOI: 10.1186/s12879-023-08883-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Sepsis is a life-threatening condition caused by an excessive inflammatory response to an infection, associated with high mortality. However, the regulatory mechanism of sepsis remains unclear. RESULTS In this study, bioinformatics analysis revealed the novel key biomarkers associated with sepsis and potential regulators. Three public datasets (GSE28750, GSE57065 and GSE95233) were employed to recognize the differentially expressed genes (DEGs). Taking the intersection of DEGs from these three datasets, GO and KEGG pathway enrichment analysis revealed 537 shared DEGs and their biological functions and pathways. These genes were mainly enriched in T cell activation, differentiation, lymphocyte differentiation, mononuclear cell differentiation, and regulation of T cell activation based on GO analysis. Further, pathway enrichment analysis revealed that these DEGs were significantly enriched in Th1, Th2 and Th17 cell differentiation. Additionally, five hub immune-related genes (CD3E, HLA-DRA, IL2RB, ITK and LAT) were identified from the protein-protein interaction network, and sepsis patients with higher expression of hub genes had a better prognosis. Besides, 14 drugs targeting these five hub related genes were revealed on the basis of the DrugBank database, which proved advantageous for treating immune-related diseases. CONCLUSIONS These results strengthen the new understanding of sepsis development and provide a fresh perspective into discriminating the candidate biomarkers for predicting sepsis as well as identifying new drugs for treating sepsis.
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Affiliation(s)
- Pingping Liang
- Foshan Fourth People's Hospital, Guangdong Province, Foshan, 528041, China
- Center for Infection and Immunity and Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital of Sun Yat-Sen University, Guangdong Province, Zhuhai, 519000, China
| | - Yongjian Wu
- Center for Infection and Immunity and Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital of Sun Yat-Sen University, Guangdong Province, Zhuhai, 519000, China
| | - Siying Qu
- Department of Clinical Laboratory, Zhuhai Hospital of Integrated Traditional Chinese and Western Medicine, The Second People's Hospital of Zhuhai, Guangdong Province, Zhuhai, 519020, China
| | - Muhammad Younis
- Foshan Fourth People's Hospital, Guangdong Province, Foshan, 528041, China
- Center for Infection and Immunity and Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital of Sun Yat-Sen University, Guangdong Province, Zhuhai, 519000, China
| | - Wei Wang
- Foshan Fourth People's Hospital, Guangdong Province, Foshan, 528041, China
| | - Zhilong Wu
- Foshan Fourth People's Hospital, Guangdong Province, Foshan, 528041, China.
| | - Xi Huang
- Foshan Fourth People's Hospital, Guangdong Province, Foshan, 528041, China.
- Center for Infection and Immunity and Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital of Sun Yat-Sen University, Guangdong Province, Zhuhai, 519000, China.
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Huang M, Atreya MR, Holder A, Kamaleswaran R. A MACHINE LEARNING MODEL DERIVED FROM ANALYSIS OF TIME-COURSE GENE-EXPRESSION DATASETS REVEALS TEMPORALLY STABLE GENE MARKERS PREDICTIVE OF SEPSIS MORTALITY. Shock 2023; 60:671-677. [PMID: 37752077 PMCID: PMC10662606 DOI: 10.1097/shk.0000000000002226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/28/2023]
Abstract
ABSTRACT Sepsis is associated with significant mortality and morbidity among critically ill patients admitted to intensive care units and represents a major health challenge globally. Given the significant clinical and biological heterogeneity among patients and the dynamic nature of the host immune response, identifying those at high risk of poor outcomes remains a critical challenge. Here, we performed secondary analysis of publicly available time-series gene-expression datasets from peripheral blood of patients admitted to the intensive care unit to elucidate temporally stable gene-expression markers between sepsis survivors and nonsurvivors. Using a limited set of genes that were determined to be temporally stable, we derived a dynamical model using a Support Vector Machine classifier to accurately predict the mortality of sepsis patients. Our model had robust performance in a test dataset, where patients' transcriptome was sampled at alternate time points, with an area under the curve of 0.89 (95% CI, 0.82-0.96) upon 5-fold cross-validation. We also identified 7 potential biomarkers of sepsis mortality (STAT5A, CX3CR1, LCP1, SNRPG, RPS27L, LSM5, SHCBP1) that require future validation. Pending prospective testing, our model may be used to identify sepsis patients with high risk of mortality accounting for the dynamic nature of the disease and with potential therapeutic implications.
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Affiliation(s)
- Min Huang
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, Georgia
| | - Mihir R. Atreya
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, Cincinnati, Ohio
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Andre Holder
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Rishikesan Kamaleswaran
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, Georgia
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia
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8
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Sanchez-Pinto LN, Bhavani SV, Atreya MR, Sinha P. Leveraging Data Science and Novel Technologies to Develop and Implement Precision Medicine Strategies in Critical Care. Crit Care Clin 2023; 39:627-646. [PMID: 37704331 DOI: 10.1016/j.ccc.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Precision medicine aims to identify treatments that are most likely to result in favorable outcomes for subgroups of patients with similar clinical and biological characteristics. The gaps for the development and implementation of precision medicine strategies in the critical care setting are many, but the advent of data science and multi-omics approaches, combined with the rich data ecosystem in the intensive care unit, offer unprecedented opportunities to realize the promise of precision critical care. In this article, the authors review the data-driven and technology-based approaches being leveraged to discover and implement precision medicine strategies in the critical care setting.
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Affiliation(s)
- Lazaro N Sanchez-Pinto
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA; Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA.
| | | | - Mihir R Atreya
- Division of Critical Care Medicine, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Pratik Sinha
- Division of Clinical and Translational Research, Department of Anesthesia, Washington University School of Medicine, 1 Barnes Jewish Hospital Plaza, St. Louis, MO 63110, USA; Division of Critical Care, Department of Anesthesia, Washington University School of Medicine, 1 Barnes Jewish Hospital Plaza, St. Louis, MO 63110, USA
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9
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Liu T, Wen Z, Shao L, Cui Y, Tang X, Miao H, Shi J, Jiang L, Feng S, Zhao Y, Zhang H, Liang Q, Chen D, Zhang Y, Wang C. ATF4 knockdown in macrophage impairs glycolysis and mediates immune tolerance by targeting HK2 and HIF-1α ubiquitination in sepsis. Clin Immunol 2023; 254:109698. [PMID: 37481013 DOI: 10.1016/j.clim.2023.109698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/30/2023] [Accepted: 07/18/2023] [Indexed: 07/24/2023]
Abstract
Strengthened glycolysis is crucial for the macrophage pro-inflammatory response during sepsis. Activating transcription factor 4 (ATF4) plays an important role in regulating glucose and lipid metabolic homeostasis in hepatocytes and adipocytes. However, its immunometabolic role in macrophage during sepsis remains largely unknown. In the present study, we found that the expression of ATF4 in peripheral blood mononuclear cells (PBMCs) was increased and associated with glucose metabolism in septic patients. Atf4 knockdown specifically decreased LPS-induced spleen macrophages and serum pro-inflammatory cytokines levels in mice. Moreover, Atf4 knockdown partially blocked LPS-induced pro-inflammatory cytokines, lactate accumulation and glycolytic capacity in RAW264.7. Mechanically, ATF4 binds to the promoter region of hexokinase II (HK2), and interacts with hypoxia inducible factor-1α (HIF-1α) and stabilizes HIF-1α through ubiquitination modification in response to LPS. Furthermore, ATF4-HIF-1α-HK2-glycolysis axis launches pro-inflammatory response in macrophage depending on the activation of mammalian target of rapamycin (mTOR). Importantly, Atf4 overexpression improves the decreased level of pro-inflammatory cytokines and lactate secretion and HK2 expression in LPS-induced tolerant macrophages. In conclusion, we propose a novel function of ATF4 as a crucial glycolytic activator contributing to pro-inflammatory response and improving immune tolerant in macrophage involved in sepsis. So, ATF4 could be a potential new target for immunotherapy of sepsis.
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Affiliation(s)
- Tiantian Liu
- Department of Critical Care Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, 200062 Shanghai, China; Laboratory of Critical Care Translational Medicine, Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, 200062 Shanghai, China
| | - Zhenliang Wen
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China
| | - Lujing Shao
- Department of Critical Care Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, 200062 Shanghai, China; Laboratory of Critical Care Translational Medicine, Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, 200062 Shanghai, China
| | - Yun Cui
- Department of Critical Care Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, 200062 Shanghai, China; Laboratory of Critical Care Translational Medicine, Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, 200062 Shanghai, China; Institute of Pediatric Critical Care, Shanghai Jiao Tong University, 200062, Shanghai, China
| | - Xiaomeng Tang
- Department of Critical Care Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, 200062 Shanghai, China; Laboratory of Critical Care Translational Medicine, Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, 200062 Shanghai, China
| | - Huijie Miao
- Department of Critical Care Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, 200062 Shanghai, China; Laboratory of Critical Care Translational Medicine, Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, 200062 Shanghai, China; Institute of Pediatric Critical Care, Shanghai Jiao Tong University, 200062, Shanghai, China
| | - Jingyi Shi
- Department of Critical Care Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, 200062 Shanghai, China; Laboratory of Critical Care Translational Medicine, Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, 200062 Shanghai, China; Institute of Pediatric Critical Care, Shanghai Jiao Tong University, 200062, Shanghai, China
| | - Linlin Jiang
- Department of Clinical Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Shuyun Feng
- Department of Critical Care Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, 200062 Shanghai, China; Laboratory of Critical Care Translational Medicine, Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, 200062 Shanghai, China
| | - Yilin Zhao
- Department of Critical Care Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, 200062 Shanghai, China; Laboratory of Critical Care Translational Medicine, Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, 200062 Shanghai, China
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Qiming Liang
- Research Center of Translational Medicine, Shanghai Institute of Immunology, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dechang Chen
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025 Shanghai, China..
| | - Yucai Zhang
- Department of Critical Care Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, 200062 Shanghai, China; Laboratory of Critical Care Translational Medicine, Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, 200062 Shanghai, China; Institute of Pediatric Critical Care, Shanghai Jiao Tong University, 200062, Shanghai, China.
| | - Chunxia Wang
- Department of Critical Care Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, 200062 Shanghai, China; Laboratory of Critical Care Translational Medicine, Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, 200062 Shanghai, China; Institute of Pediatric Critical Care, Shanghai Jiao Tong University, 200062, Shanghai, China.
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10
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Wang J, Cai J, Yue L, Zhou X, Hu C, Zhu H. Identification of Potential Biomarkers of Septic Shock Based on Pathway and Transcriptome Analyses of Immune-Related Genes. Genet Res (Camb) 2023; 2023:9991613. [PMID: 37575977 PMCID: PMC10423089 DOI: 10.1155/2023/9991613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/19/2023] [Accepted: 07/03/2023] [Indexed: 08/15/2023] Open
Abstract
Immunoregulation is crucial to septic shock (SS) but has not been clearly explained. Our aim was to explore potential biomarkers for SS by pathway and transcriptional analyses of immune-related genes to improve early detection. GSE57065 and GSE95233 microarray data were used to screen differentially expressed genes (DEGs) in SS. Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analyses of DEGs were performed, and correlations between immune cell and pathway enrichment scores were analyzed. The predictive value of candidate genes was evaluated by receiver operating characteristic (ROC) curves. GSE66099, GSE4607, and GSE13904 datasets were used for external validation. Blood samples from six patients and six controls were collected for validation by qRT-PCR and western blotting. In total, 550 DEGs in SS were identified; these genes were involved in the immune response, inflammation, and infection. Immune-related pathways and levels of infiltration of CD4 + TCM, CD8 + T cells, and preadipocytes differed between SS cases and controls. Seventeen genes were identified as potential biomarkers of SS (areas under ROC curves >0.9). The downregulation of CD8A, CD247, CD3G, LCK, and HLA-DRA in SS was experimentally confirmed. We identified several immune-related biomarkers in SS that may improve early identification of disease risk.
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Affiliation(s)
- Jie Wang
- Department of Critical Care Medicine, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, China
| | - Jie Cai
- Department of Critical Care Medicine, HUST Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, Guangdong 518052, China
| | - Linlin Yue
- Department of Critical Care Medicine, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, China
| | - Xixi Zhou
- Department of Critical Care Medicine, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, China
| | - Chunlin Hu
- Department of Emergency Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080 Guangdong, China
| | - Hongquan Zhu
- Department of Critical Care Medicine, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, China
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11
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Bhavani SV, Xiong L, Pius A, Semler M, Qian ET, Verhoef PA, Robichaux C, Coopersmith CM, Churpek MM. Comparison of time series clustering methods for identifying novel subphenotypes of patients with infection. J Am Med Inform Assoc 2023; 30:1158-1166. [PMID: 37043759 PMCID: PMC10198539 DOI: 10.1093/jamia/ocad063] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/06/2023] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
OBJECTIVE Severe infection can lead to organ dysfunction and sepsis. Identifying subphenotypes of infected patients is essential for personalized management. It is unknown how different time series clustering algorithms compare in identifying these subphenotypes. MATERIALS AND METHODS Patients with suspected infection admitted between 2014 and 2019 to 4 hospitals in Emory healthcare were included, split into separate training and validation cohorts. Dynamic time warping (DTW) was applied to vital signs from the first 8 h of hospitalization, and hierarchical clustering (DTW-HC) and partition around medoids (DTW-PAM) were used to cluster patients into subphenotypes. DTW-HC, DTW-PAM, and a previously published group-based trajectory model (GBTM) were evaluated for agreement in subphenotype clusters, trajectory patterns, and subphenotype associations with clinical outcomes and treatment responses. RESULTS There were 12 473 patients in training and 8256 patients in validation cohorts. DTW-HC, DTW-PAM, and GBTM models resulted in 4 consistent vitals trajectory patterns with significant agreement in clustering (71-80% agreement, P < .001): group A was hyperthermic, tachycardic, tachypneic, and hypotensive. Group B was hyperthermic, tachycardic, tachypneic, and hypertensive. Groups C and D had lower temperatures, heart rates, and respiratory rates, with group C normotensive and group D hypotensive. Group A had higher odds ratio of 30-day inpatient mortality (P < .01) and group D had significant mortality benefit from balanced crystalloids compared to saline (P < .01) in all 3 models. DISCUSSION DTW- and GBTM-based clustering algorithms applied to vital signs in infected patients identified consistent subphenotypes with distinct clinical outcomes and treatment responses. CONCLUSION Time series clustering with distinct computational approaches demonstrate similar performance and significant agreement in the resulting subphenotypes.
