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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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2
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Burnham KL, Milind N, Lee W, Kwok AJ, Cano-Gamez K, Mi Y, Geoghegan CG, Zhang P, McKechnie S, Soranzo N, Hinds CJ, Knight JC, Davenport EE. eQTLs identify regulatory networks and drivers of variation in the individual response to sepsis. CELL GENOMICS 2024:100587. [PMID: 38897207 DOI: 10.1016/j.xgen.2024.100587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/27/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024]
Abstract
Sepsis is a clinical syndrome of life-threatening organ dysfunction caused by a dysregulated response to infection, for which disease heterogeneity is a major obstacle to developing targeted treatments. We have previously identified gene-expression-based patient subgroups (sepsis response signatures [SRS]) informative for outcome and underlying pathophysiology. Here, we aimed to investigate the role of genetic variation in determining the host transcriptomic response and to delineate regulatory networks underlying SRS. Using genotyping and RNA-sequencing data on 638 adult sepsis patients, we report 16,049 independent expression (eQTLs) and 32 co-expression module (modQTLs) quantitative trait loci in this disease context. We identified significant interactions between SRS and genotype for 1,578 SNP-gene pairs and combined transcription factor (TF) binding site information (SNP2TFBS) and predicted regulon activity (DoRothEA) to identify candidate upstream regulators. Overall, these approaches identified putative mechanistic links between host genetic variation, cell subtypes, and the individual transcriptomic response to infection.
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Affiliation(s)
- Katie L Burnham
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Nikhil Milind
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; University of Cambridge, Cambridge, UK
| | - Wanseon Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Andrew J Kwok
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kiki Cano-Gamez
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yuxin Mi
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Ping Zhang
- Centre for Human Genetics, University of Oxford, Oxford, UK; Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
| | | | - Nicole Soranzo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Charles J Hinds
- Centre for Translational Medicine & Therapeutics, William Harvey Research Institute, Faculty of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Julian C Knight
- Centre for Human Genetics, University of Oxford, Oxford, UK; Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK.
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3
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Mi Y, Burnham KL, Charles PD, Heilig R, Vendrell I, Whalley J, Torrance HD, Antcliffe DB, May SM, Neville MJ, Berridge G, Hutton P, Geoghegan CG, Radhakrishnan J, Nesvizhskii AI, Yu F, Davenport EE, McKechnie S, Davies R, O'Callaghan DJP, Patel P, Del Arroyo AG, Karpe F, Gordon AC, Ackland GL, Hinds CJ, Fischer R, Knight JC. High-throughput mass spectrometry maps the sepsis plasma proteome and differences in patient response. Sci Transl Med 2024; 16:eadh0185. [PMID: 38838133 DOI: 10.1126/scitranslmed.adh0185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 05/08/2024] [Indexed: 06/07/2024]
Abstract
Sepsis, the dysregulated host response to infection causing life-threatening organ dysfunction, is a global health challenge requiring better understanding of pathophysiology and new therapeutic approaches. Here, we applied high-throughput tandem mass spectrometry to delineate the plasma proteome for sepsis and comparator groups (noninfected critical illness, postoperative inflammation, and healthy volunteers) involving 2612 samples (from 1611 patients) and 4553 liquid chromatography-mass spectrometry analyses acquired through a single batch of continuous measurements, with a throughput of 100 samples per day. We show how this scale of data can delineate proteins, pathways, and coexpression modules in sepsis and be integrated with paired leukocyte transcriptomic data (837 samples from n = 649 patients). We mapped the plasma proteomic landscape of the host response in sepsis, including changes over time, and identified features relating to etiology, clinical phenotypes (including organ failures), and severity. This work reveals subphenotypes informative for sepsis response state, disease processes, and outcome; identifies potential biomarkers; and advances opportunities for a precision medicine approach to sepsis.
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Affiliation(s)
- Yuxin Mi
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Katie L Burnham
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Philip D Charles
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Raphael Heilig
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Iolanda Vendrell
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford OX3 7BN, UK
| | - Justin Whalley
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Hew D Torrance
- Division of Anaesthetics, Pain Medicine and Intensive Care, Imperial College, London SW7 2AZ, UK
| | - David B Antcliffe
- Division of Anaesthetics, Pain Medicine and Intensive Care, Imperial College, London SW7 2AZ, UK
- Department of Critical Care, Imperial College Healthcare NHS Trust, London W2 1NY, UK
| | - Shaun M May
- Translational Medicine and Therapeutics, William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Matt J Neville
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LE, UK
- NIHR Oxford Biomedical Research Centre, Oxford OX3 9DU, UK
| | - Georgina Berridge
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Paula Hutton
- Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7JX, UK
| | - Cyndi G Geoghegan
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Jayachandran Radhakrishnan
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | | | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Emma E Davenport
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Stuart McKechnie
- Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7JX, UK
| | - Roger Davies
- Division of Anaesthetics, Pain Medicine and Intensive Care, Imperial College, London SW7 2AZ, UK
| | - David J P O'Callaghan
- Division of Anaesthetics, Pain Medicine and Intensive Care, Imperial College, London SW7 2AZ, UK
- Department of Critical Care, Imperial College Healthcare NHS Trust, London W2 1NY, UK
| | - Parind Patel
- Department of Critical Care, Imperial College Healthcare NHS Trust, London W2 1NY, UK
| | - Ana G Del Arroyo
- Translational Medicine and Therapeutics, William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Fredrik Karpe
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LE, UK
- NIHR Oxford Biomedical Research Centre, Oxford OX3 9DU, UK
| | - Anthony C Gordon
- Division of Anaesthetics, Pain Medicine and Intensive Care, Imperial College, London SW7 2AZ, UK
- Department of Critical Care, Imperial College Healthcare NHS Trust, London W2 1NY, UK
| | - Gareth L Ackland
- Translational Medicine and Therapeutics, William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Charles J Hinds
- Translational Medicine and Therapeutics, William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford OX3 7BN, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, Oxford OX3 9DU, UK
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4
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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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5
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Stevens J, Tezel O, Bonnefil V, Hapstack M, Atreya MR. Biological basis of critical illness subclasses: from the bedside to the bench and back again. Crit Care 2024; 28:186. [PMID: 38812006 PMCID: PMC11137966 DOI: 10.1186/s13054-024-04959-3] [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: 03/09/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
Critical illness syndromes including sepsis, acute respiratory distress syndrome, and acute kidney injury (AKI) are associated with high in-hospital mortality and long-term adverse health outcomes among survivors. Despite advancements in care, clinical and biological heterogeneity among patients continues to hamper identification of efficacious therapies. Precision medicine offers hope by identifying patient subclasses based on clinical, laboratory, biomarker and 'omic' data and potentially facilitating better alignment of interventions. Within the previous two decades, numerous studies have made strides in identifying gene-expression based endotypes and clinico-biomarker based phenotypes among critically ill patients associated with differential outcomes and responses to treatment. In this state-of-the-art review, we summarize the biological similarities and differences across the various subclassification schemes among critically ill patients. In addition, we highlight current translational gaps, the need for advanced scientific tools, human-relevant disease models, to gain a comprehensive understanding of the molecular mechanisms underlying critical illness subclasses.