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Affiliation(s)
- Sivasubramanium V Bhavani
- Department of Medicine, Emory University, Atlanta, Georgia, USA
- Emory Critical Care Center, Atlanta, Georgia, USA
| | - Li Xiong
- Department of Computer Science, Emory University, Atlanta, Georgia, USA
| | - Abish Pius
- Department of Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Matthew Semler
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Edward T Qian
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Philip A Verhoef
- Department of Medicine, University of Hawaii John A. Burns School of Medicine, Honolulu, Hawaii, USA
- Hawaii Permanente Medical Group, Honolulu, Hawaii, USA
| | - Chad Robichaux
- Department of Biomedical Informatics, Emory University, Atlanta, Georgia, USA
| | - Craig M Coopersmith
- Emory Critical Care Center, Atlanta, Georgia, USA
- Department of Surgery, Emory University, Atlanta, Georgia, USA
| | - Matthew M Churpek
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin, USA
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12
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Abstract
Heterogeneity in sepsis and acute respiratory distress syndrome (ARDS) is increasingly being recognized as one of the principal barriers to finding efficacious targeted therapies. The advent of multiple high-throughput biological data ("omics"), coupled with the widespread access to increased computational power, has led to the emergence of phenotyping in critical care. Phenotyping aims to use a multitude of data to identify homogenous subgroups within an otherwise heterogenous population. Increasingly, phenotyping schemas are being applied to sepsis and ARDS to increase understanding of these clinical conditions and identify potential therapies. Here we present a selective review of the biological phenotyping schemas applied to sepsis and ARDS. Further, we outline some of the challenges involved in translating these conceptual findings to bedside clinical decision-making tools.
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Affiliation(s)
- Pratik Sinha
- Division of Clinical & Translational Research and Division of Critical Care, Department of Anesthesia, Washington University, St. Louis, Missouri, USA;
| | - Nuala J Meyer
- Division of Pulmonary, Allergy, and Critical Care Medicine; Center for Translational Lung Biology; and Lung Biology Institute, University of Pennsylvania Perelman School of Medicine; Philadelphia, Pennsylvania, USA
| | - Carolyn S Calfee
- Division of Pulmonary, Critical Care, Allergy & Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA
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13
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Bhavani SV, Semler M, Qian ET, Verhoef PA, Robichaux C, Churpek MM, Coopersmith CM. Development and validation of novel sepsis subphenotypes using trajectories of vital signs. Intensive Care Med 2022; 48:1582-1592. [PMID: 36152041 PMCID: PMC9510534 DOI: 10.1007/s00134-022-06890-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/06/2022] [Indexed: 12/15/2022]
Abstract
PURPOSE Sepsis is a heterogeneous syndrome and identification of sub-phenotypes is essential. This study used trajectories of vital signs to develop and validate sub-phenotypes and investigated the interaction of sub-phenotypes with treatment using randomized controlled trial data. METHODS All patients with suspected infection admitted to four academic hospitals in Emory Healthcare between 2014-2017 (training cohort) and 2018-2019 (validation cohort) were included. Group-based trajectory modeling was applied to vital signs from the first 8 h of hospitalization to develop and validate vitals trajectory sub-phenotypes. The associations between sub-phenotypes and outcomes were evaluated in patients with sepsis. The interaction between sub-phenotype and treatment with balanced crystalloids versus saline was tested in a secondary analysis of SMART (Isotonic Solutions and Major Adverse Renal Events Trial). RESULTS There were 12,473 patients with suspected infection in training and 8256 patients in validation cohorts, and 4 vitals trajectory sub-phenotypes were found. Group A (N = 3483, 28%) were hyperthermic, tachycardic, tachypneic, and hypotensive. Group B (N = 1578, 13%) were hyperthermic, tachycardic, tachypneic (not as pronounced as Group A) and hypertensive. Groups C (N = 4044, 32%) and D (N = 3368, 27%) had lower temperatures, heart rates, and respiratory rates, with Group C normotensive and Group D hypotensive. In the 6,919 patients with sepsis, Groups A and B were younger while Groups C and D were older. Group A had the lowest prevalence of congestive heart failure, hypertension, diabetes mellitus, and chronic kidney disease, while Group B had the highest prevalence. Groups A and D had the highest vasopressor use (p < 0.001 for all analyses above). In logistic regression, 30-day mortality was significantly higher in Groups A and D (p < 0.001 and p = 0.03, respectively). In the SMART trial, sub-phenotype significantly modified treatment effect (p = 0.03). Group D had significantly lower odds of mortality with balanced crystalloids compared to saline (odds ratio (OR) 0.39, 95% confidence interval (CI) 0.23-0.67, p < 0.001). CONCLUSION Sepsis sub-phenotypes based on vital sign trajectory were consistent across cohorts, had distinct outcomes, and different responses to treatment with balanced crystalloids versus saline.
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Affiliation(s)
- Sivasubramanium V Bhavani
- Department of Medicine, Emory University, Atlanta, GA, USA.
- Emory Critical Care Center, Atlanta, GA, USA.
- Division of Pulmonary, Allergy, Critical Care & Sleep Medicine, Emory University School of Medicine, 615 Michael St., Atlanta, GA, 30322, USA.
| | - Matthew Semler
- Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Edward T Qian
- Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Philip A Verhoef
- Department of Medicine, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA
- Hawaii Permanente Medical Group, Honolulu, HI, USA
| | - Chad Robichaux
- Department of Biomedical Informatics, Emory University, Atlanta, GA, USA
| | - Matthew M Churpek
- Department of Medicine, University of Wisconsin, Madison, WI, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - Craig M Coopersmith
- Emory Critical Care Center, Atlanta, GA, USA
- Department of Surgery, Emory University, Atlanta, GA, USA
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14
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Abstract
PURPOSE OF REVIEW Sleep is particularly important for critically ill patients. Here, we review the latest evidence on how sleep and circadian disruption in the intensive care unit (ICU) affects physiology and clinical outcomes, as well as the most recent advances in sleep and circadian rhythm promoting interventions including therapeutics. RECENT FINDINGS On a molecular level, clock genes dysrhythmia and altered immunity are clearly linked, particularly in sepsis. Melatonin may also be associated with insulin sensitivity in ICU patients. Clinically, changes in sleep architecture are associated with delirium, and sleep-promoting interventions in the form of multifaceted care bundles may reduce its incidence. Regarding medications, one recent randomized controlled trial (RCT) on melatonin showed no difference in sleep quality or incidence of delirium. SUMMARY Further investigation is needed to establish the clinical relevance of sleep and circadian disruption in the ICU. For interventions, standardized protocols of sleep promotion bundles require validation by larger multicenter trials. Administratively, such protocols should be individualized to both organizational and independent patient needs. Incorporating pharmacotherapy such as melatonin and nocturnal dexmedetomidine requires further evaluation in large RCTs.
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Affiliation(s)
- Eugenia Y Lee
- Interdepartmental Division of Critical Care Medicine, University of Toronto
| | - M Elizabeth Wilcox
- Interdepartmental Division of Critical Care Medicine, University of Toronto
- Department of Medicine, University Health Network, Toronto, Canada
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15
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Gong T, Liu Y, Tian Z, Zhang M, Gao H, Peng Z, Yin S, Cheung CW, Liu Y. Identification of immune-related endoplasmic reticulum stress genes in sepsis using bioinformatics and machine learning. Front Immunol 2022; 13:995974. [PMID: 36203606 PMCID: PMC9530749 DOI: 10.3389/fimmu.2022.995974] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/02/2022] [Indexed: 11/18/2022] Open
Abstract
Background Sepsis-induced apoptosis of immune cells leads to widespread depletion of key immune effector cells. Endoplasmic reticulum (ER) stress has been implicated in the apoptotic pathway, although little is known regarding its role in sepsis-related immune cell apoptosis. The aim of this study was to develop an ER stress-related prognostic and diagnostic signature for sepsis through bioinformatics and machine learning algorithms on the basis of the differentially expressed genes (DEGs) between healthy controls and sepsis patients. Methods The transcriptomic datasets that include gene expression profiles of sepsis patients and healthy controls were downloaded from the GEO database. The immune-related endoplasmic reticulum stress hub genes associated with sepsis patients were identified using the new comprehensive machine learning algorithm and bioinformatics analysis which includes functional enrichment analyses, consensus clustering, weighted gene coexpression network analysis (WGCNA), and protein-protein interaction (PPI) network construction. Next, the diagnostic model was established by logistic regression and the molecular subtypes of sepsis were obtained based on the significant DEGs. Finally, the potential diagnostic markers of sepsis were screened among the significant DEGs, and validated in multiple datasets. Results Significant differences in the type and abundance of infiltrating immune cell populations were observed between the healthy control and sepsis patients. The immune-related ER stress genes achieved strong stability and high accuracy in predicting sepsis patients. 10 genes were screened as potential diagnostic markers for sepsis among the significant DEGs, and were further validated in multiple datasets. In addition, higher expression levels of SCAMP5 mRNA and protein were observed in PBMCs isolated from sepsis patients than healthy donors (n = 5). Conclusions We established a stable and accurate signature to evaluate the diagnosis of sepsis based on the machine learning algorithms and bioinformatics. SCAMP5 was preliminarily identified as a diagnostic marker of sepsis that may affect its progression by regulating ER stress.
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Affiliation(s)
- Ting Gong
- Department of Anesthesiology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yongbin Liu
- Department of Radiology, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Zhiyuan Tian
- Department of Anesthesiology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Min Zhang
- Department of Anesthesiology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Hejun Gao
- Department of Anesthesiology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Zhiyong Peng
- Department of Anesthesiology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Shuang Yin
- Department of Anesthesiology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
- *Correspondence: Youtan Liu, ; Chi Wai Cheung, ; Shuang Yin,
| | - Chi Wai Cheung
- Department of Anesthesiology, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- *Correspondence: Youtan Liu, ; Chi Wai Cheung, ; Shuang Yin,
| | - Youtan Liu
- Department of Anesthesiology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China
- *Correspondence: Youtan Liu, ; Chi Wai Cheung, ; Shuang Yin,
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16
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Bain CR, Myles PS, Taylor R, Trahair H, Lee YP, Croft L, Peyton PJ, Painter T, Chan MTV, Wallace S, Corcoran T, Shaw AD, Paul E, Ziemann M, Bozaoglu K. Methylomic and transcriptomic characterization of postoperative systemic inflammatory dysregulation. Transl Res 2022; 247:79-98. [PMID: 35470009 DOI: 10.1016/j.trsl.2022.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/04/2022] [Accepted: 04/14/2022] [Indexed: 12/17/2022]
Abstract
In this study, we define and validate a state of postoperative systemic inflammatory dysregulation (PSID) based on postoperative phenotypic extremes of plasma C-reactive protein concentration following major abdominal surgery. PSID manifested clinically with significantly higher rates of sepsis, complications, longer hospital stays and poorer short, and long-term outcomes. We hypothesized that PSID will be associated with, and potentially predicted by, altered patterns of genome-wide peripheral blood mononuclear cell differential DNA methylation and gene expression. We identified altered DNA methylation and differential gene expression in specific immune and metabolic pathways during PSID. Our findings suggest that dysregulation results in, or from, dramatic changes in differential DNA methylation and highlights potential targets for early detection and treatment. The combination of altered DNA methylation and gene expression suggests that dysregulation is mediated at multiple levels within specific gene sets and hence, nonspecific anti-inflammatory treatments such as corticosteroids alone are unlikely to represent an effective therapeutic strategy.
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Affiliation(s)
- Chris R Bain
- Genomics and Systems Biology Laboratory, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Anesthesiology and Perioperative Medicine, Alfred Hospital, Melbourne Victoria, Australia; Department of Anesthesiology and Perioperative Medicine, Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia.
| | - Paul S Myles
- Department of Anesthesiology and Perioperative Medicine, Alfred Hospital, Melbourne Victoria, Australia; Department of Anesthesiology and Perioperative Medicine, Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
| | - Rachael Taylor
- Genomics and Systems Biology Laboratory, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Hugh Trahair
- Genomics and Systems Biology Laboratory, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Yin Peng Lee
- Genomics Centre, School of life and environmental sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds, Victoria, Australia
| | - Larry Croft
- Genomics Centre, School of life and environmental sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds, Victoria, Australia
| | - Philip J Peyton
- Department of Anesthesia, The Austin Hospital and Department of Critical Care, Melbourne Medical School, University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas Painter
- Department of Anesthesia, Royal Adelaide Hospital, Discipline of Acute Care Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Matthew T V Chan
- Department of Anesthesia and Intensive Care, The Chinese Universtiy of Hong Kong, Hong Kong Special Administrative Region, China
| | - Sophie Wallace
- Department of Anesthesiology and Perioperative Medicine, Alfred Hospital, Melbourne Victoria, Australia; Department of Anesthesiology and Perioperative Medicine, Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
| | - Tomás Corcoran
- Department of Anesthesia and Pain Medicine, Royal Perth Hospital, School of Medicine and Pharmacology, University of Western Australia, Perth, Western Australia, Australia; School of Public Health and Preventative Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University, Victoria, Australia
| | - Andrew D Shaw
- Department of Anesthesiology and Critical Care Medicine, Duke University Medical Center, Durham, North Carolina; Department of Intensive Care and Resuscitation, Cleveland Clinic, Cleveland, Ohio
| | - Eldho Paul
- Australian and New Zealand Intensive Care Research Centre, School of Public Health and Preventive Medicine, Monash University, Victoria, Australia
| | - Mark Ziemann
- Genomics Centre, School of life and environmental sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds, Victoria, Australia; Epigenetics in Human Health and Disease Laboratory, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Kiymet Bozaoglu
- Genomics and Systems Biology Laboratory, Baker IDI Heart and Diabetes Institute, Melbourne, Victoria, Australia; Murdoch Children's Research Institute and Department of Pediatrics, University of Melbourne, Victoria, Australia
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17
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Lukaszewski RA, Jones HE, Gersuk VH, Russell P, Simpson A, Brealey D, Walker J, Thomas M, Whitehouse T, Ostermann M, Koch A, Zacharowski K, Kruhoffer M, Chaussabel D, Singer M. Presymptomatic diagnosis of postoperative infection and sepsis using gene expression signatures. Intensive Care Med 2022; 48:1133-1143. [PMID: 35831640 PMCID: PMC9281215 DOI: 10.1007/s00134-022-06769-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 05/29/2022] [Indexed: 12/11/2022]
Abstract
Purpose Early accurate diagnosis of infection ± organ dysfunction (sepsis) remains a major challenge in clinical practice. Utilizing effective biomarkers to identify infection and impending organ dysfunction before the onset of clinical signs and symptoms would enable earlier investigation and intervention. To our knowledge, no prior study has specifically examined the possibility of pre-symptomatic detection of sepsis. Methods Blood samples and clinical/laboratory data were collected daily from 4385 patients undergoing elective surgery. An adjudication panel identified 154 patients with definite postoperative infection, of whom 98 developed sepsis. Transcriptomic profiling and subsequent RT-qPCR were undertaken on sequential blood samples taken postoperatively from these patients in the three days prior to the onset of symptoms. Comparison was made against postoperative day-, age-, sex- and procedure- matched patients who had an uncomplicated recovery (n =151) or postoperative inflammation without infection (n =148). Results Specific gene signatures optimized to predict infection or sepsis in the three days prior to clinical presentation were identified in initial discovery cohorts. Subsequent classification using machine learning with cross-validation with separate patient cohorts and their matched controls gave high Area Under the Receiver Operator Curve (AUC) values. These allowed discrimination of infection from uncomplicated recovery (AUC 0.871), infectious from non-infectious systemic inflammation (0.897), sepsis from other postoperative presentations (0.843), and sepsis from uncomplicated infection (0.703). Conclusion Host biomarker signatures may be able to identify postoperative infection or sepsis up to three days in advance of clinical recognition. If validated in future studies, these signatures offer potential diagnostic utility for postoperative management of deteriorating or high-risk surgical patients and, potentially, other patient populations. Supplementary Information The online version contains supplementary material available at 10.1007/s00134-022-06769-z.
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Affiliation(s)
- Roman A. Lukaszewski
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire UK
- Bloomsbury Institute of Intensive Care Medicine, Division of Medicine, University College London, London, UK
| | - Helen E. Jones
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire UK
| | | | - Paul Russell
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire UK
- Salisbury NHS Foundation Trust, Salisbury, Wiltshire UK
| | - Andrew Simpson
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire UK
| | - David Brealey
- Bloomsbury Institute of Intensive Care Medicine, Division of Medicine, University College London, London, UK
- Division of Critical Care and, NIHR University College London Hospitals Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, London, UK
| | - Jonathan Walker
- Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool, UK
| | - Matt Thomas
- University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Tony Whitehouse
- University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, Edgbaston, Birmingham, UK
| | - Marlies Ostermann
- Intensive Care Unit, Guy’s and St Thomas’s, NHS Foundation Trust, London, UK
| | - Alexander Koch
- Klinikum Esslingen, 73707 Esslingen, Germany
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany
| | - Kai Zacharowski
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany
| | | | - Damien Chaussabel
- Benaroya Research Institute, Seattle, WA 98101-2795 USA
- Laboratory of Translational Systems Immunology, Sidra Medicine, Doha, Qatar
| | - Mervyn Singer
- Bloomsbury Institute of Intensive Care Medicine, Division of Medicine, University College London, London, UK
- Division of Critical Care and, NIHR University College London Hospitals Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, London, UK
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18
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Córneo E, Michels M, Abatti M, Vieira A, Gonçalves RC, Gabriel FF, Borges H, Goulart A, da Silva Matos N, Dominguini D, Varela R, Valvassori S, Dal-Pizzol F. Enriched environment causes epigenetic changes in hippocampus and improves long-term cognitive function in sepsis. Sci Rep 2022; 12:11529. [PMID: 35798809 PMCID: PMC9262921 DOI: 10.1038/s41598-022-14660-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 06/10/2022] [Indexed: 11/16/2022] Open
Abstract
Sepsis is defined as a life-threatening organ dysfunction caused by an inappropriate host response to infection. The presence of oxidative stress and inflammatory mediators in sepsis leads to dysregulated gene expression, leading to a hyperinflammatory response. Environmental conditions play an important role in various pathologies depending on the stimulus it presents. A standard environment condition (SE) may offer reduced sensory and cognitive stimulation, but an enriched environment improves spatial learning, prevents cognitive deficits induced by disease stress, and is an important modulator of epigenetic enzymes. The study evaluated the epigenetic alterations and the effects of the environmental enrichment (EE) protocol in the brain of animals submitted to sepsis by cecal ligation and perforation (CLP). Male Wistar rats were divided into sham and CLP at 24 h, 72 h, 10 days and 30 days after sepsis. Other male Wistar rats were distributed in a SE or in EE for forty-five days. Behavioral tests, analysis of epigenetic enzymes:histone acetylase (HAT), histone deacetylase (HDAC) and DNA methyltransferase (DNMT), biochemical and synaptic plasticity analyzes were performed. An increase in HDAC and DNMT activities was observed at 72 h, 10 days and 30 days. There was a positive correlation between epigenetic enzymes DNMT and HDAC 24 h, 10 days and 30 days. After EE, HDAC and DNMT enzyme activity decreased, cognitive impairment was reversed, IL1-β levels decreased and there was an increase in PSD-95 levels in the hippocampus. Interventions in environmental conditions can modulate the outcomes of long-term cognitive consequences associated with sepsis, supporting the idea of the potential benefits of EE.
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Affiliation(s)
- Emily Córneo
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Av. Universitária, 1105, Criciúma, SC, 88806000, Brazil.
| | - Monique Michels
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Av. Universitária, 1105, Criciúma, SC, 88806000, Brazil
| | - Mariane Abatti
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Av. Universitária, 1105, Criciúma, SC, 88806000, Brazil
| | - Andriele Vieira
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Av. Universitária, 1105, Criciúma, SC, 88806000, Brazil
| | - Renata Casagrande Gonçalves
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Av. Universitária, 1105, Criciúma, SC, 88806000, Brazil
| | - Filipe Fernandes Gabriel
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Av. Universitária, 1105, Criciúma, SC, 88806000, Brazil
| | - Heloisa Borges
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Av. Universitária, 1105, Criciúma, SC, 88806000, Brazil
| | - Amanda Goulart
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Av. Universitária, 1105, Criciúma, SC, 88806000, Brazil
| | - Natan da Silva Matos
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Av. Universitária, 1105, Criciúma, SC, 88806000, Brazil
| | - Diogo Dominguini
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Av. Universitária, 1105, Criciúma, SC, 88806000, Brazil
| | - Roger Varela
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil
| | - Samira Valvassori
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil
| | - Felipe Dal-Pizzol
- Laboratory of Experimental Pathophysiology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Av. Universitária, 1105, Criciúma, SC, 88806000, Brazil
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19
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Kreitmann L, Bodinier M, Fleurie A, Imhoff K, Cazalis MA, Peronnet E, Cerrato E, Tardiveau C, Conti F, Llitjos JF, Textoris J, Monneret G, Blein S, Brengel-Pesce K. Mortality Prediction in Sepsis With an Immune-Related Transcriptomics Signature: A Multi-Cohort Analysis. Front Med (Lausanne) 2022; 9:930043. [PMID: 35847809 PMCID: PMC9280291 DOI: 10.3389/fmed.2022.930043] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/08/2022] [Indexed: 12/29/2022] Open
Abstract
Background Novel biomarkers are needed to progress toward individualized patient care in sepsis. The immune profiling panel (IPP) prototype has been designed as a fully-automated multiplex tool measuring expression levels of 26 genes in sepsis patients to explore immune functions, determine sepsis endotypes and guide personalized clinical management. The performance of the IPP gene set to predict 30-day mortality has not been extensively characterized in heterogeneous cohorts of sepsis patients. Methods Publicly available microarray data of sepsis patients with widely variable demographics, clinical characteristics and ethnical background were co-normalized, and the performance of the IPP gene set to predict 30-day mortality was assessed using a combination of machine learning algorithms. Results We collected data from 1,801 arrays sampled on sepsis patients and 598 sampled on controls in 17 studies. When gene expression was assayed at day 1 following admission (1,437 arrays sampled on sepsis patients, of whom 1,161 were alive and 276 (19.2%) were dead at day 30), the IPP gene set showed good performance to predict 30-day mortality, with an area under the receiving operating characteristics curve (AUROC) of 0.710 (CI 0.652-0.768). Importantly, there was no statistically significant improvement in predictive performance when training the same models with all genes common to the 17 microarray studies (n = 7,122 genes), with an AUROC = 0.755 (CI 0.697-0.813, p = 0.286). In patients with gene expression data sampled at day 3 following admission or later, the IPP gene set had higher performance, with an AUROC = 0.804 (CI 0.643-0.964), while the total gene pool had an AUROC = 0.787 (CI 0.610-0.965, p = 0.811). Conclusion Using pooled publicly-available gene expression data from multiple cohorts, we showed that the IPP gene set, an immune-related transcriptomics signature conveys relevant information to predict 30-day mortality when sampled at day 1 following admission. Our data also suggests that higher predictive performance could be obtained when assaying gene expression at later time points during the course of sepsis. Prospective studies are needed to confirm these findings using the IPP gene set on its dedicated measurement platform.
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Affiliation(s)
- Louis Kreitmann
- EA 7426 “Pathophysiology of Injury-Induced Immunosuppression”, Joint Research Unit Université Claude Bernard Lyon 1 – Hospices Civils de Lyon – bioMérieux, Lyon, France
- Open Innovation and Partnerships (OIP), bioMérieux S.A., Marcy-l’Étoile, France
| | - Maxime Bodinier
- EA 7426 “Pathophysiology of Injury-Induced Immunosuppression”, Joint Research Unit Université Claude Bernard Lyon 1 – Hospices Civils de Lyon – bioMérieux, Lyon, France
- Open Innovation and Partnerships (OIP), bioMérieux S.A., Marcy-l’Étoile, France
| | - Aurore Fleurie
- EA 7426 “Pathophysiology of Injury-Induced Immunosuppression”, Joint Research Unit Université Claude Bernard Lyon 1 – Hospices Civils de Lyon – bioMérieux, Lyon, France
- Open Innovation and Partnerships (OIP), bioMérieux S.A., Marcy-l’Étoile, France
| | - Katia Imhoff
- Data Science, bioMérieux S.A., Marcy-l’Etoile, France
| | - Marie-Angelique Cazalis
- EA 7426 “Pathophysiology of Injury-Induced Immunosuppression”, Joint Research Unit Université Claude Bernard Lyon 1 – Hospices Civils de Lyon – bioMérieux, Lyon, France
- Open Innovation and Partnerships (OIP), bioMérieux S.A., Marcy-l’Étoile, France
| | - Estelle Peronnet
- EA 7426 “Pathophysiology of Injury-Induced Immunosuppression”, Joint Research Unit Université Claude Bernard Lyon 1 – Hospices Civils de Lyon – bioMérieux, Lyon, France
- Open Innovation and Partnerships (OIP), bioMérieux S.A., Marcy-l’Étoile, France
| | - Elisabeth Cerrato
- EA 7426 “Pathophysiology of Injury-Induced Immunosuppression”, Joint Research Unit Université Claude Bernard Lyon 1 – Hospices Civils de Lyon – bioMérieux, Lyon, France
- Open Innovation and Partnerships (OIP), bioMérieux S.A., Marcy-l’Étoile, France
| | - Claire Tardiveau
- EA 7426 “Pathophysiology of Injury-Induced Immunosuppression”, Joint Research Unit Université Claude Bernard Lyon 1 – Hospices Civils de Lyon – bioMérieux, Lyon, France
- Open Innovation and Partnerships (OIP), bioMérieux S.A., Marcy-l’Étoile, France
| | - Filippo Conti
- EA 7426 “Pathophysiology of Injury-Induced Immunosuppression”, Joint Research Unit Université Claude Bernard Lyon 1 – Hospices Civils de Lyon – bioMérieux, Lyon, France
- Immunology Laboratory, Edouard Herriot Hospital – Hospices Civils de Lyon, Lyon, France
| | - Jean-François Llitjos
- EA 7426 “Pathophysiology of Injury-Induced Immunosuppression”, Joint Research Unit Université Claude Bernard Lyon 1 – Hospices Civils de Lyon – bioMérieux, Lyon, France
- Open Innovation and Partnerships (OIP), bioMérieux S.A., Marcy-l’Étoile, France
- Anaesthesia and Critical Care Medicine Department, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France
| | | | - Guillaume Monneret
- EA 7426 “Pathophysiology of Injury-Induced Immunosuppression”, Joint Research Unit Université Claude Bernard Lyon 1 – Hospices Civils de Lyon – bioMérieux, Lyon, France
- Immunology Laboratory, Edouard Herriot Hospital – Hospices Civils de Lyon, Lyon, France
| | - Sophie Blein
- Data Science, bioMérieux S.A., Marcy-l’Etoile, France
| | - Karen Brengel-Pesce
- EA 7426 “Pathophysiology of Injury-Induced Immunosuppression”, Joint Research Unit Université Claude Bernard Lyon 1 – Hospices Civils de Lyon – bioMérieux, Lyon, France
- Open Innovation and Partnerships (OIP), bioMérieux S.A., Marcy-l’Étoile, France
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20
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Hamilton A, Rizzo R, Brod S, Ono M, Perretti M, Cooper D, D'Acquisto F. The immunomodulatory effects of social isolation in mice are linked to temperature control. Brain Behav Immun 2022; 102:179-194. [PMID: 35217174 DOI: 10.1016/j.bbi.2022.02.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/17/2022] [Accepted: 02/18/2022] [Indexed: 12/25/2022] Open
Abstract
Living in isolation is considered an emerging societal problem that negatively affects the physical wellbeing of its sufferers in ways that we are just starting to appreciate. This study investigates the immunomodulatory effects of social isolation in mice, utilising a two-week program of sole cage occupancy followed by the testing of immune-inflammatory resilience to bacterial sepsis. Our results revealed that mice housed in social isolation showed an increased ability to clear bacterial infection compared to control socially housed animals. These effects were associated with specific changes in whole blood gene expression profile and an increased production of classical pro-inflammatory cytokines. Interestingly, equipping socially isolated mice with artificial nests as a substitute for their natural huddling behaviour reversed the increased resistance to bacterial sepsis. Together these results suggest that the control of body temperature through social housing and huddling behaviour are important factors in the regulation of the host immune response to infection in mice and might provide another example of the many ways by which living conditions influence immunity.