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Affiliation(s)
- Joseph Stevens
- Division of Immunobiology, Graduate Program, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Oğuzhan Tezel
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Valentina Bonnefil
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45627, USA
| | - Matthew Hapstack
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Mihir R Atreya
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45627, USA.
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6
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Schlapbach LJ, Ganesamoorthy D, Wilson C, Raman S, George S, Snelling PJ, Phillips N, Irwin A, Sharp N, Le Marsney R, Chavan A, Hempenstall A, Bialasiewicz S, MacDonald AD, Grimwood K, Kling JC, McPherson SJ, Blumenthal A, Kaforou M, Levin M, Herberg JA, Gibbons KS, Coin LJM. Host gene expression signatures to identify infection type and organ dysfunction in children evaluated for sepsis: a multicentre cohort study. THE LANCET. CHILD & ADOLESCENT HEALTH 2024; 8:325-338. [PMID: 38513681 DOI: 10.1016/s2352-4642(24)00017-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 03/23/2024]
Abstract
BACKGROUND Sepsis is defined as dysregulated host response to infection that leads to life-threatening organ dysfunction. Biomarkers characterising the dysregulated host response in sepsis are lacking. We aimed to develop host gene expression signatures to predict organ dysfunction in children with bacterial or viral infection. METHODS This cohort study was done in emergency departments and intensive care units of four hospitals in Queensland, Australia, and recruited children aged 1 month to 17 years who, upon admission, underwent a diagnostic test, including blood cultures, for suspected sepsis. Whole-blood RNA sequencing of blood was performed with Illumina NovaSeq (San Diego, CA, USA). Samples with completed phenotyping, monitoring, and RNA extraction by March 31, 2020, were included in the discovery cohort; samples collected or completed thereafter and by Oct 27, 2021, constituted the Rapid Paediatric Infection Diagnosis in Sepsis (RAPIDS) internal validation cohort. An external validation cohort was assembled from RNA sequencing gene expression count data from the observational European Childhood Life-threatening Infectious Disease Study (EUCLIDS), which recruited children with severe infection in nine European countries between 2012 and 2016. Feature selection approaches were applied to derive novel gene signatures for disease class (bacterial vs viral infection) and disease severity (presence vs absence of organ dysfunction 24 h post-sampling). The primary endpoint was the presence of organ dysfunction 24 h after blood sampling in the presence of confirmed bacterial versus viral infection. Gene signature performance is reported as area under the receiver operating characteristic curves (AUCs) and 95% CI. FINDINGS Between Sept 25, 2017, and Oct 27, 2021, 907 patients were enrolled. Blood samples from 595 patients were included in the discovery cohort, and samples from 312 children were included in the RAPIDS validation cohort. We derived a ten-gene disease class signature that achieved an AUC of 94·1% (95% CI 90·6-97·7) in distinguishing bacterial from viral infections in the RAPIDS validation cohort. A ten-gene disease severity signature achieved an AUC of 82·2% (95% CI 76·3-88·1) in predicting organ dysfunction within 24 h of sampling in the RAPIDS validation cohort. Used in tandem, the disease class and disease severity signatures predicted organ dysfunction within 24 h of sampling with an AUC of 90·5% (95% CI 83·3-97·6) for patients with predicted bacterial infection and 94·7% (87·8-100·0) for patients with predicted viral infection. In the external EUCLIDS validation dataset (n=362), the disease class and disease severity predicted organ dysfunction at time of sampling with an AUC of 70·1% (95% CI 44·1-96·2) for patients with predicted bacterial infection and 69·6% (53·1-86·0) for patients with predicted viral infection. INTERPRETATION In children evaluated for sepsis, novel host transcriptomic signatures specific for bacterial and viral infection can identify dysregulated host response leading to organ dysfunction. FUNDING Australian Government Medical Research Future Fund Genomic Health Futures Mission, Children's Hospital Foundation Queensland, Brisbane Diamantina Health Partners, Emergency Medicine Foundation, Gold Coast Hospital Foundation, Far North Queensland Foundation, Townsville Hospital and Health Services SERTA Grant, and Australian Infectious Diseases Research Centre.
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Affiliation(s)
- Luregn J Schlapbach
- Children's Intensive Care Research Program, Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia; Department of Intensive Care and Neonatology, and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland; Paediatric Intensive Care Unit, Queensland Children's Hospital, Children's Health Queensland, Brisbane, QLD, Australia.
| | - Devika Ganesamoorthy
- Children's Intensive Care Research Program, Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Clare Wilson
- Section of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Sainath Raman
- Children's Intensive Care Research Program, Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia; Paediatric Intensive Care Unit, Queensland Children's Hospital, Children's Health Queensland, Brisbane, QLD, Australia
| | - Shane George
- Children's Intensive Care Research Program, Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia; Department of Emergency Medicine, Gold Coast University Hospital, Southport, QLD, Australia; School of Medicine and Dentistry and the Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
| | - Peter J Snelling
- Department of Emergency Medicine, Gold Coast University Hospital, Southport, QLD, Australia; School of Medicine and Dentistry and the Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
| | - Natalie Phillips
- Children's Intensive Care Research Program, Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia; Emergency Department, Queensland Children's Hospital, Children's Health Queensland, Brisbane, QLD, Australia
| | - Adam Irwin
- Faculty of Medicine, UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia; Infection Management and Prevention Services, Queensland Children's Hospital, Children's Health Queensland, Brisbane, QLD, Australia
| | - Natalie Sharp
- Children's Intensive Care Research Program, Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia; Paediatric Intensive Care Unit, Queensland Children's Hospital, Children's Health Queensland, Brisbane, QLD, Australia
| | - Renate Le Marsney
- Children's Intensive Care Research Program, Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Arjun Chavan
- Paediatric Intensive Care Unit, Townsville University Hospital, Townsville, QLD, Australia
| | | | - Seweryn Bialasiewicz
- School of Chemistry and Molecular Biosciences, The Australian Centre for Ecogenomics, and Queensland Paediatric Infectious Diseases Laboratory, The University of Queensland, Brisbane, QLD, Australia
| | - Anna D MacDonald
- Children's Intensive Care Research Program, Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Keith Grimwood
- School of Medicine and Dentistry and the Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia; Department of Infectious Disease and Paediatrics, Gold Coast Health, Southport, QLD, Australia
| | - Jessica C Kling
- Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | | | - Antje Blumenthal
- Frazer Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Myrsini Kaforou
- Section of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Michael Levin
- Section of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Jethro A Herberg
- Section of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Kristen S Gibbons
- Children's Intensive Care Research Program, Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Lachlan J M Coin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia; Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
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7
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Abstract
Sepsis syndromes have been recognized since antiquity yet still pose significant challenges to modern medicine. One of the biggest challenges lies in the heterogeneity of triggers and its protean clinical manifestations, as well as its rapidly progressive and lethal nature. Thus, there is a critical need for biomarkers that can quickly and accurately detect sepsis onset and predict treatment response. In this review, we will briefly describe the current consensus definitions of sepsis and the ideal features of a biomarker. We will then delve into currently available and in-development markers of pathogens, hosts, and their interactions that together comprise the sepsis syndrome.