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Affiliation(s)
- Alice Hamilton
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Raffaella Rizzo
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Samuel Brod
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Masahiro Ono
- University of London Imperial College Science Technology & Medicine, Department of Life Science, Faculty of Natural Science, London SW7 2AZ, England
| | - Mauro Perretti
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Dianne Cooper
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Fulvio D'Acquisto
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK; School of Life and Health Science, University of Roehampton, London SW15, 4JD, UK.
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21
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Hernandez-Beeftink T, Marcelino-Rodríguez I, Guillen-Guio B, Rodríguez-Pérez H, Lorenzo-Salazar JM, Corrales A, Díaz-de Usera A, González-Montelongo R, Domínguez D, Espinosa E, Villar J, Flores C. Admixture Mapping of Sepsis in European Individuals With African Ancestries. Front Med (Lausanne) 2022; 9:754440. [PMID: 35345767 PMCID: PMC8957104 DOI: 10.3389/fmed.2022.754440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/24/2022] [Indexed: 11/30/2022] Open
Abstract
Sepsis is a severe systemic inflammatory response to infections that is accompanied by organ dysfunction. Although the ancestral genetic background is a relevant factor for sepsis susceptibility, there is a lack of studies using the genetic singularities of a recently admixed population to identify loci involved in sepsis susceptibility. Here we aimed to discover new sepsis loci by completing the first admixture mapping study of sepsis in Canary Islanders, leveraging their distinctive genetic makeup as a mixture of Europeans and African ancestries. We used a case-control approach and inferred local ancestry blocks from genome-wide data from 113,414 polymorphisms genotyped in 343 patients with sepsis and 410 unrelated controls, all ascertained for grandparental origin in the Canary Islands (Spain). Deviations in local ancestries between cases and controls were tested using logistic regressions, followed by fine-mapping analyses based on imputed genotypes, in silico functional assessments, and gene expression analysis centered on the region of interest. The admixture mapping analysis detected that local European ancestry in a locus spanning 1.2 megabases of chromosome 8p23.1 was associated with sepsis (lowest p = 1.37 × 10−4; Odds Ratio [OR] = 0.51; 95%CI = 0.40–0.66). Fine-mapping studies prioritized the variant rs13249564 within intron 1 of MFHAS1 gene associated with sepsis (p = 9.94 × 10−4; OR = 0.65; 95%CI = 0.50–0.84). Functional and gene expression analyses focused on 8p23.1 allowed us to identify alternative genes with possible biological plausibility such as defensins, which are well-known effector molecules of innate immunity. By completing the first admixture mapping study of sepsis, our results revealed a new genetic locus (8p23.1) harboring a number of genes with plausible implications in sepsis susceptibility.
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Affiliation(s)
- Tamara Hernandez-Beeftink
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Research Unit, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - Itahisa Marcelino-Rodríguez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Beatriz Guillen-Guio
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Héctor Rodríguez-Pérez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Jose M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Almudena Corrales
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | | | - David Domínguez
- Department of Anesthesiology, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Elena Espinosa
- Department of Anesthesiology, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - 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
| | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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22
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Yao L, Rey DA, Bulgarelli L, Kast R, Osborn J, Van Ark E, Fang LT, Lau B, Lam H, Teixeira LM, Neto AS, Bellomo R, Deliberato RO. Gene Expression Scoring of Immune Activity Levels for Precision Use of Hydrocortisone in Vasodilatory Shock. Shock 2022; 57:384-391. [PMID: 35081076 PMCID: PMC8868213 DOI: 10.1097/shk.0000000000001910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/06/2021] [Accepted: 01/07/2022] [Indexed: 11/26/2022]
Abstract
PURPOSE Among patients with vasodilatory shock, gene expression scores may identify different immune states. We aimed to test whether such scores are robust in identifying patients' immune state and predicting response to hydrocortisone treatment in vasodilatory shock. MATERIALS AND METHODS We selected genes to generate continuous scores to define previously established subclasses of sepsis. We used these scores to identify a patient's immune state. We evaluated the potential for these states to assess the differential effect of hydrocortisone in two randomized clinical trials of hydrocortisone versus placebo in vasodilatory shock. RESULTS We initially identified genes associated with immune-adaptive, immune-innate, immune-coagulant functions. From these genes, 15 were most relevant to generate expression scores related to each of the functions. These scores were used to identify patients as immune-adaptive prevalent (IA-P) and immune-innate prevalent (IN-P). In IA-P patients, hydrocortisone therapy increased 28-day mortality in both trials (43.3% vs 14.7%, P = 0.028) and (57.1% vs 0.0%, P = 0.99). In IN-P patients, this effect was numerically reversed. CONCLUSIONS Gene expression scores identified the immune state of vasodilatory shock patients, one of which (IA-P) identified those who may be harmed by hydrocortisone. Gene expression scores may help advance the field of personalized medicine.
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Affiliation(s)
- Lijing Yao
- Department of Clinical Data Science, Endpoint Health Inc, Palo Alto, California
| | - Diego Ariel Rey
- Department of Clinical Data Science, Endpoint Health Inc, Palo Alto, California
| | - Lucas Bulgarelli
- Department of Clinical Data Science, Endpoint Health Inc, Palo Alto, California
| | - Rachel Kast
- Department of Clinical Data Science, Endpoint Health Inc, Palo Alto, California
| | - Jeff Osborn
- Department of Clinical Data Science, Endpoint Health Inc, Palo Alto, California
| | - Emily Van Ark
- Department of Clinical Data Science, Endpoint Health Inc, Palo Alto, California
| | - Li Tai Fang
- Department of Clinical Data Science, Endpoint Health Inc, Palo Alto, California
| | - Bayo Lau
- Bioinformatics Department, HypaHub Inc, San Jose, California, USA
| | - Hugo Lam
- Bioinformatics Department, HypaHub Inc, San Jose, California, USA
| | | | - Ary Serpa Neto
- Department of Critical Care Medicine, Hospital Israelita Albert Einstein, São Paulo, Brazil
- Australian and New Zealand Intensive Care Research Centre (ANZIC-RC), School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
- Department of Critical Care, Melbourne Medical School, University of Melbourne, Austin Hospital, Melbourne, Australia
- Data Analytics Research and Evaluation (DARE) Centre, Austin Hospital, Melbourne, Australia
| | - Rinaldo Bellomo
- Australian and New Zealand Intensive Care Research Centre (ANZIC-RC), School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
- Department of Critical Care, Melbourne Medical School, University of Melbourne, Austin Hospital, Melbourne, Australia
- Data Analytics Research and Evaluation (DARE) Centre, Austin Hospital, Melbourne, Australia
- Department of Intensive Care, Austin Hospital, Melbourne, Australia
- Department of Intensive Care, Royal Melbourne Hospital, Melbourne, Australia
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23
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Poole J, Kitchen GB. Circadian regulation of innate immunity in animals and humans and implications for human disease. Semin Immunopathol 2022; 44:183-192. [PMID: 35169890 PMCID: PMC8853148 DOI: 10.1007/s00281-022-00921-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/03/2022] [Indexed: 01/19/2023]
Abstract
Circadian rhythms are 24-h oscillating variations in physiology generated by the core circadian clock. There is now a wide body of evidence showing circadian regulation of the immune system. Innate immune cells contain the molecular circadian clock which drives rhythmic responses, from the magnitude of the inflammatory response to the numbers of circulating immune cells varying throughout the day. This leads to rhythmic presentation of disease clinically, for example the classic presentation of nocturnal asthma or the sudden development of pulmonary oedema from acute myocardial infarction first thing in the morning.
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Affiliation(s)
- Joanna Poole
- Southmead Hospital, North Bristol Trust, Southmead Rd, Bristol, BS10 5NB, UK
| | - Gareth B Kitchen
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, M13 9PT, UK.
- Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK.
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24
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Li M, Huang H, Ke C, Tan L, Wu J, Xu S, Tu X. Identification of a novel four-gene diagnostic signature for patients with sepsis by integrating weighted gene co-expression network analysis and support vector machine algorithm. Hereditas 2022; 159:14. [PMID: 35184762 PMCID: PMC8859894 DOI: 10.1186/s41065-021-00215-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/29/2021] [Indexed: 11/17/2022] Open
Abstract
Sepsis is a life-threatening condition in which the immune response is directed towards the host tissues, causing organ failure. Since sepsis does not present with specific symptoms, its diagnosis is often delayed. The lack of diagnostic accuracy results in a non-specific diagnosis, and to date, a standard diagnostic test to detect sepsis in patients remains lacking. Therefore, it is vital to identify sepsis-related diagnostic genes. This study aimed to conduct an integrated analysis to assess the immune scores of samples from patients diagnosed with sepsis and normal samples, followed by weighted gene co-expression network analysis (WGCNA) to identify immune infiltration-related genes and potential transcriptome markers in sepsis. Furthermore, gene regulatory networks were established to screen diagnostic markers for sepsis based on the protein-protein interaction networks involving these immune infiltration-related genes. Moreover, we integrated WGCNA with the support vector machine (SVM) algorithm to build a diagnostic model for sepsis. Results showed that the immune score was significantly lower in the samples from patients with sepsis than in normal samples. A total of 328 and 333 genes were positively and negatively correlated with the immune score, respectively. Using the MCODE plugin in Cytoscape, we identified four modules, and through functional annotation, we found that these modules were related to the immune response. Gene Ontology functional enrichment analysis showed that the identified genes were associated with functions such as neutrophil degranulation, neutrophil activation in the immune response, neutrophil activation, and neutrophil-mediated immunity. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed the enrichment of pathways such as primary immunodeficiency, Th1- and Th2-cell differentiation, T-cell receptor signaling pathway, and natural killer cell-mediated cytotoxicity. Finally, we identified a four-gene signature, containing the hub genes LCK, CCL5, ITGAM, and MMP9, and established a model that could be used to diagnose patients with sepsis.
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25
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She H, Hu Y, Zhou Y, Tan L, Zhu Y, Ma C, Wu Y, Chen W, Wang L, Zhang Z, Wang L, Liu L, Li T. Protective Effects of Dexmedetomidine on Sepsis-Induced Vascular Leakage by Alleviating Ferroptosis via Regulating Metabolic Reprogramming. J Inflamm Res 2021; 14:6765-6782. [PMID: 34916824 PMCID: PMC8670891 DOI: 10.2147/jir.s340420] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/03/2021] [Indexed: 12/15/2022] Open
Abstract
Introduction Vascular leakage plays a vital role in sepsis-induced multi-organ dysfunction. Currently, no specific measures are available for vascular leakage. Ferroptosis, as a recently recognized form of cell death, plays a crucial role in cell dysfunction. It is still unknown whether ferroptosis participates in the occurrence of organ dysfunction following sepsis. Our previous study showed that dexmedetomidine (Dex) could alleviate sepsis-induced organ dysfunction. However, whether the mechanism is related to ferroptosis is not clear. Methods The publicly available datasets of septic patients were reanalyzed, and septic models in vivo and vitro by cecal ligation and puncture and lipopolysaccharide-stimulated vascular endothelial cells (VECs) were applied. The occurrence of ferroptosis in septic patients and rats was observed, and the protective effects of Dex on ferroptosis, and related mechanisms on regulating metabolic reprogramming and mitochondrial fission were further studied. Results The transcriptomics data of patients from the GEO database showed that ferroptosis was closely related to sepsis. Sepsis induced significant ferroptosis in VECs by metabolomics analysis. The level of lipid peroxidation was increased in VECs, and the mitochondrial cristae was decreased after sepsis. Metabolomics analysis showed that Dex activated the pentose phosphate pathway and increased glutathione in VECs via up-regulation of G6PD expression. Dex could antagonize sepsis-induced the decrease in the level of Nrf2. The Nrf2 inhibitor reversed the protective effect of Dex on ferroptosis. Further study showed that Dex significantly alleviated sepsis-induced mitochondrial over-division, improved mitochondrial function, and decreased ROS, further inhibiting the ferroptosis of VECs. Dex alleviated the permeability of vessels by reducing ferroptosis and enhanced the intercellular junction of VECs. Conclusion Dex protects vascular leakage following sepsis by inhibiting ferroptosis. The mechanism is mainly related to metabolic reprogramming via Nrf2 up-regulation and inhibition of mitochondrial fission.