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Affiliation(s)
- Maya Cohen
- Division of Pulmonary, Critical Care, and Sleep Medicine, Alpert/Brown Medical School, Providence, RI, USA
| | - Debasree Banerjee
- Division of Pulmonary, Critical Care, and Sleep Medicine, Alpert/Brown Medical School, Providence, RI, USA
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8
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Cajander S, Kox M, Scicluna BP, Weigand MA, Mora RA, Flohé SB, Martin-Loeches I, Lachmann G, Girardis M, Garcia-Salido A, Brunkhorst FM, Bauer M, Torres A, Cossarizza A, Monneret G, Cavaillon JM, Shankar-Hari M, Giamarellos-Bourboulis EJ, Winkler MS, Skirecki T, Osuchowski M, Rubio I, Bermejo-Martin JF, Schefold JC, Venet F. Profiling the dysregulated immune response in sepsis: overcoming challenges to achieve the goal of precision medicine. THE LANCET. RESPIRATORY MEDICINE 2024; 12:305-322. [PMID: 38142698 DOI: 10.1016/s2213-2600(23)00330-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 08/14/2023] [Accepted: 08/24/2023] [Indexed: 12/26/2023]
Abstract
Sepsis is characterised by a dysregulated host immune response to infection. Despite recognition of its significance, immune status monitoring is not implemented in clinical practice due in part to the current absence of direct therapeutic implications. Technological advances in immunological profiling could enhance our understanding of immune dysregulation and facilitate integration into clinical practice. In this Review, we provide an overview of the current state of immune profiling in sepsis, including its use, current challenges, and opportunities for progress. We highlight the important role of immunological biomarkers in facilitating predictive enrichment in current and future treatment scenarios. We propose that multiple immune and non-immune-related parameters, including clinical and microbiological data, be integrated into diagnostic and predictive combitypes, with the aid of machine learning and artificial intelligence techniques. These combitypes could form the basis of workable algorithms to guide clinical decisions that make precision medicine in sepsis a reality and improve patient outcomes.
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Affiliation(s)
- Sara Cajander
- Department of Infectious Diseases, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Matthijs Kox
- Department of Intensive Care Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Brendon P Scicluna
- Department of Applied Biomedical Science, Faculty of Health Sciences, Mater Dei hospital, University of Malta, Msida, Malta; Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Markus A Weigand
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Raquel Almansa Mora
- Department of Cell Biology, Genetics, Histology and Pharmacology, University of Valladolid, Valladolid, Spain
| | - Stefanie B Flohé
- Department of Trauma, Hand, and Reconstructive Surgery, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ignacio Martin-Loeches
- St James's Hospital, Dublin, Ireland; Hospital Clinic, Institut D'Investigacions Biomediques August Pi i Sunyer, Universidad de Barcelona, Barcelona, Spain
| | - Gunnar Lachmann
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Anesthesiology and Operative Intensive Care Medicine, Berlin, Germany
| | - Massimo Girardis
- Department of Intensive Care and Anesthesiology, University Hospital of Modena, Modena, Italy
| | - Alberto Garcia-Salido
- Hospital Infantil Universitario Niño Jesús, Pediatric Critical Care Unit, Madrid, Spain
| | - Frank M Brunkhorst
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany
| | - Michael Bauer
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany; Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - Antoni Torres
- Pulmonology Department. Hospital Clinic of Barcelona, University of Barcelona, Ciberes, IDIBAPS, ICREA, Barcelona, Spain
| | - Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Guillaume Monneret
- Immunology Laboratory, Hôpital E Herriot - Hospices Civils de Lyon, Lyon, France; Université Claude Bernard Lyon-1, Hôpital E Herriot, Lyon, France
| | | | - Manu Shankar-Hari
- Centre for Inflammation Research, Institute of Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | | | - Martin Sebastian Winkler
- Department of Anesthesiology and Intensive Care, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Tomasz Skirecki
- Department of Translational Immunology and Experimental Intensive Care, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Marcin Osuchowski
- Ludwig Boltzmann Institute for Traumatology, The Research Center in Cooperation with AUVA, Vienna, Austria
| | - Ignacio Rubio
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany; Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - Jesus F Bermejo-Martin
- Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain; School of Medicine, Universidad de Salamanca, Salamanca, Spain; Centro de Investigación Biomédica en Red en Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Joerg C Schefold
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Fabienne Venet
- Immunology Laboratory, Hôpital E Herriot - Hospices Civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie, Inserm U1111, CNRS, UMR5308, Ecole Normale Supeérieure de Lyon, Universiteé Claude Bernard-Lyon 1, Lyon, France.
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9
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Shankar-Hari M, Calandra T, Soares MP, Bauer M, Wiersinga WJ, Prescott HC, Knight JC, Baillie KJ, Bos LDJ, Derde LPG, Finfer S, Hotchkiss RS, Marshall J, Openshaw PJM, Seymour CW, Venet F, Vincent JL, Le Tourneau C, Maitland-van der Zee AH, McInnes IB, van der Poll T. Reframing sepsis immunobiology for translation: towards informative subtyping and targeted immunomodulatory therapies. THE LANCET. RESPIRATORY MEDICINE 2024; 12:323-336. [PMID: 38408467 PMCID: PMC11025021 DOI: 10.1016/s2213-2600(23)00468-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/27/2023] [Accepted: 12/07/2023] [Indexed: 02/28/2024]
Abstract
Sepsis is a common and deadly condition. Within the current model of sepsis immunobiology, the framing of dysregulated host immune responses into proinflammatory and immunosuppressive responses for the testing of novel treatments has not resulted in successful immunomodulatory therapies. Thus, the recent focus has been to parse observable heterogeneity into subtypes of sepsis to enable personalised immunomodulation. In this Personal View, we highlight that many fundamental immunological concepts such as resistance, disease tolerance, resilience, resolution, and repair are not incorporated into the current sepsis immunobiology model. The focus for addressing heterogeneity in sepsis should be broadened beyond subtyping to encompass the identification of deterministic molecular networks or dominant mechanisms. We explicitly reframe the dysregulated host immune responses in sepsis as altered homoeostasis with pathological disruption of immune-driven resistance, disease tolerance, resilience, and resolution mechanisms. Our proposal highlights opportunities to identify novel treatment targets and could enable successful immunomodulation in the future.
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Affiliation(s)
- Manu Shankar-Hari
- Institute for Regeneration and Repair, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, UK.
| | - Thierry Calandra
- Service of Immunology and Allergy, Center of Human Immunology Lausanne, Department of Medicine and Department of Laboratory Medicine and Pathology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | | | - Michael Bauer
- Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - W Joost Wiersinga
- Center for Experimental and Molecular Medicine and Division of Infectious Diseases, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Hallie C Prescott
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Julian C Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kenneth J Baillie
- Institute for Regeneration and Repair, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, UK
| | - Lieuwe D J Bos
- Department of Intensive Care, Academic Medical Center, Amsterdam, Netherlands
| | - Lennie P G Derde
- Intensive Care Center, University Medical Center Utrecht, Utrecht, Netherlands
| | - Simon Finfer
- Critical Care Division, The George Institute for Global Health, University of New South Wales, Sydney, NSW, Australia
| | - Richard S Hotchkiss
- Department of Anesthesiology and Critical Care Medicine, Washington University School of Medicine in St Louis, St Louis, MO, USA
| | - John Marshall
- Interdepartmental Division of Critical Care, University of Toronto, Toronto, ON, Canada
| | | | - Christopher W Seymour
- Department of Critical Care Medicine, The Clinical Research, Investigation, and Systems Modeling of Acute illness (CRISMA) Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Fabienne Venet
- Immunology Laboratory, Edouard Herriot Hospital, Hospices Civils de Lyon, Lyon, France
| | | | - Christophe Le Tourneau
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris-Saclay University, Paris, France
| | - Anke H Maitland-van der Zee
- Department of Pulmonary Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Iain B McInnes
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine and Division of Infectious Diseases, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
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10
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Robey RC, Logue C, Caird CA, Hansel J, Hellyer TP, Simpson J, Dark P, Mathioudakis AG, Felton T. Immunomodulatory drugs in sepsis: a systematic review and meta-analysis. Anaesthesia 2024. [PMID: 38523060 DOI: 10.1111/anae.16263] [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] [Accepted: 02/05/2024] [Indexed: 03/26/2024]
Abstract
Dysregulation of the host immune response has a central role in the pathophysiology of sepsis. There has been much interest in immunomodulatory drugs as potential therapeutic adjuncts in sepsis. We conducted a systematic review and meta-analysis of randomised controlled trials evaluating the safety and clinical effectiveness of immunomodulatory drugs as adjuncts to standard care in the treatment of adults with sepsis. Our primary outcomes were serious adverse events and all-cause mortality. Fifty-six unique, eligible randomised controlled trials were identified, assessing a range of interventions including cytokine inhibitors; anti-inflammatories; immune cell stimulators; platelet pathway inhibitors; and complement inhibitors. At 1-month follow-up, the use of cytokine inhibitors was associated with a decreased risk of serious adverse events, based on 11 studies involving 7138 patients (RR (95%CI) 0.95 (0.90-1.00), I2 = 0%). The only immunomodulatory drugs associated with an increased risk of serious adverse events were toll-like receptor 4 antagonists (RR (95%CI) 1.18 (1.04-1.34), I2 = 0% (two trials, 567 patients)). Based on 18 randomised controlled trials, involving 11,075 patients, cytokine inhibitors reduced 1-month mortality (RR (95%CI) 0.88 (0.78-0.98), I2 = 57%). Mortality reduction was also shown in the subgroup of 13 randomised controlled trials that evaluated anti-tumour necrosis factor α interventions (RR (95%CI) 0.93 (0.87-0.99), I2 = 0%). Anti-inflammatory drugs had the largest apparent effect on mortality at 2 months at any dose (two trials, 228 patients, RR (95%CI) 0.64 (0.51-0.80), I2 = 0%) and at 3 months at any dose (three trials involving 277 patients, RR (95%CI) 0.67 (0.55-0.81), I2 = 0%). These data indicate that, except for toll-like receptor 4 antagonists, there is no evidence of safety concerns for the use of immunomodulatory drugs in sepsis, and they may show some short-term mortality benefit for selected drugs.
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Affiliation(s)
- R C Robey
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - C Logue
- Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - C A Caird
- Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - J Hansel
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - T P Hellyer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - J Simpson
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - P Dark
- University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Critical Care Unit, Northern Care Alliance NHS Foundation Trust, Salford Care Organisation, Salford, UK
| | - A G Mathioudakis
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - T Felton
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
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11
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Leite GGF, de Brabander J, Michels EHA, Butler JM, Cremer OL, Scicluna BP, Sweeney TE, Reyes M, Salomao R, Peters-Sengers H, van der Poll T. Monocyte state 1 (MS1) cells in critically ill patients with sepsis or non-infectious conditions: association with disease course and host response. Crit Care 2024; 28:88. [PMID: 38504349 PMCID: PMC10953179 DOI: 10.1186/s13054-024-04868-5] [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: 11/17/2023] [Accepted: 03/11/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Sepsis is a life-threatening condition arising from an aberrant host response to infection. Recent single-cell RNA sequencing investigations identified an immature bone-marrow-derived CD14+ monocyte phenotype with immune suppressive properties termed "monocyte state 1" (MS1) in patients with sepsis. Our objective was to determine the association of MS1 cell profiles with disease presentation, outcomes, and host response characteristics. METHODS We used the transcriptome deconvolution method (CIBERSORTx) to estimate the percentage of MS1 cells from blood RNA profiles of patients with sepsis admitted to the intensive care unit (ICU). We compared these profiles to ICU patients without infection and to healthy controls. Host response dysregulation was further studied by gene co-expression network and gene set enrichment analyses of blood leukocytes, and measurement of 15 plasma biomarkers indicative of pathways implicated in sepsis pathogenesis. RESULTS Sepsis patients (n = 332) were divided into three equally-sized groups based on their MS1 cell levels (low, intermediate, and high). MS1 groups did not differ in demographics or comorbidities. The intermediate and high MS1 groups presented with higher disease severity and more often had shock. MS1 cell abundance did not differ between survivors and non-survivors, or between patients who did or did not acquire a secondary infection. Higher MS1 cell percentages were associated with downregulation of lymphocyte-related and interferon response genes in blood leukocytes, with concurrent upregulation of inflammatory response pathways, including tumor necrosis factor signaling via nuclear factor-κB. Previously described sepsis host response transcriptomic subtypes showed different MS1 cell abundances, and MS1 cell percentages positively correlated with the "quantitative sepsis response signature" and "molecular degree of perturbation" scores. Plasma biomarker levels, indicative of inflammation, endothelial cell activation, and coagulation activation, were largely similar between MS1 groups. In ICU patients without infection (n = 215), MS1 cell percentages and their relation with disease severity, shock, and host response dysregulation were highly similar to those in sepsis patients. CONCLUSIONS High MS1 cell percentages are associated with increased disease severity and shock in critically ill patients with sepsis or a non-infectious condition. High MS1 cell abundance likely indicates broad immune dysregulation, entailing not only immunosuppression but also anomalies reflecting exaggerated inflammatory responses.