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Affiliation(s)
- Han She
- Department of Anesthesiology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China.,State Key Laboratory of Trauma, Burns and Combined Injury, Second Department of Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Yi Hu
- Department of Anesthesiology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Yuanqun Zhou
- State Key Laboratory of Trauma, Burns and Combined Injury, Second Department of Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Lei Tan
- Department of Anesthesiology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Yu Zhu
- State Key Laboratory of Trauma, Burns and Combined Injury, Second Department of Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Chunhua Ma
- State Key Laboratory of Trauma, Burns and Combined Injury, Second Department of Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Yue Wu
- State Key Laboratory of Trauma, Burns and Combined Injury, Second Department of Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Wei Chen
- Department of Anesthesiology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Li Wang
- State Key Laboratory of Trauma, Burns and Combined Injury, Second Department of Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Zisen Zhang
- State Key Laboratory of Trauma, Burns and Combined Injury, Second Department of Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Li Wang
- Department of Anesthesiology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Liangming Liu
- State Key Laboratory of Trauma, Burns and Combined Injury, Second Department of Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Tao Li
- State Key Laboratory of Trauma, Burns and Combined Injury, Second Department of Research Institute of Surgery, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
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Bouwman W, Verhaegh W, van de Stolpe A. Androgen Receptor Pathway Activity Assay for Sepsis Diagnosis and Prediction of Favorable Prognosis. Front Med (Lausanne) 2021; 8:767145. [PMID: 34888328 PMCID: PMC8650119 DOI: 10.3389/fmed.2021.767145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/01/2021] [Indexed: 12/17/2022] Open
Abstract
Introduction: Sepsis is a life-threatening complication of a bacterial infection. It is hard to predict which patients with a bacterial infection will develop sepsis, and accurate and timely diagnosis as well as assessment of prognosis is difficult. Aside from antibiotics-based treatment of the causative infection and supportive measures, treatment options have remained limited. Better understanding of the immuno-pathophysiology of sepsis is expected to lead to improved diagnostic and therapeutic solutions. Functional activity of the innate (inflammatory) and adaptive immune response is controlled by a dedicated set of cellular signal transduction pathways, that are active in the various immune cell types. To develop an immune response-based diagnostic assay for sepsis and provide novel therapeutic targets, signal transduction pathway activities have been analyzed in whole blood samples from patients with sepsis. Methods: A validated and previously published set of signal transduction pathway (STP) assays, enabling determination of immune cell function, was used to analyze public Affymetrix expression microarray data from clinical studies containing data from pediatric and adult patients with sepsis. STP assays enable quantitative measurement of STP activity on individual patient sample data, and were used to calculate activity of androgen receptor (AR), estrogen receptor (ER), JAK-STAT1/2, JAK-STAT3, Notch, Hedgehog, TGFβ, FOXO-PI3K, MAPK-AP1, and NFκB signal transduction pathways. Results: Activity of AR and TGFβ pathways was increased in children and adults with sepsis. Using the mean plus two standard deviations of normal pathway activity (in healthy individuals) as threshold for abnormal STP activity, diagnostic assay parameters were determined. For diagnosis of pediatric sepsis, the AR pathway assay showed high sensitivity (77%) and specificity (97%), with a positive prediction value (PPV) of 99% and negative prediction value (NPV) of 50%. For prediction of favorable prognosis (survival), PPV was 95%, NPV was 21%. The TGFβ pathway activity assay performed slightly less for diagnosing sepsis, with a sensitivity of 64% and specificity of 98% (PPV 99%, NPV 39%). Conclusion: The AR and TGFβ pathways have an immunosuppressive role, suggesting a causal relation between increased pathway activity and sepsis immunopathology. STP assays have been converted to qPCR assays for further evaluation of clinical utility for sepsis diagnosis and prediction of prognosis, as well as for prediction of risk at developing sepsis in patients with a bacterial infection. STPs may present novel therapeutic targets in sepsis.
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Oliveira RADC, Imparato DO, Fernandes VGS, Cavalcante JVF, Albanus RD, Dalmolin RJS. Reverse Engineering of the Pediatric Sepsis Regulatory Network and Identification of Master Regulators. Biomedicines 2021; 9:biomedicines9101297. [PMID: 34680414 PMCID: PMC8533457 DOI: 10.3390/biomedicines9101297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 01/04/2023] Open
Abstract
Sepsis remains a leading cause of death in ICUs all over the world, with pediatric sepsis accounting for a high percentage of mortality in pediatric ICUs. Its complexity makes it difficult to establish a consensus on genetic biomarkers and therapeutic targets. A promising strategy is to investigate the regulatory mechanisms involved in sepsis progression, but there are few studies regarding gene regulation in sepsis. This work aimed to reconstruct the sepsis regulatory network and identify transcription factors (TFs) driving transcriptional states, which we refer to here as master regulators. We used public gene expression datasets to infer the co-expression network associated with sepsis in a retrospective study. We identified a set of 15 TFs as potential master regulators of pediatric sepsis, which were divided into two main clusters. The first cluster corresponded to TFs with decreased activity in pediatric sepsis, and GATA3 and RORA, as well as other TFs previously implicated in the context of inflammatory response. The second cluster corresponded to TFs with increased activity in pediatric sepsis and was composed of TRIM25, RFX2, and MEF2A, genes not previously described as acting in a coordinated way in pediatric sepsis. Altogether, these results show how a subset of master regulators TF can drive pathological transcriptional states, with implications for sepsis biology and treatment.
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Affiliation(s)
- Raffael Azevedo de Carvalho Oliveira
- Bioinformatics Multidisciplinary Environment–BioME, Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal 59078-400, Brazil; (R.A.d.C.O.); (D.O.I.); (V.G.S.F.); (J.V.F.C.)
| | - Danilo Oliveira Imparato
- Bioinformatics Multidisciplinary Environment–BioME, Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal 59078-400, Brazil; (R.A.d.C.O.); (D.O.I.); (V.G.S.F.); (J.V.F.C.)
| | - Vítor Gabriel Saldanha Fernandes
- Bioinformatics Multidisciplinary Environment–BioME, Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal 59078-400, Brazil; (R.A.d.C.O.); (D.O.I.); (V.G.S.F.); (J.V.F.C.)
| | - João Vitor Ferreira Cavalcante
- Bioinformatics Multidisciplinary Environment–BioME, Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal 59078-400, Brazil; (R.A.d.C.O.); (D.O.I.); (V.G.S.F.); (J.V.F.C.)
| | - Ricardo D’Oliveira Albanus
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Rodrigo Juliani Siqueira Dalmolin
- Bioinformatics Multidisciplinary Environment–BioME, Instituto Metrópole Digital, Universidade Federal do Rio Grande do Norte, Natal 59078-400, Brazil; (R.A.d.C.O.); (D.O.I.); (V.G.S.F.); (J.V.F.C.)
- Department of Biochemistry–DBQ–CB, Federal University of Rio Grande do Norte, Natal 59064-741, Brazil
- Correspondence:
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Schaack D, Weigand MA, Uhle F. Comparison of machine-learning methodologies for accurate diagnosis of sepsis using microarray gene expression data. PLoS One 2021; 16:e0251800. [PMID: 33999966 PMCID: PMC8128240 DOI: 10.1371/journal.pone.0251800] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/04/2021] [Indexed: 11/27/2022] Open
Abstract
We investigate the feasibility of molecular-level sample classification of sepsis using microarray gene expression data merged by in silico meta-analysis. Publicly available data series were extracted from NCBI Gene Expression Omnibus and EMBL-EBI ArrayExpress to create a comprehensive meta-analysis microarray expression set (meta-expression set). Measurements had to be obtained via microarray-technique from whole blood samples of adult or pediatric patients with sepsis diagnosed based on international consensus definition immediately after admission to the intensive care unit. We aggregate trauma patients, systemic inflammatory response syndrome (SIRS) patients, and healthy controls in a non-septic entity. Differential expression (DE) analysis is compared with machine-learning-based solutions like decision tree (DT), random forest (RF), support vector machine (SVM), and deep-learning neural networks (DNNs). We evaluated classifier training and discrimination performance in 100 independent iterations. To test diagnostic resilience, we gradually degraded expression data in multiple levels. Clustering of expression values based on DE genes results in partial identification of sepsis samples. In contrast, RF, SVM, and DNN provide excellent diagnostic performance measured in terms of accuracy and area under the curve (>0.96 and >0.99, respectively). We prove DNNs as the most resilient methodology, virtually unaffected by targeted removal of DE genes. By surpassing most other published solutions, the presented approach substantially augments current diagnostic capability in intensive care medicine.
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Affiliation(s)
- Dominik Schaack
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
- * E-mail:
| | - Markus A. Weigand
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Florian Uhle
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
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Zheng X, Leung KS, Wong MH, Cheng L. Long non-coding RNA pairs to assist in diagnosing sepsis. BMC Genomics 2021; 22:275. [PMID: 33863291 PMCID: PMC8050902 DOI: 10.1186/s12864-021-07576-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
Background Sepsis is the major cause of death in Intensive Care Unit (ICU) globally. Molecular detection enables rapid diagnosis that allows early intervention to minimize the death rate. Recent studies showed that long non-coding RNAs (lncRNAs) regulate proinflammatory genes and are related to the dysfunction of organs in sepsis. Identifying lncRNA signature with absolute abundance is challenging because of the technical variation and the systematic experimental bias. Results Cohorts (n = 768) containing whole blood lncRNA profiling of sepsis patients in the Gene Expression Omnibus (GEO) database were included. We proposed a novel diagnostic strategy that made use of the relative expressions of lncRNA pairs, which are reversed between sepsis patients and normal controls (eg. lncRNAi > lncRNAj in sepsis patients and lncRNAi < lncRNAj in normal controls), to identify 14 lncRNA pairs as a sepsis diagnostic signature. The signature was then applied to independent cohorts (n = 644) to evaluate its predictive performance across different ages and normalization methods. Comparing to common machine learning models and existing signatures, SepSigLnc consistently attains better performance on the validation cohorts from the same age group (AUC = 0.990 & 0.995 in two cohorts) and across different groups (AUC = 0.878 on average), as well as cohorts processed by an alternative normalization method (AUC = 0.953 on average). Functional analysis demonstrates that the lncRNA pairs in SepsigLnc are functionally similar and tend to implicate in the same biological processes including cell fate commitment and cellular response to steroid hormone stimulus. Conclusion Our study identified 14 lncRNA pairs as signature that can facilitate the diagnosis of septic patients at an intervenable point when clinical manifestations are not dramatic. Also, the computational procedure can be generalized to a standard procedure for discovering diagnostic molecule signatures. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07576-4.
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Affiliation(s)
- Xubin Zheng
- Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen, 518020, China.,Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Kwong-Sak Leung
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Man-Hon Wong
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Lixin Cheng
- Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen, 518020, China.
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Tang Y, Yang X, Shu H, Yu Y, Pan S, Xu J, Shang Y. Bioinformatic analysis identifies potential biomarkers and therapeutic targets of septic-shock-associated acute kidney injury. Hereditas 2021; 158:13. [PMID: 33863396 PMCID: PMC8052759 DOI: 10.1186/s41065-021-00176-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/30/2021] [Indexed: 01/22/2023] Open
Abstract
Background Sepsis and septic shock are life-threatening diseases with high mortality rate in intensive care unit (ICU). Acute kidney injury (AKI) is a common complication of sepsis, and its occurrence is a poor prognostic sign to septic patients. We analyzed co-differentially expressed genes (co-DEGs) to explore relationships between septic shock and AKI and reveal potential biomarkers and therapeutic targets of septic-shock-associated AKI (SSAKI). Methods Two gene expression datasets (GSE30718 and GSE57065) were downloaded from the Gene Expression Omnibus (GEO). The GSE57065 dataset included 28 septic shock patients and 25 healthy volunteers and blood samples were collected within 0.5, 24 and 48 h after shock. Specimens of GSE30718 were collected from 26 patients with AKI and 11 control patents. AKI-DEGs and septic-shock-DEGs were identified using the two datasets. Subsequently, Gene Ontology (GO) functional analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and protein-protein interaction (PPI) network analysis were performed to elucidate molecular mechanisms of DEGs. We also evaluated co-DEGs and corresponding predicted miRNAs involved in septic shock and AKI. Results We identified 62 DEGs in AKI specimens and 888, 870, and 717 DEGs in septic shock blood samples within 0.5, 24 and 48 h, respectively. The hub genes of EGF and OLFM4 may be involved in AKI and QPCT, CKAP4, PRKCQ, PLAC8, PRC1, BCL9L, ATP11B, KLHL2, LDLRAP1, NDUFAF1, IFIT2, CSF1R, HGF, NRN1, GZMB, and STAT4 may be associated with septic shock. Besides, co-DEGs of VMP1, SLPI, PTX3, TIMP1, OLFM4, LCN2, and S100A9 coupled with corresponding predicted miRNAs, especially miR-29b-3p, miR-152-3p, and miR-223-3p may be regarded as promising targets for the diagnosis and treatment of SSAKI in the future. Conclusions Septic shock and AKI are related and VMP1, SLPI, PTX3, TIMP1, OLFM4, LCN2, and S100A9 genes are significantly associated with novel biomarkers involved in the occurrence and development of SSAKI. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-021-00176-y.
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Affiliation(s)
- Yun Tang
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1277, Jiefang Avenue, Wuhan, 430022, China
| | - Xiaobo Yang
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1277, Jiefang Avenue, Wuhan, 430022, China
| | - Huaqing Shu
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1277, Jiefang Avenue, Wuhan, 430022, China
| | - Yuan Yu
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1277, Jiefang Avenue, Wuhan, 430022, China
| | - Shangwen Pan
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1277, Jiefang Avenue, Wuhan, 430022, China
| | - Jiqian Xu
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1277, Jiefang Avenue, Wuhan, 430022, China
| | - You Shang
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1277, Jiefang Avenue, Wuhan, 430022, China.
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Kim KS, Jekarl DW, Yoo J, Lee S, Kim M, Kim Y. Immune gene expression networks in sepsis: A network biology approach. PLoS One 2021; 16:e0247669. [PMID: 33667236 PMCID: PMC7935325 DOI: 10.1371/journal.pone.0247669] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 02/10/2021] [Indexed: 12/29/2022] Open
Abstract
To study the dysregulated host immune response to infection in sepsis, gene expression profiles from the Gene Expression Omnibus (GEO) datasets GSE54514, GSE57065, GSE64456, GSE95233, GSE66099 and GSE72829 were selected. From the Kyoto Encyclopedia of Genes and Genomes (KEGG) immune system pathways, 998 unique genes were selected, and genes were classified as follows based on gene annotation from KEGG, Gene Ontology, and Reactome: adaptive immunity, antigen presentation, cytokines and chemokines, complement, hematopoiesis, innate immunity, leukocyte migration, NK cell activity, platelet activity, and signaling. After correlation matrix formation, correlation coefficient of 0.8 was selected for network generation and network analysis. Total transcriptome was analyzed for differentially expressed genes (DEG), followed by gene set enrichment analysis. The network topological structure revealed that adaptive immunity tended to form a prominent and isolated cluster in sepsis. Common genes within the cluster from the 6 datasets included CD247, CD8A, ITK, LAT, and LCK. The clustering coefficient and modularity parameters were increased in 5/6 and 4/6 datasets in the sepsis group that seemed to be associated with functional aspect of the network. GSE95233 revealed that the nonsurvivor group showed a prominent and isolated adaptive immunity cluster, whereas the survivor group had isolated complement-coagulation and platelet-related clusters. T cell receptor signaling (TCR) pathway and antigen processing and presentation pathway were down-regulated in 5/6 and 4/6 datasets, respectively. Complement and coagulation, Fc gamma, epsilon related signaling pathways were up-regulated in 5/6 datasets. Altogether, network and gene set enrichment analysis showed that adaptive-immunity-related genes along with TCR pathway were down-regulated and isolated from immune the network that seemed to be associated with unfavorable prognosis. Prominence of platelet and complement-coagulation-related genes in the immune network was associated with survival in sepsis. Complement-coagulation pathway was up-regulated in the sepsis group that was associated with favorable prognosis. Network and gene set enrichment analysis supported elucidation of sepsis pathogenesis.
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Affiliation(s)
- Kyung Soo Kim
- Department of Thoracic and Cardiovascular Surgery, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Dong Wook Jekarl
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Laboratory for Development and Evaluation Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
- * E-mail:
| | - Jaeeun Yoo
- Laboratory for Development and Evaluation Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Department of Laboratory Medicine, Incheon St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seungok Lee
- Laboratory for Development and Evaluation Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Department of Laboratory Medicine, Incheon St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Laboratory for Development and Evaluation Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Laboratory for Development and Evaluation Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Lorente-Pozo S, Navarrete P, Garzón MJ, Lara-Cantón I, Beltrán-García J, Osca-Verdegal R, Mena-Mollá S, García-López E, Vento M, Pallardó FV, García-Giménez JL. DNA Methylation Analysis to Unravel Altered Genetic Pathways Underlying Early Onset and Late Onset Neonatal Sepsis. A Pilot Study. Front Immunol 2021; 12:622599. [PMID: 33659006 PMCID: PMC7917190 DOI: 10.3389/fimmu.2021.622599] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Neonatal sepsis is a systemic condition widely affecting preterm infants and characterized by pro-inflammatory and anti-inflammatory responses. However, its pathophysiology is not yet fully understood. Epigenetics regulates the immune system, and its alteration leads to the impaired immune response underlying sepsis. DNA methylation may contribute to sepsis-induced immunosuppression which, if persistent, will cause long-term adverse effects in neonates. Objective: To analyze the methylome of preterm infants in order to determine whether there are DNA methylation marks that may shed light on the pathophysiology of neonatal sepsis. Design: Prospective observational cohort study performed in the neonatal intensive care unit (NICU) of a tertiary care center. Patients: Eligible infants were premature ≤32 weeks admitted to the NICU with clinical suspicion of sepsis. The methylome analysis was performed in DNA from blood using Infinium Human Methylation EPIC microarrays to uncover methylation marks. Results: Methylation differential analysis revealed an alteration of methylation levels in genomic regions involved in inflammatory pathways which participate in both the innate and the adaptive immune response. Moreover, differences between early and late onset sepsis as compared to normal controls were assessed. Conclusions: DNA methylation marks can serve as a biomarker for neonatal sepsis and even contribute to differentiating between early and late onset sepsis.
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Affiliation(s)
- Sheila Lorente-Pozo
- Neonatal Research Group, Health Research Institute La Fe, Valencia, Spain.,Division of Neonatology, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Paula Navarrete
- EpiDisease S.L. (Spin-off From the CIBER-ISCIII), Parc Científic de la Universitat de València, Paterna, Spain
| | - María José Garzón
- EpiDisease S.L. (Spin-off From the CIBER-ISCIII), Parc Científic de la Universitat de València, Paterna, Spain
| | - Inmaculada Lara-Cantón
- Neonatal Research Group, Health Research Institute La Fe, Valencia, Spain.,Division of Neonatology, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Jesús Beltrán-García
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain.,Department Fisiología, Facultad de Medicina y Odontología, Universidad de Valencia-INCLIVA, Valencia, Spain
| | - Rebeca Osca-Verdegal
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain.,Department Fisiología, Facultad de Medicina y Odontología, Universidad de Valencia-INCLIVA, Valencia, Spain
| | - Salvador Mena-Mollá
- EpiDisease S.L. (Spin-off From the CIBER-ISCIII), Parc Científic de la Universitat de València, Paterna, Spain.,Department Fisiología, Facultad de Medicina y Odontología, Universidad de Valencia-INCLIVA, Valencia, Spain
| | - Eva García-López
- EpiDisease S.L. (Spin-off From the CIBER-ISCIII), Parc Científic de la Universitat de València, Paterna, Spain
| | - Máximo Vento
- Neonatal Research Group, Health Research Institute La Fe, Valencia, Spain.,Division of Neonatology, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Federico V Pallardó
- EpiDisease S.L. (Spin-off From the CIBER-ISCIII), Parc Científic de la Universitat de València, Paterna, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain.,Department Fisiología, Facultad de Medicina y Odontología, Universidad de Valencia-INCLIVA, Valencia, Spain
| | - José Luis García-Giménez
- EpiDisease S.L. (Spin-off From the CIBER-ISCIII), Parc Científic de la Universitat de València, Paterna, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain.,Department Fisiología, Facultad de Medicina y Odontología, Universidad de Valencia-INCLIVA, Valencia, Spain
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Systemic viral spreading and defective host responses are associated with fatal Lassa fever in macaques. Commun Biol 2021; 4:27. [PMID: 33398113 PMCID: PMC7782745 DOI: 10.1038/s42003-020-01543-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022] Open
Abstract
Lassa virus (LASV) is endemic in West Africa and induces a viral hemorrhagic fever (VHF) with up to 30% lethality among clinical cases. The mechanisms involved in control of Lassa fever or, in contrast, the ensuing catastrophic illness and death are poorly understood. We used the cynomolgus monkey model to reproduce the human disease with asymptomatic to mild or fatal disease. After initial replication at the inoculation site, LASV reached the secondary lymphoid organs. LASV did not spread further in nonfatal disease and was rapidly controlled by balanced innate and T-cell responses. Systemic viral dissemination occurred during severe disease. Massive replication, a cytokine/chemokine storm, defective T-cell responses, and multiorgan failure were observed. Clinical, biological, immunological, and transcriptomic parameters resembled those observed during septic-shock syndrome, suggesting that similar pathogenesis is induced during Lassa fever. The outcome appears to be determined early, as differentially expressed genes in PBMCs were associated with fatal and non-fatal Lassa fever outcome very early after infection. These results provide a full characterization and important insights into Lassa fever pathogenesis and could help to develop early diagnostic tools.
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34
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Zhao Q, Xu N, Guo H, Li J. Identification of the Diagnostic Signature of Sepsis Based on Bioinformatic Analysis of Gene Expression and Machine Learning. Comb Chem High Throughput Screen 2020; 25:21-28. [PMID: 33280594 DOI: 10.2174/1386207323666201204130031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/26/2020] [Accepted: 11/08/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Sepsis is a life-threatening disease caused by the dysregulated host response to the infection and the major cause of death of patients in the intensive care unit (ICU). OBJECTIVE Early diagnosis of sepsis could significantly reduce in-hospital mortality. Though generated from infection, the development of sepsis follows its own psychological process and disciplines, alters with gender, health status and other factors. Hence, the analysis of mass data by bioinformatics tools and machine learning is a promising method for exploring early diagnosis. METHODS We collected miRNA and mRNA expression data of sepsis blood samples from Gene Expression Omnibus (GEO) and ArrayExpress databases, screened out differentially expressed genes (DEGs) by R software, predicted miRNA targets on TargetScanHuman and miRTarBase websites, conducted Gene Ontology (GO) term and KEGG pathway enrichment analysis based on overlapping DEGs. The STRING database and Cytoscape were used to build protein-protein interaction (PPI) network and predict hub genes. Then we constructed a Random Forest model by using the hub genes to assess sample type. RESULTS Bioinformatic analysis of GEO dataset revealed 46 overlapping DEGs in sepsis. The PPI network analysis identified five hub genes, SOCS3, KBTBD6, FBXL5, FEM1C and WSB1. Random Forest model based on these five hub genes was used to assess GSE95233 and GSE95233 datasets, and the area under the curve (AUC) of ROC was 0.900 and 0.7988, respectively, which confirmed the efficacy of this model. CONCLUSION The integrated analysis of gene expression in sepsis and the effective Random Forest model built in this study may provide promising diagnostic methods for sepsis.
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Affiliation(s)
- Qian Zhao
- Department of Emergency, Hebei General Hospital, Shijiazhuang, 050051,China
| | - Ning Xu
- Department of Emergency, Hebei General Hospital, Shijiazhuang, 050051,China
| | - Hui Guo
- Department of Emergency, Hebei General Hospital, Shijiazhuang, 050051,China
| | - Jianguo Li
- Department of Emergency, Hebei General Hospital, Shijiazhuang, 050051,China
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35
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Identification of Potential Biomarkers and Immune Features of Sepsis Using Bioinformatics Analysis. Mediators Inflamm 2020; 2020:3432587. [PMID: 33132754 PMCID: PMC7568774 DOI: 10.1155/2020/3432587] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/26/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022] Open
Abstract
Sepsis remains a major global concern and is associated with high mortality and morbidity despite improvements in its management. Markers currently in use have shortcomings such as a lack of specificity and failures in the early detection of sepsis. In this study, we aimed to identify key genes involved in the molecular mechanisms of sepsis and search for potential new biomarkers and treatment targets for sepsis using bioinformatics analyses. Three datasets (GSE95233, GSE57065, and GSE28750) associated with sepsis were downloaded from the public functional genomics data repository Gene Expression Omnibus. Differentially expressed genes (DEGs) were identified using R packages (Affy and limma). Functional enrichment of the DEGs was analyzed with the DAVID database. Protein-protein interaction networks were derived using the STRING database and visualized using Cytoscape software. Potential biomarker genes were analyzed using receiver operating characteristic (ROC) curves in the R package (pROC). The three datasets included 156 whole blood RNA samples from 89 sepsis patients and 67 healthy controls. Between the two groups, 568 DEGs were identified, among which 315 were upregulated and 253 were downregulated in the septic group. These genes were enriched for pathways mainly involved in the innate immune response, T-cell biology, antigen presentation, and natural killer cell function. ROC analyses identified nine genes—LRG1, ELANE, TP53, LCK, TBX21, ZAP70, CD247, ITK, and FYN—as potential new biomarkers for sepsis. Real-time PCR confirmed that the expression of seven of these genes was in accordance with the microarray results. This study revealed imbalanced immune responses at the transcriptomic level during early sepsis and identified nine genes as potential biomarkers for sepsis.
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36
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Tallon J, Browning B, Couenne F, Bordes C, Venet F, Nony P, Gueyffier F, Moucadel V, Monneret G, Tayakout-Fayolle M. Dynamical modeling of pro- and anti-inflammatory cytokines in the early stage of septic shock. In Silico Biol 2020; 14:101-121. [PMID: 32597796 PMCID: PMC7505012 DOI: 10.3233/isb-200474] [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] [Indexed: 01/09/2023]
Abstract
A dynamical model of the pathophysiological behaviors of IL18 and IL10 cytokines with their receptors is tested against data for the case of early sepsis. The proposed approach considers the surroundings (organs and bone marrow) and the different subsystems (cells and cyctokines). The interactions between blood cells, cytokines and the surroundings are described via mass balances. Cytokines are adsorbed onto associated receptors at the cell surface. The adsorption is described by the Langmuir model and gives rise to the production of more cytokines and associated receptors inside the cell. The quantities of pro and anti-inflammatory cytokines present in the body are combined to give global information via an inflammation level function which describes the patient’s state. Data for parameter estimation comes from the Sepsis 48 H database. Comparisons between patient data and simulations are presented and are in good agreement. For the IL18/IL10 cytokine pair, 5 key parameters have been found. They are linked to pro-inflammatory IL18 cytokine and show that the early sepsis is driven by components of inflammatory character.
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Affiliation(s)
- J Tallon
- Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, Villeurbanne, France
| | - B Browning
- Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, Villeurbanne, France
| | - F Couenne
- Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, Villeurbanne, France
| | - C Bordes
- Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, Villeurbanne, France
| | - F Venet
- Hospices Civils de Lyon, LYON Cedex 03 - France
| | - P Nony
- Université Claude Bernard Lyon 1, CNRS, LBBE UMR 5558, Lyon, France
| | - F Gueyffier
- Université Claude Bernard Lyon 1, CNRS, LBBE UMR 5558, Lyon, France
| | | | - G Monneret
- Hospices Civils de Lyon, LYON Cedex 03 - France
| | - M Tayakout-Fayolle
- Université Claude Bernard Lyon 1, CNRS, LAGEPP UMR 5007, Villeurbanne, France
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37
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Lu J, Li Q, Wu Z, Zhong Z, Ji P, Li H, He C, Feng J, Zhang J. Two gene set variation indexes as potential diagnostic tool for sepsis. Am J Transl Res 2020; 12:2749-2759. [PMID: 32655806 PMCID: PMC7344106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/26/2020] [Indexed: 06/11/2023]
Abstract
Accurate diagnosis of sepsis remains challenging, new markers or combinations of markers are urgently needed. In the present study, we screened differentially expressed genes (DEGs) between sepsis and non-sepsis blood samples across three previously published gene expression data sets. Common upregulated and downregulated DEGs were ranked according to their average functional similarity. The ten genes (OLFM4, ORM1, CEP55, S100A12, S100P, LRG1, CEACAM8, MS4A4A, PLSCR1, and IL1R2) with the largest average functional similarity among the common upregulated genes and another ten genes (THEMIS, IL2RB, CD2, IL7R, CD3E, KLRB1, PVRIG, CCRR3, TGFBR3, and PLEKHA1) with the largest average functional similarity among the common downregulated genes were separately identified as the upregulated crucial gene set and the downregulated crucial gene set. Gene set variation analysis (GSVA) was used to obtain the GSVA index of each sample against the two crucial gene sets. Both the two crucial GSVA indexes may be robust markers for sepsis with high area under ROC curve. The diagnostic utility of the upregulated GSVA index was validated in another independent data set. Functional analyses revealed several sepsis-related pathways. In conclusion, we proposed two sepsis-related gene sets across multiple data sets and created two GSVA indexes with promising diagnostic value.