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Affiliation(s)
- Giuseppe G F Leite
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC, Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
- Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil.
| | - Justin de Brabander
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC, Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Erik H A Michels
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC, Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Joe M Butler
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC, Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Olaf L Cremer
- Department of Intensive Care Medicine, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Brendon P Scicluna
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC, Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Department of Applied Biomedical Science, Faculty of Health Sciences, Mater Dei Hospital, University of Malta, Msida, Malta
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | | | - Miguel Reyes
- Department of Infectious Diseases, Genentech, South San Francisco, USA
| | - Reinaldo Salomao
- Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Hessel Peters-Sengers
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC, Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Department of Epidemiology and Data Science, Amsterdam UMC, Location Vrije Universiteit, Amsterdam, The Netherlands
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC, Location University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Division of Infectious Diseases, Amsterdam UMC, Location University of Amsterdam, Amsterdam, The Netherlands
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12
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Kyriazopoulou E, Hasin-Brumshtein Y, Midic U, Poulakou G, Milionis H, Metallidis S, Astriti M, Fragkou A, Rapti A, Taddei E, Kalomenidis I, Chrysos G, Angheben A, Kainis I, Alexiou Z, Castelli F, Serino FS, Bakakos P, Nicastri E, Tzavara V, Ioannou S, Dagna L, Dimakou K, Tzatzagou G, Chini M, Bassetti M, Kotsis V, Tsoukalas DG, Selmi C, Konstantinou A, Samarkos M, Doumas M, Masgala A, Pagkratis K, Argyraki A, Akinosoglou K, Symbardi S, Netea MG, Panagopoulos P, Dalekos GN, Liesenfeld O, Sweeney TE, Khatri P, Giamarellos-Bourboulis EJ. Transitions of blood immune endotypes and improved outcome by anakinra in COVID-19 pneumonia: an analysis of the SAVE-MORE randomized controlled trial. Crit Care 2024; 28:73. [PMID: 38475786 PMCID: PMC10935809 DOI: 10.1186/s13054-024-04852-z] [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: 01/11/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Endotype classification may guide immunomodulatory management of patients with bacterial and viral sepsis. We aimed to identify immune endotypes and transitions associated with response to anakinra (human interleukin 1 receptor antagonist) in participants in the SAVE-MORE trial. METHODS Adult patients hospitalized with radiological findings of PCR-confirmed severe pneumonia caused by SARS-CoV-2 and plasma-soluble urokinase plasminogen activator receptor levels of ≥ 6 ng/ml in the SAVE-MORE trial (NCT04680949) were characterized at baseline and days 4 and 7 of treatment using a previously defined 33-messenger RNA classifier to assign an immunological endotype in blood. Endpoints were changes in endotypes and progression to severe respiratory failure (SRF) associated with anakinra treatment. RESULTS At baseline, 23.2% of 393 patients were designated as inflammopathic, 41.1% as adaptive, and 35.7% as coagulopathic. Only 23.9% were designated as the same endotype at days 4 and 7 compared to baseline, while all other patients transitioned between endotypes. Anakinra-treated patients were more likely to remain in the adaptive endotype during 7-day treatment (24.4% vs. 9.9%; p < 0.001). Anakinra also protected patients with coagulopathic endotype at day 7 against SRF compared to placebo (27.8% vs. 55.9%; p = 0.013). CONCLUSION We identify an association between endotypes defined using blood transcriptome and anakinra therapy for COVID-19 pneumonia, with anakinra-treated patients shifting toward endotypes associated with a better outcome, mainly the adaptive endotype. Trial registration ClinicalTrials.gov, NCT04680949, December 23, 2020.
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Affiliation(s)
- Evdoxia Kyriazopoulou
- 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | | | - Garyfallia Poulakou
- 3rd Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Haralampos Milionis
- 1st Department of Internal Medicine, Medical School, University of Ioannina, Ioannina, Greece
| | - Simeon Metallidis
- 1st Department of Internal Medicine, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Myrto Astriti
- 1st Department of Internal Medicine, G. Gennimatas General Hospital of Athens, Athens, Greece
| | | | - Aggeliki Rapti
- 2nd Department of Pulmonary Medicine, Sotiria General Hospital of Chest Diseases, Athens, Greece
| | - Eleonora Taddei
- Dipartimento Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Gemelli IRCCS, Rome, Italy
| | - Ioannis Kalomenidis
- 1st Department of Critical Care and Pulmonary Medicine, Medical School, National and Kapodistrian University of Athens, Evangelismos General Hospital, Athens, Greece
| | - Georgios Chrysos
- 2nd Department of Internal Medicine, Tzaneio General Hospital of Piraeus, Athens, Greece
| | - Andrea Angheben
- Department of Infectious - Tropical Diseases and Microbiology, IRCSS Sacro Cuore Hospital, Negrar, Verona, Italy
| | - Ilias Kainis
- 10th Department of Pulmonary Medicine, Sotiria General Hospital of Chest Diseases of Athens, Athens, Greece
| | - Zoi Alexiou
- 2nd Department of Internal Medicine, Thriasio General Hospital of Eleusis, Athens, Greece
| | - Francesco Castelli
- Spedali Civili, Brescia ASST Spedali Civili Hospital, University of Brescia, Brescia, Italy
| | | | - Petros Bakakos
- 1st Department of Chest Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Emanuele Nicastri
- Department of Internal Medicine, Spallanzani Institute of Rome, Rome, Italy
| | - Vasiliki Tzavara
- 1st Department of Internal Medicine, Korgialeneion-Benakeion General Hospital, Athens, Greece
| | - Sofia Ioannou
- Department of Therapeutics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Lorenzo Dagna
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases (UnIRAR), IRCCS Ospedale San Raffaele and Vita-Salute San Raffaele University, Milan, Italy
| | - Katerina Dimakou
- 5th Department of Pulmonary Medicine, Sotiria General Hospital of Chest Diseases, Athens, Athens, Greece
| | - Glykeria Tzatzagou
- 1st Department of Internal Medicine, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Maria Chini
- 3rd Department of Internal Medicine and Infectious Diseases Unit, Korgialeneion-Benakeion General Hospital, Athens, Greece
| | - Matteo Bassetti
- Infectious Diseases Clinic, Ospedale Policlinico San Martino IRCCS and Department of Health Sciences, University of Genova, Genova, Italy
| | - Vasileios Kotsis
- 3rd Department of Internal Medicine, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dionysios G Tsoukalas
- 4th Department of Pulmonary Medicine, Sotiria General Hospital of Chest Diseases, Athens, Greece
| | - Carlo Selmi
- Department of Biomedical Sciences, Humanitas University and IRCCS Humanitas Research Hospital, Milan, Italy
| | - Alexandra Konstantinou
- 1st Department of Internal Medicine, Asklepieio General Hospital of Voula, Voula, Greece
| | - Michael Samarkos
- 1st Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Michael Doumas
- 2nd Department of Propedeutic Medicine, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Aikaterini Masgala
- 2nd Department of Internal Medicine, Konstantopouleio General Hospital, Athens, Greece
| | | | - Aikaterini Argyraki
- Department of Internal Medicine, Sotiria General Hospital of Chest Diseases, Athens, Greece
| | | | - Styliani Symbardi
- 1st Department of Internal Medicine, Thriasio General Hospital of Eleusis, Athens, Greece
| | - Mihai G Netea
- Department of Internal Medicine and Center for Infectious Diseases, Radboud University, Nijmegen, The Netherlands
- Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Periklis Panagopoulos
- 2nd Department of Internal Medicine, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - George N Dalekos
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
| | | | | | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Evangelos J Giamarellos-Bourboulis
- 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
- 4th Department of Internal Medicine, ATTIKON University Hospital, 1 Rimini Street, 124 62, Athens, Greece.