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Affiliation(s)
- Junyu Lu
- Intensive Care Unit, The Second Affiliated Hospital of Guangxi Medical UniversityNanning 530007, China
| | - Qian Li
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical UniversityNanning 530007, China
| | - Zimeng Wu
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical UniversityNanning 530007, China
| | - Zhimei Zhong
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical UniversityNanning 530007, China
| | - Pan Ji
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical UniversityNanning 530007, China
| | - Hongyuan Li
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical UniversityNanning 530007, China
| | - Cuiying He
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical UniversityNanning 530007, China
| | - Jihua Feng
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical UniversityNanning 530007, China
| | - Jianfeng Zhang
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical UniversityNanning 530007, China
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38
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Mayhew MB, Buturovic L, Luethy R, Midic U, Moore AR, Roque JA, Shaller BD, Asuni T, Rawling D, Remmel M, Choi K, Wacker J, Khatri P, Rogers AJ, Sweeney TE. A generalizable 29-mRNA neural-network classifier for acute bacterial and viral infections. Nat Commun 2020; 11:1177. [PMID: 32132525 PMCID: PMC7055276 DOI: 10.1038/s41467-020-14975-w] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 02/13/2020] [Indexed: 02/07/2023] Open
Abstract
Improved identification of bacterial and viral infections would reduce morbidity from sepsis, reduce antibiotic overuse, and lower healthcare costs. Here, we develop a generalizable host-gene-expression-based classifier for acute bacterial and viral infections. We use training data (N = 1069) from 18 retrospective transcriptomic studies. Using only 29 preselected host mRNAs, we train a neural-network classifier with a bacterial-vs-other area under the receiver-operating characteristic curve (AUROC) 0.92 (95% CI 0.90–0.93) and a viral-vs-other AUROC 0.92 (95% CI 0.90–0.93). We then apply this classifier, inflammatix-bacterial-viral-noninfected-version 1 (IMX-BVN-1), without retraining, to an independent cohort (N = 163). In this cohort, IMX-BVN-1 AUROCs are: bacterial-vs.-other 0.86 (95% CI 0.77–0.93), and viral-vs.-other 0.85 (95% CI 0.76–0.93). In patients enrolled within 36 h of hospital admission (N = 70), IMX-BVN-1 AUROCs are: bacterial-vs.-other 0.92 (95% CI 0.83–0.99), and viral-vs.-other 0.91 (95% CI 0.82–0.98). With further study, IMX-BVN-1 could provide a tool for assessing patients with suspected infection and sepsis at hospital admission. Diagnosing acute infections based on transcriptional host response shows promise, but generalizability is wanting. Here, the authors use a co-normalization framework to train a classifier to diagnose acute infections and apply it to independent data on a targeted diagnostic platform.
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Affiliation(s)
- Michael B Mayhew
- Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA
| | | | - Roland Luethy
- Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA
| | - Uros Midic
- Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA
| | - Andrew R Moore
- Department of Medicine, Stanford University, Palo Alto, CA, 94305, USA
| | - Jonasel A Roque
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Stanford University, Palo Alto, CA, 94305, USA
| | - Brian D Shaller
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Stanford University, Palo Alto, CA, 94305, USA
| | - Tola Asuni
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Stanford University, Palo Alto, CA, 94305, USA
| | - David Rawling
- Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA
| | - Melissa Remmel
- Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA
| | - Kirindi Choi
- Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA
| | - James Wacker
- Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infections, Stanford University, Palo Alto, CA, 94305, USA.,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Palo Alto, CA, 94305, USA
| | - Angela J Rogers
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Stanford University, Palo Alto, CA, 94305, USA
| | - Timothy E Sweeney
- Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA.
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39
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Payen D. Immunity check should be performed for all patients with septic shock? No. Intensive Care Med 2020; 46:506-509. [PMID: 32123990 DOI: 10.1007/s00134-019-05923-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/28/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Didier Payen
- Anesthesiology and Critical Care, UFR de Médecine Villemin, Université Paris 7 Paris Cité Sorbonne, Paris, France.
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40
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Brusletto BS, Løberg EM, Hellerud BC, Goverud IL, Berg JP, Olstad OK, Gopinathan U, Brandtzaeg P, Øvstebø R. Extensive Changes in Transcriptomic "Fingerprints" and Immunological Cells in the Large Organs of Patients Dying of Acute Septic Shock and Multiple Organ Failure Caused by Neisseria meningitidis. Front Cell Infect Microbiol 2020; 10:42. [PMID: 32154187 PMCID: PMC7045056 DOI: 10.3389/fcimb.2020.00042] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/22/2020] [Indexed: 12/16/2022] Open
Abstract
Background: Patients developing meningococcal septic shock reveal levels of Neisseria meningitidis (106-108/mL) and endotoxin (101-103 EU/mL) in the circulation and organs, leading to acute cardiovascular, pulmonary and renal failure, coagulopathy and a high case fatality rate within 24 h. Objective: To investigate transcriptional profiles in heart, lungs, kidneys, liver, and spleen and immunostain key inflammatory cells and proteins in post mortem formalin-fixed, paraffin-embedded (FFPE) tissue samples from meningococcal septic shock patients. Patients and Methods: Total RNA was isolated from FFPE and fresh frozen (FF) tissue samples from five patients and two controls (acute non-infectious death). Differential expression of genes was detected using Affymetrix microarray analysis. Lung and heart tissue samples were immunostained for T-and B cells, macrophages, neutrophils and the inflammatory markers PAI-1 and MCP-1. Inflammatory mediators were quantified in lysates from FF tissues. Results: The transcriptional profiles showed a complex pattern of protein-coding and non-coding RNAs with significant regulation of pathways associated with organismal death, cell death and survival, leukocyte migration, cellular movement, proliferation of cells, cell-to-cell signaling, immune cell trafficking, and inflammatory responses in an organ-specific clustering manner. The canonical pathways including acute phase response-, EIF2-, TREM1-, IL-6-, HMBG1-, PPAR signaling, and LXR/RXR activation were associated with acute heart, pulmonary, and renal failure. Fewer genes were regulated in the liver and particularly in the spleen. The main upstream regulators were TNF, IL-1β, IL-6, RICTOR, miR-6739-3p, and CD3. Increased numbers of inflammatory cells (CD68+, MPO+, CD3+, and CD20+) were found in lungs and heart. PAI-1 inhibiting fibrinolysis and MCP-1 attracting leukocyte were found significantly present in the septic tissue samples compared to the controls. Conclusions: FFPE tissue samples can be suitable for gene expression studies as well as immunostaining of specific cells or molecules. The most pronounced gene expression patterns were found in the organs with highest levels of Neisseria meningitidis DNA. Thousands of protein-coding and non-coding RNA transcripts were altered in lungs, heart and kidneys. We identified specific biomarker panels both protein-coding and non-coding RNA transcripts, which differed from organ to organ. Involvement of many genes and pathways add up and the combined effect induce organ failure.
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Affiliation(s)
- Berit Sletbakk Brusletto
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Else Marit Løberg
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Pathology, Oslo University Hospital, Oslo, Norway
| | | | - Ingeborg Løstegaard Goverud
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Jens Petter Berg
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Unni Gopinathan
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Petter Brandtzaeg
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Pediatrics, Oslo University Hospital, Oslo, Norway
| | - Reidun Øvstebø
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
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41
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Evankovich J, Lear T, Baldwin C, Chen Y, White V, Villandre J, Londino J, Liu Y, McVerry B, Kitsios GD, Mallampalli RK, Chen BB. Toll-like Receptor 8 Stability Is Regulated by Ring Finger 216 in Response to Circulating MicroRNAs. Am J Respir Cell Mol Biol 2020; 62:157-167. [PMID: 31385713 PMCID: PMC6993540 DOI: 10.1165/rcmb.2018-0373oc] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 08/01/2019] [Indexed: 01/16/2023] Open
Abstract
TLR8 (Toll-like receptor 8) is an intracellular pattern recognition receptor that senses RNA in endosomes to initiate innate immune signaling through NF-κB, and mechanisms regulating TLR8 protein abundance are not completely understood. Protein degradation is a cellular process controlling protein concentrations, accomplished largely through ubiquitin transfer directed by E3 ligase proteins to substrates. In the present study, we show that TLR8 has a short half-life in THP-1 monocytes (∼1 h) and that TLR8 is ubiquitinated and degraded in the proteasome. Treatment with the TLR8 agonist R848 causes rapid depletion of TLR8 concentrations at early time points, an effect blocked by proteasomal inhibition. We show a novel role for RNF216 (ring finger protein 216), an E3 ligase that targets TLR8 for ubiquitination and degradation. RNF216 overexpression reduces TLR8 concentrations, whereas RNF216 knockdown stabilizes TLR8. We describe a potential role for TLR8 activation by circulating RNA ligands in humans with acute respiratory distress syndrome (ARDS): Plasma and extracted RNA fractions from subjects with ARDS activated TLR8 in vitro. MicroRNA (miRNA) expression profiling revealed several circulating miRNAs from subjects with ARDS. miRNA mimics promoted TLR8 proteasomal degradation in THP-1 cells. These data show that TLR8 proteasomal disposal through RNF216 in response to RNA ligands regulates TLR8 cellular concentrations and may have implications for innate immune signaling. In addition, TLR8 activation by circulating RNA ligands may be a previously underrecognized stimulus contributing to excessive innate immune signaling characteristic of ARDS.
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Affiliation(s)
- John Evankovich
- Department of Medicine, Acute Lung Injury Center of Excellence
| | - Travis Lear
- Department of Environmental and Occupational Health, School of Public Health
| | | | | | - Virginia White
- Department of Medicine, Acute Lung Injury Center of Excellence
| | - John Villandre
- Department of Medicine, Acute Lung Injury Center of Excellence
| | - James Londino
- Department of Medicine, The Ohio State University, Columbus, Ohio; and
| | - Yuan Liu
- Department of Medicine, Acute Lung Injury Center of Excellence
- Aging Institute
- McGowan Institute for Regenerative Medicine
| | - Bryan McVerry
- Department of Medicine, Acute Lung Injury Center of Excellence
| | - Georgios D. Kitsios
- Department of Medicine, Acute Lung Injury Center of Excellence
- Center for Medicine and the Microbiome, and
| | - Rama K. Mallampalli
- Department of Medicine, Acute Lung Injury Center of Excellence
- Department of Medicine, The Ohio State University, Columbus, Ohio; and
- Medical Specialty Service Line, Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania
| | - Bill B. Chen
- Department of Medicine, Acute Lung Injury Center of Excellence
- Aging Institute
- Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
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Braga D, Barcella M, Herpain A, Aletti F, Kistler EB, Bollen Pinto B, Bendjelid K, Barlassina C. A longitudinal study highlights shared aspects of the transcriptomic response to cardiogenic and septic shock. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2019; 23:414. [PMID: 31856860 PMCID: PMC6921511 DOI: 10.1186/s13054-019-2670-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 11/12/2019] [Indexed: 12/13/2022]
Abstract
Background Septic shock (SS) and cardiogenic shock (CS) are two types of circulatory shock with a different etiology. Several studies have described the molecular alterations in SS patients, whereas the molecular factors involved in CS have been poorly investigated. We aimed to assess in the whole blood of CS and SS patients, using septic patients without shock (SC) as controls, transcriptomic modifications that occur over 1 week after ICU admission and are common to the two types of shock. Methods We performed whole blood RNA sequencing in 21 SS, 11 CS, and 5 SC. In shock patients, blood samples were collected within 16 h from ICU admission (T1), 48 h after ICU admission (T2), and at day 7 or before discharge (T3). In controls, blood samples were available at T1 and T2. Gene expression changes over time have been studied in CS, SS, and SC separately with a paired analysis. Genes with p value < 0.01 (Benjamini-Hochberg multiple test correction) were defined differentially expressed (DEGs). We used gene set enrichment analysis (GSEA) to identify the biological processes and transcriptional regulators significantly enriched in both types of shock. Results In both CS and SS patients, GO terms of inflammatory response and pattern recognition receptors (PRRs) were downregulated following ICU admission, whereas gene sets of DNA replication were upregulated. At the gene level, we observed that alarmins, interleukin receptors, PRRs, inflammasome, and DNA replication genes significantly changed their expression in CS and SS, but not in SC. Analysis of transcription factor targets showed in both CS and SS patients, an enrichment of CCAAT-enhancer-binding protein beta (CEBPB) targets in genes downregulated over time and an enrichment of E2F targets in genes with an increasing expression trend. Conclusions This pilot study supports, within the limits of a small sample size, the role of alarmins, PRRs, DNA replication, and immunoglobulins in the pathophysiology of circulatory shock, either in the presence of infection or not. We hypothesize that these genes could be potential targets of therapeutic interventions in CS and SS. Trial registration ClinicalTrials.gov, NCT02141607. Registered 19 May 2014.
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Affiliation(s)
- Daniele Braga
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, 20142, Milano, Italy. .,Fondazione Filarete, 20139, Milano, Italy.
| | - Matteo Barcella
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, 20142, Milano, Italy.,Fondazione Filarete, 20139, Milano, Italy
| | - Antoine Herpain
- Department of Intensive Care, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Federico Aletti
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Erik B Kistler
- Department of Anestesiology & Critical Care, University of California, San Diego, USA
| | - Bernardo Bollen Pinto
- Department of Anaesthesia, Pharmacology and Intensive Care, Geneva University Hospitals, Geneva, Switzerland
| | - Karim Bendjelid
- Department of Anaesthesia, Pharmacology and Intensive Care, Geneva University Hospitals, Geneva, Switzerland
| | - Cristina Barlassina
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, 20142, Milano, Italy.,Fondazione Filarete, 20139, Milano, Italy
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43
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Davis FM, Schaller MA, denDekker A, Joshi AD, Kimball AS, Evanoff H, Wilke C, Obi AT, Melvin WJ, Cavassani K, Scola M, Carson B, Moser S, Blanc V, Engoren M, Moore BB, Kunkel SL, Gallagher KA. Sepsis Induces Prolonged Epigenetic Modifications in Bone Marrow and Peripheral Macrophages Impairing Inflammation and Wound Healing. Arterioscler Thromb Vasc Biol 2019; 39:2353-2366. [PMID: 31644352 PMCID: PMC6818743 DOI: 10.1161/atvbaha.119.312754] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Sepsis represents an acute life-threatening disorder resulting from a dysregulated host response. For patients who survive sepsis, there remains long-term consequences, including impaired inflammation, as a result of profound immunosuppression. The mechanisms involved in this long-lasting deficient immune response are poorly defined. Approach and Results: Sepsis was induced using the murine model of cecal ligation and puncture. Following a full recovery period from sepsis physiology, mice were subjected to our wound healing model and wound macrophages (CD11b+, CD3-, CD19-, Ly6G-) were sorted. Post-sepsis mice demonstrated impaired wound healing and decreased reepithelization in comparison to controls. Further, post-sepsis bone marrow-derived macrophages and wound macrophages exhibited decreased expression of inflammatory cytokines vital for wound repair (IL [interleukin]-1β, IL-12, and IL-23). To evaluate if decreased inflammatory gene expression was secondary to epigenetic modification, we conducted chromatin immunoprecipitation on post-sepsis bone marrow-derived macrophages and wound macrophages. This demonstrated decreased expression of Mll1, an epigenetic enzyme, and impaired histone 3 lysine 4 trimethylation (activation mark) at NFκB (nuclear factor kappa-light-chain-enhancer of activated B cells)-binding sites on inflammatory gene promoters in bone marrow-derived macrophages and wound macrophages from postcecal ligation and puncture mice. Bone marrow transplantation studies demonstrated epigenetic modifications initiate in bone marrow progenitor/stem cells following sepsis resulting in lasting impairment in peripheral macrophage function. Importantly, human peripheral blood leukocytes from post-septic patients demonstrate a significant reduction in MLL1 compared with nonseptic controls. CONCLUSIONS These data demonstrate that severe sepsis induces stable mixed-lineage leukemia 1-mediated epigenetic modifications in the bone marrow, which are passed to peripheral macrophages resulting in impaired macrophage function and deficient wound healing persisting long after sepsis recovery.
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Affiliation(s)
- Frank M. Davis
- Section of Vascular Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
| | - Matthew A. Schaller
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Florida, Gainesville, FL
| | - Aaron denDekker
- Section of Vascular Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
| | - Amrita D. Joshi
- Section of Vascular Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
| | - Andrew S. Kimball
- Section of Vascular Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
| | - Holly Evanoff
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Carol Wilke
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Andrea T. Obi
- Section of Vascular Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
| | - William J Melvin
- Section of Vascular Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
| | - Karen Cavassani
- Urological Oncology, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Melissa Scola
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Beau Carson
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Stephanie Moser
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI
| | - Victoria Blanc
- Biorepository Office of Research, University of Michigan, Ann Arbor, MI
| | - Milo Engoren
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI
| | - Bethany B. Moore
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
- Department Microbiology and Immunology, University of Michigan, Ann Arbor, MI
| | | | - Katherine A. Gallagher
- Section of Vascular Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
- Department Microbiology and Immunology, University of Michigan, Ann Arbor, MI
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44
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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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Unsupervised Analysis of Transcriptomics in Bacterial Sepsis Across Multiple Datasets Reveals Three Robust Clusters. Crit Care Med 2019. [PMID: 29537985 DOI: 10.1097/ccm.0000000000003084] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVES To find and validate generalizable sepsis subtypes using data-driven clustering. DESIGN We used advanced informatics techniques to pool data from 14 bacterial sepsis transcriptomic datasets from eight different countries (n = 700). SETTING Retrospective analysis. SUBJECTS Persons admitted to the hospital with bacterial sepsis. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS A unified clustering analysis across 14 discovery datasets revealed three subtypes, which, based on functional analysis, we termed "Inflammopathic, Adaptive, and Coagulopathic." We then validated these subtypes in nine independent datasets from five different countries (n = 600). In both discovery and validation data, the Adaptive subtype is associated with a lower clinical severity and lower mortality rate, and the Coagulopathic subtype is associated with higher mortality and clinical coagulopathy. Further, these clusters are statistically associated with clusters derived by others in independent single sepsis cohorts. CONCLUSIONS The three sepsis subtypes may represent a unifying framework for understanding the molecular heterogeneity of the sepsis syndrome. Further study could potentially enable a precision medicine approach of matching novel immunomodulatory therapies with septic patients most likely to benefit.
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Morrow KN, Coopersmith CM, Ford ML. IL-17, IL-27, and IL-33: A Novel Axis Linked to Immunological Dysfunction During Sepsis. Front Immunol 2019; 10:1982. [PMID: 31507598 PMCID: PMC6713916 DOI: 10.3389/fimmu.2019.01982] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 08/05/2019] [Indexed: 12/11/2022] Open
Abstract
Sepsis is a major cause of morbidity and mortality worldwide despite numerous attempts to identify effective therapeutics. While some sepsis deaths are attributable to tissue damage caused by inflammation, most mortality is the result of prolonged immunosuppression. Ex vivo, immunosuppression during sepsis is evidenced by a sharp decrease in the production of pro-inflammatory cytokines by T cells and other leukocytes and increased lymphocyte apoptosis. This allows suppressive cytokines to exert a greater inhibitory effect on lymphocytes upon antigen exposure. While some pre-clinical and clinical trials have demonstrated utility in targeting cytokines that promote lymphocyte survival, this has not led to the approval of any therapies for clinical use. As cytokines with a more global impact on the immune system are also altered by sepsis, they represent novel and potentially valuable therapeutic targets. Recent evidence links interleukin (IL)-17, IL-27, and IL-33 to alterations in the immune response during sepsis using patient serum and murine models of peritonitis and pneumonia. Elevated levels of IL-17 and IL-27 are found in the serum of pediatric and adult septic patients early after sepsis onset and have been proposed as diagnostic biomarkers. In contrast, IL-33 levels increase in patient serum during the immunosuppressive stage of sepsis and remain high for more than 5 months after recovery. All three cytokines contribute to immunological dysfunction during sepsis by disrupting the balance between type 1, 2, and 17 immune responses. This review will describe how IL-17, IL-27, and IL-33 exert these effects during sepsis and their potential as therapeutic targets.
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Affiliation(s)
- Kristen N Morrow
- Immunology and Molecular Pathogenesis Program, Laney Graduate School, Emory University, Atlanta, GA, United States.,Department of Surgery, Emory University School of Medicine, Atlanta, GA, United States
| | - Craig M Coopersmith
- Department of Surgery, Emory University School of Medicine, Atlanta, GA, United States.,Emory Critical Care Center, Emory University School of Medicine, Atlanta, GA, United States
| | - Mandy L Ford
- Department of Surgery, Emory University School of Medicine, Atlanta, GA, United States.,Emory Transplant Center, Emory University School of Medicine, Atlanta, GA, United States
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47
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Activated peripheral blood mononuclear cell mediators trigger astrocyte reactivity. Brain Behav Immun 2019; 80:879-888. [PMID: 31176000 DOI: 10.1016/j.bbi.2019.05.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 12/23/2022] Open
Abstract
Sepsis is characterized by a severe and disseminated inflammation. In the central nervous system, sepsis promotes synaptic dysfunction and permanent cognitive impairment. Besides sepsis-induced neuronal dysfunction, glial cell response has been gaining considerable attention with microglial activation as a key player. By contrast, astrocytes' role during acute sepsis is still underexplored. Astrocytes are specialized immunocompetent cells involved in brain surveillance. In this context, the potential communication between the peripheral immune system and astrocytes during acute sepsis still remains unclear. We hypothesized that peripheral blood mononuclear cell (PBMC) mediators are able to affect the brain during an episode of acute sepsis. With this in mind, we first performed a data-driven transcriptome analysis of blood from septic patients to identify common features among independent clinical studies. Our findings evidenced pronounced impairment in energy-related signaling pathways in the blood of septic patients. Since astrocytes are key for brain energy homeostasis, we decided to investigate the communication between PBMC mediators and astrocytes in a rat model of acute sepsis, induced by cecal ligation and perforation (CLP). In the CLP animals, we identified widespread in vivo brain glucose hypometabolism. Ex vivo analyses demonstrated astrocyte reactivity along with reduced glutamate uptake capacity during sepsis. Also, by exposing cultured astrocytes to mediators released by PBMCs from CLP animals, we reproduced the energetic failure observed in vivo. Finally, by pharmacologically inhibiting phosphoinositide 3-kinase (PI3K), a central metabolic pathway downregulated in the blood of septic patients and reduced in the CLP rat brain, we mimicked the PBMC mediators effect on glutamate uptake but not on glucose metabolism. These results suggest that PBMC mediators are capable of directly mediating astrocyte reactivity and contribute to the brain energetic failure observed in acute sepsis. Moreover, the evidence of PI3K participation in this process indicates a potential target for therapeutic modulation.
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Mierzchala-Pasierb M, Krzystek-Korpacka M, Lesnik P, Adamik B, Placzkowska S, Serek P, Gamian A, Lipinska-Gediga M. Interleukin-18 serum levels in sepsis: Correlation with disease severity and inflammatory markers. Cytokine 2019; 120:22-27. [PMID: 31003186 DOI: 10.1016/j.cyto.2019.04.003] [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: 11/17/2018] [Revised: 03/11/2019] [Accepted: 04/05/2019] [Indexed: 12/19/2022]
Abstract
PURPOSE Sepsis is defined as a life-threatening organ dysfunction caused by a dysregulated host response to infection and a syndrome shaped by pathogen and host factors with characteristic that evolve over time. The study was conducted to evaluate the prognostic and discriminative value of IL-18 assessment in comparison to PCT, CRP, WBC in early stage of sepsis and septic shock. METHODS An observational and prospective study was conducted in the group of 40 ICU patients with diagnosis of sepsis or septic shock, serum PCT, IL-18, CRP and WBC measurements were performed on admission, and on the 2nd, 3rd and 5th therapy day. The level of IL-18 was determined with commercially available test according to manufacturer's protocol. RESULTS There were no statistically significant differences in IL-18 levels in survivors vs non-survivors and in sepsis vs septic shock subgroups the IL-18 levels were statistically significant in the course of the study except for the 5th day. CONCLUSION The PCT, CRP and WBC levels revealed no significant differences between any analyzed subgroups in all time points during study. According to our results the IL-18 is a biomarker better differentiating sepsis and septic shock status than PCT, CRP and WBC but with no prognostic impact.
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Affiliation(s)
| | | | - Patrycja Lesnik
- Department of Anesthesiology and Intensive Therapy, 4th Military Hospital of Wroclaw, Weigla 5, 50-981 Wroclaw, Poland; Department of Pathophysiology, Wroclaw Medical University, Marcinkowskiego 1, 50-368 Wroclaw, Poland.
| | - Barbara Adamik
- Department of Anesthesiology and Intensive Therapy, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland.
| | - Sylwia Placzkowska
- Diagnostics Laboratory for Teaching and Research, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland.
| | - Pawel Serek
- Department of Medical Biochemistry, Wroclaw Medical University, Chalubinskiego 10, 50-368 Wroclaw, Poland.
| | - Andrzej Gamian
- Department of Medical Biochemistry, Wroclaw Medical University, Chalubinskiego 10, 50-368 Wroclaw, Poland.
| | - Malgorzata Lipinska-Gediga
- Department of Anesthesiology and Intensive Therapy, 4th Military Hospital of Wroclaw, Weigla 5, 50-981 Wroclaw, Poland; Faculty of Health Science, Wroclaw Medical University, Wroclaw, Poland.
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Heterogeneity in sepsis: new biological evidence with clinical applications. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2019; 23:80. [PMID: 30850013 PMCID: PMC6408778 DOI: 10.1186/s13054-019-2372-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This article is one of ten reviews selected from the Annual Update in Intensive Care and Emergency Medicine 2019. Other selected articles can be found online at https://www.biomedcentral.com/collections/annualupdate2019. Further information about the Annual Update in Intensive Care and Emergency Medicine is available from http://www.springer.com/series/8901.
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von Knethen A, Brüne B. Histone Deacetylation Inhibitors as Therapy Concept in Sepsis. Int J Mol Sci 2019; 20:ijms20020346. [PMID: 30654448 PMCID: PMC6359123 DOI: 10.3390/ijms20020346] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 12/15/2022] Open
Abstract
Sepsis is characterized by dysregulated gene expression, provoking a hyper-inflammatory response occurring in parallel to a hypo-inflammatory reaction. This is often associated with multi-organ failure, leading to the patient’s death. Therefore, reprogramming of these pro- and anti-inflammatory, as well as immune-response genes which are involved in acute systemic inflammation, is a therapy approach to prevent organ failure and to improve sepsis outcomes. Considering epigenetic, i.e., reversible, modifications of chromatin, not altering the DNA sequence as one tool to adapt the expression profile, inhibition of factors mediating these changes is important. Acetylation of histones by histone acetyltransferases (HATs) and initiating an open-chromatin structure leading to its active transcription is counteracted by histone deacetylases (HDACs). Histone deacetylation triggers a compact nucleosome structure preventing active transcription. Hence, inhibiting the activity of HDACs by specific inhibitors can be used to restore the expression profile of the cells. It can be assumed that HDAC inhibitors will reduce the expression of pro-, as well as anti-inflammatory mediators, which blocks sepsis progression. However, decreased cytokine expression might also be unfavorable, because it can be associated with decreased bacterial clearance.
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Affiliation(s)
- Andreas von Knethen
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt/Main, 60590 Frankfurt, Germany.
- Fraunhofer⁻IME, Project Group Translational Medicine and Pharmacology (TMP), 60596 Frankfurt, Germany.
| | - Bernhard Brüne
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt/Main, 60590 Frankfurt, Germany.
- Fraunhofer⁻IME, Project Group Translational Medicine and Pharmacology (TMP), 60596 Frankfurt, Germany.
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