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13
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Yang Q, Langston JC, Prosniak R, Pettigrew S, Zhao H, Perez E, Edelmann H, Mansoor N, Merali C, Merali S, Marchetti N, Prabhakarpandian B, Kiani MF, Kilpatrick LE. Distinct functional neutrophil phenotypes in sepsis patients correlate with disease severity. Front Immunol 2024; 15:1341752. [PMID: 38524125 PMCID: PMC10957777 DOI: 10.3389/fimmu.2024.1341752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 03/26/2024] Open
Abstract
Purpose Sepsis is a clinical syndrome defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. Sepsis is a highly heterogeneous syndrome with distinct phenotypes that impact immune function and response to infection. To develop targeted therapeutics, immunophenotyping is needed to identify distinct functional phenotypes of immune cells. In this study, we utilized our Organ-on-Chip assay to categorize sepsis patients into distinct phenotypes using patient data, neutrophil functional analysis, and proteomics. Methods Following informed consent, neutrophils and plasma were isolated from sepsis patients in the Temple University Hospital ICU (n=45) and healthy control donors (n=7). Human lung microvascular endothelial cells (HLMVEC) were cultured in the Organ-on-Chip and treated with buffer or cytomix ((TNF/IL-1β/IFNγ). Neutrophil adhesion and migration across HLMVEC in the Organ-on-Chip were used to categorize functional neutrophil phenotypes. Quantitative label-free global proteomics was performed on neutrophils to identify differentially expressed proteins. Plasma levels of sepsis biomarkers and neutrophil extracellular traps (NETs) were determined by ELISA. Results We identified three functional phenotypes in critically ill ICU sepsis patients based on ex vivo neutrophil adhesion and migration patterns. The phenotypes were classified as: Hyperimmune characterized by enhanced neutrophil adhesion and migration, Hypoimmune that was unresponsive to stimulation, and Hybrid with increased adhesion but blunted migration. These functional phenotypes were associated with distinct proteomic signatures and differentiated sepsis patients by important clinical parameters related to disease severity. The Hyperimmune group demonstrated higher oxygen requirements, increased mechanical ventilation, and longer ICU length of stay compared to the Hypoimmune and Hybrid groups. Patients with the Hyperimmune neutrophil phenotype had significantly increased circulating neutrophils and elevated plasma levels NETs. Conclusion Neutrophils and NETs play a critical role in vascular barrier dysfunction in sepsis and elevated NETs may be a key biomarker identifying the Hyperimmune group. Our results establish significant associations between specific neutrophil functional phenotypes and disease severity and identify important functional parameters in sepsis pathophysiology that may provide a new approach to classify sepsis patients for specific therapeutic interventions.
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Affiliation(s)
- Qingliang Yang
- Department of Mechanical Engineering, College of Engineering, Temple University, Philadelphia, PA, United States
| | - Jordan C. Langston
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, PA, United States
| | - Roman Prosniak
- Department of Thoracic Medicine and Surgery, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Samantha Pettigrew
- Department of Thoracic Medicine and Surgery, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Huaqing Zhao
- Department of Biomedical Education and Data Science, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Edwin Perez
- Center for Inflammation and Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Hannah Edelmann
- Center for Inflammation and Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Nadia Mansoor
- Center for Inflammation and Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Carmen Merali
- School of Pharmacy, Temple University, Philadelphia, PA, United States
| | - Salim Merali
- School of Pharmacy, Temple University, Philadelphia, PA, United States
| | - Nathaniel Marchetti
- Department of Thoracic Medicine and Surgery, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | | | - Mohammad F. Kiani
- Department of Mechanical Engineering, College of Engineering, Temple University, Philadelphia, PA, United States
- Department of Bioengineering, College of Engineering, Temple University, Philadelphia, PA, United States
| | - Laurie E. Kilpatrick
- Department of Thoracic Medicine and Surgery, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
- Center for Inflammation and Lung Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
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14
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Santacroce E, D'Angerio M, Ciobanu AL, Masini L, Lo Tartaro D, Coloretti I, Busani S, Rubio I, Meschiari M, Franceschini E, Mussini C, Girardis M, Gibellini L, Cossarizza A, De Biasi S. Advances and Challenges in Sepsis Management: Modern Tools and Future Directions. Cells 2024; 13:439. [PMID: 38474403 DOI: 10.3390/cells13050439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Sepsis, a critical condition marked by systemic inflammation, profoundly impacts both innate and adaptive immunity, often resulting in lymphopenia. This immune alteration can spare regulatory T cells (Tregs) but significantly affects other lymphocyte subsets, leading to diminished effector functions, altered cytokine profiles, and metabolic changes. The complexity of sepsis stems not only from its pathophysiology but also from the heterogeneity of patient responses, posing significant challenges in developing universally effective therapies. This review emphasizes the importance of phenotyping in sepsis to enhance patient-specific diagnostic and therapeutic strategies. Phenotyping immune cells, which categorizes patients based on clinical and immunological characteristics, is pivotal for tailoring treatment approaches. Flow cytometry emerges as a crucial tool in this endeavor, offering rapid, low cost and detailed analysis of immune cell populations and their functional states. Indeed, this technology facilitates the understanding of immune dysfunctions in sepsis and contributes to the identification of novel biomarkers. Our review underscores the potential of integrating flow cytometry with omics data, machine learning and clinical observations to refine sepsis management, highlighting the shift towards personalized medicine in critical care. This approach could lead to more precise interventions, improving outcomes in this heterogeneously affected patient population.
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Affiliation(s)
- Elena Santacroce
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Miriam D'Angerio
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Alin Liviu Ciobanu
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Linda Masini
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Domenico Lo Tartaro
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Irene Coloretti
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Stefano Busani
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Ignacio Rubio
- Department of Anesthesiology and Intensive Care Medicine, Center for Sepsis Control and Care, Jena University Hospital, 07747 Jena, Germany
| | - Marianna Meschiari
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Erica Franceschini
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Cristina Mussini
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Massimo Girardis
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Lara Gibellini
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Sara De Biasi
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy
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15
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Feinstein M, Katz D, Demaria S, Hofer IS. Remote Monitoring and Artificial Intelligence: Outlook for 2050. Anesth Analg 2024; 138:350-357. [PMID: 38215713 PMCID: PMC10794024 DOI: 10.1213/ane.0000000000006712] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024]
Abstract
Remote monitoring and artificial intelligence will become common and intertwined in anesthesiology by 2050. In the intraoperative period, technology will lead to the development of integrated monitoring systems that will integrate multiple data streams and allow anesthesiologists to track patients more effectively. This will free up anesthesiologists to focus on more complex tasks, such as managing risk and making value-based decisions. This will also enable the continued integration of remote monitoring and control towers having profound effects on coverage and practice models. In the PACU and ICU, the technology will lead to the development of early warning systems that can identify patients who are at risk of complications, enabling early interventions and more proactive care. The integration of augmented reality will allow for better integration of diverse types of data and better decision-making. Postoperatively, the proliferation of wearable devices that can monitor patient vital signs and track their progress will allow patients to be discharged from the hospital sooner and receive care at home. This will require increased use of telemedicine, which will allow patients to consult with doctors remotely. All of these advances will require changes to legal and regulatory frameworks that will enable new workflows that are different from those familiar to today's providers.
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Affiliation(s)
- Max Feinstein
- Department of Anesthesiology Pain and Perioperative Medicine, Icahn School of Medicine at Mount Sinai
| | - Daniel Katz
- Department of Anesthesiology Pain and Perioperative Medicine, Icahn School of Medicine at Mount Sinai
| | - Samuel Demaria
- Department of Anesthesiology Pain and Perioperative Medicine, Icahn School of Medicine at Mount Sinai
| | - Ira S. Hofer
- Department of Anesthesiology Pain and Perioperative Medicine, Icahn School of Medicine at Mount Sinai
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16
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Yang CS, Coopersmith CM, Lyons JD. Cell death proteins in sepsis: key players and modern therapeutic approaches. Front Immunol 2024; 14:1347401. [PMID: 38274794 PMCID: PMC10808706 DOI: 10.3389/fimmu.2023.1347401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
Cell death proteins play a central role in host immune signaling during sepsis. These interconnected mechanisms trigger cell demise via apoptosis, necroptosis, and pyroptosis while also driving inflammatory signaling. Targeting cell death mediators with novel therapies may correct the dysregulated inflammation seen during sepsis and improve outcomes for septic patients.
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Affiliation(s)
- Chloe S. Yang
- Department of Surgery, Emory University, Atlanta, GA, United States
| | - Craig M. Coopersmith
- Department of Surgery, Emory University, Atlanta, GA, United States
- Emory Critical Care Center, Emory University, Atlanta, GA, United States
| | - John D. Lyons
- Department of Surgery, Emory University, Atlanta, GA, United States
- Emory Critical Care Center, Emory University, Atlanta, GA, United States
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17
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de Kok JWTM, van Rosmalen F, Koeze J, Keus F, van Kuijk SMJ, Castela Forte J, Schnabel RM, Driessen RGH, van Herpt TTW, Sels JWEM, Bergmans DCJJ, Lexis CPH, van Doorn WPTM, Meex SJR, Xu M, Borrat X, Cavill R, van der Horst ICC, van Bussel BCT. Deep embedded clustering generalisability and adaptation for integrating mixed datatypes: two critical care cohorts. Sci Rep 2024; 14:1045. [PMID: 38200252 PMCID: PMC10781731 DOI: 10.1038/s41598-024-51699-z] [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: 08/14/2023] [Accepted: 01/08/2024] [Indexed: 01/12/2024] Open
Abstract
We validated a Deep Embedded Clustering (DEC) model and its adaptation for integrating mixed datatypes (in this study, numerical and categorical variables). Deep Embedded Clustering (DEC) is a promising technique capable of managing extensive sets of variables and non-linear relationships. Nevertheless, DEC cannot adequately handle mixed datatypes. Therefore, we adapted DEC by replacing the autoencoder with an X-shaped variational autoencoder (XVAE) and optimising hyperparameters for cluster stability. We call this model "X-DEC". We compared DEC and X-DEC by reproducing a previous study that used DEC to identify clusters in a population of intensive care patients. We assessed internal validity based on cluster stability on the development dataset. Since generalisability of clustering models has insufficiently been validated on external populations, we assessed external validity by investigating cluster generalisability onto an external validation dataset. We concluded that both DEC and X-DEC resulted in clinically recognisable and generalisable clusters, but X-DEC produced much more stable clusters.
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Affiliation(s)
- Jip W T M de Kok
- Department of Intensive Care Medicine, Maastricht University Medical Centre+, P. Debyelaan, 25, 6229 HX, Maastricht, The Netherlands.
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands.
| | - Frank van Rosmalen
- Department of Intensive Care Medicine, Maastricht University Medical Centre+, P. Debyelaan, 25, 6229 HX, Maastricht, The Netherlands
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Jacqueline Koeze
- Department of Critical Care, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Frederik Keus
- Department of Critical Care, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Sander M J van Kuijk
- Department of Clinical Epidemiology and Medical Technical Assessment, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - José Castela Forte
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Bernoulli Institute for Mathematics, Computer Science and Artificial Intelligence, University of Groningen, Groningen, The Netherlands
| | - Ronny M Schnabel
- Department of Intensive Care Medicine, Maastricht University Medical Centre+, P. Debyelaan, 25, 6229 HX, Maastricht, The Netherlands
| | - Rob G H Driessen
- Department of Intensive Care Medicine, Maastricht University Medical Centre+, P. Debyelaan, 25, 6229 HX, Maastricht, The Netherlands
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
- Department of Cardiology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Thijs T W van Herpt
- Department of Intensive Care Medicine, Maastricht University Medical Centre+, P. Debyelaan, 25, 6229 HX, Maastricht, The Netherlands
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Jan-Willem E M Sels
- Department of Intensive Care Medicine, Maastricht University Medical Centre+, P. Debyelaan, 25, 6229 HX, Maastricht, The Netherlands
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
- Department of Cardiology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Dennis C J J Bergmans
- Department of Intensive Care Medicine, Maastricht University Medical Centre+, P. Debyelaan, 25, 6229 HX, Maastricht, The Netherlands
- School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Chris P H Lexis
- Department of Intensive Care Medicine, Maastricht University Medical Centre+, P. Debyelaan, 25, 6229 HX, Maastricht, The Netherlands
| | - William P T M van Doorn
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
- Department of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Steven J R Meex
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
- Department of Clinical Chemistry, Central Diagnostic Laboratory, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Minnan Xu
- Takeda Pharmaceuticals, Deerfield, IL, USA
| | - Xavier Borrat
- Department of Biostatistics Harvard T.H, Chan School of Public Health, Boston, MA, USA
- Anaesthesiology and Critical Care Department, Hospital Clinic de Barcelona, Barcelona, Spain
- Medical Informatics Department, Hospital Clinic de Barcelona, Barcelona, Spain
| | - Rachel Cavill
- Department of Advanced Computing Sciences, Maastricht University, Maastricht, The Netherlands
| | - Iwan C C van der Horst
- Department of Intensive Care Medicine, Maastricht University Medical Centre+, P. Debyelaan, 25, 6229 HX, Maastricht, The Netherlands
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Bas C T van Bussel
- Department of Intensive Care Medicine, Maastricht University Medical Centre+, P. Debyelaan, 25, 6229 HX, Maastricht, The Netherlands
- Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
- Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, The Netherlands
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18
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Liu D, Langston JC, Prabhakarpandian B, Kiani MF, Kilpatrick LE. The critical role of neutrophil-endothelial cell interactions in sepsis: new synergistic approaches employing organ-on-chip, omics, immune cell phenotyping and in silico modeling to identify new therapeutics. Front Cell Infect Microbiol 2024; 13:1274842. [PMID: 38259971 PMCID: PMC10800980 DOI: 10.3389/fcimb.2023.1274842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
Sepsis is a global health concern accounting for more than 1 in 5 deaths worldwide. Sepsis is now defined as life-threatening organ dysfunction caused by a dysregulated host response to infection. Sepsis can develop from bacterial (gram negative or gram positive), fungal or viral (such as COVID) infections. However, therapeutics developed in animal models and traditional in vitro sepsis models have had little success in clinical trials, as these models have failed to fully replicate the underlying pathophysiology and heterogeneity of the disease. The current understanding is that the host response to sepsis is highly diverse among patients, and this heterogeneity impacts immune function and response to infection. Phenotyping immune function and classifying sepsis patients into specific endotypes is needed to develop a personalized treatment approach. Neutrophil-endothelium interactions play a critical role in sepsis progression, and increased neutrophil influx and endothelial barrier disruption have important roles in the early course of organ damage. Understanding the mechanism of neutrophil-endothelium interactions and how immune function impacts this interaction can help us better manage the disease and lead to the discovery of new diagnostic and prognosis tools for effective treatments. In this review, we will discuss the latest research exploring how in silico modeling of a synergistic combination of new organ-on-chip models incorporating human cells/tissue, omics analysis and clinical data from sepsis patients will allow us to identify relevant signaling pathways and characterize specific immune phenotypes in patients. Emerging technologies such as machine learning can then be leveraged to identify druggable therapeutic targets and relate them to immune phenotypes and underlying infectious agents. This synergistic approach can lead to the development of new therapeutics and the identification of FDA approved drugs that can be repurposed for the treatment of sepsis.
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Affiliation(s)
- Dan Liu
- Department of Bioengineering, Temple University, Philadelphia, PA, United States
| | - Jordan C. Langston
- Department of Bioengineering, Temple University, Philadelphia, PA, United States
| | | | - Mohammad F. Kiani
- Department of Bioengineering, Temple University, Philadelphia, PA, United States
- Department of Mechanical Engineering, Temple University, Philadelphia, PA, United States
- Department of Radiation Oncology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Laurie E. Kilpatrick
- Center for Inflammation and Lung Research, Department of Microbiology, Immunology and Inflammation, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
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19
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Levine AR, Calfee CS. Subphenotypes of Acute Respiratory Distress Syndrome: Advancing Towards Precision Medicine. Tuberc Respir Dis (Seoul) 2024; 87:1-11. [PMID: 37675452 PMCID: PMC10758309 DOI: 10.4046/trd.2023.0104] [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: 07/26/2023] [Revised: 08/25/2023] [Accepted: 09/06/2023] [Indexed: 09/08/2023] Open
Abstract
Acute respiratory distress syndrome (ARDS) is a common cause of severe hypoxemia defined by the acute onset of bilateral non-cardiogenic pulmonary edema. The diagnosis is made by defined consensus criteria. Supportive care, including prevention of further injury to the lungs, is the only treatment that conclusively improves outcomes. The inability to find more advanced therapies is due, in part, to the highly sensitive but relatively non-specific current syndromic consensus criteria, combining a heterogenous population of patients under the umbrella of ARDS. With few effective therapies, the morality rate remains 30% to 40%. Many subphenotypes of ARDS have been proposed to cluster patients with shared combinations of observable or measurable traits. Subphenotyping patients is a strategy to overcome heterogeneity to advance clinical research and eventually identify treatable traits. Subphenotypes of ARDS have been proposed based on radiographic patterns, protein biomarkers, transcriptomics, and/or machine-based clustering of clinical and biological variables. Some of these strategies have been reproducible across patient cohorts, but at present all have practical limitations to their implementation. Furthermore, there is no agreement on which strategy is the most appropriate. This review will discuss the current strategies for subphenotyping patients with ARDS, including the strengths and limitations, and the future directions of ARDS subphenotyping.
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Affiliation(s)
- Andrea R. Levine
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Carolyn S. Calfee
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
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20
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Atreya MR, Banerjee S, Lautz AJ, Alder MN, Varisco BM, Wong HR, Muszynski JA, Hall MW, Sanchez-Pinto LN, Kamaleswaran R. Machine learning-driven identification of the gene-expression signature associated with a persistent multiple organ dysfunction trajectory in critical illness. EBioMedicine 2024; 99:104938. [PMID: 38142638 PMCID: PMC10788426 DOI: 10.1016/j.ebiom.2023.104938] [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: 09/20/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/26/2023] Open
Abstract
BACKGROUND Multiple organ dysfunction syndrome (MODS) disproportionately drives morbidity and mortality among critically ill patients. However, we lack a comprehensive understanding of its pathobiology. Identification of genes associated with a persistent MODS trajectory may shed light on underlying biology and allow for accurate prediction of those at-risk. METHODS Secondary analyses of publicly available gene-expression datasets. Supervised machine learning (ML) was used to identify a parsimonious set of genes associated with a persistent MODS trajectory in a training set of pediatric septic shock. We optimized model parameters and tested risk-prediction capabilities in independent validation and test datasets, respectively. We compared model performance relative to an established gene-set predictive of sepsis mortality. FINDINGS Patients with a persistent MODS trajectory had 568 differentially expressed genes and characterized by a dysregulated innate immune response. Supervised ML identified 111 genes associated with the outcome of interest on repeated cross-validation, with an AUROC of 0.87 (95% CI: 0.85-0.88) in the training set. The optimized model, limited to 20 genes, achieved AUROCs ranging from 0.74 to 0.79 in the validation and test sets to predict those with persistent MODS, regardless of host age and cause of organ dysfunction. Our classifier demonstrated reproducibility in identifying those with persistent MODS in comparison with a published gene-set predictive of sepsis mortality. INTERPRETATION We demonstrate the utility of supervised ML driven identification of the genes associated with persistent MODS. Pending validation in enriched cohorts with a high burden of organ dysfunction, such an approach may inform targeted delivery of interventions among at-risk patients. FUNDING H.R.W.'s NIHR35GM126943 award supported the work detailed in this manuscript. Upon his death, the award was transferred to M.N.A. M.R.A., N.S.P, and R.K were supported by NIHR21GM151703. R.K. was supported by R01GM139967.
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Affiliation(s)
- Mihir R Atreya
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, Cincinnati, 45229, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.
| | - Shayantan Banerjee
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600 036, India
| | - Andrew J Lautz
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, Cincinnati, 45229, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Matthew N Alder
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, Cincinnati, 45229, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Brian M Varisco
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, Cincinnati, 45229, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Hector R Wong
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, Cincinnati, 45229, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Jennifer A Muszynski
- Division of Critical Care Medicine, Nationwide Children's Hospital, Columbus, 43205, OH, USA; Department of Pediatrics, Ohio State University, Columbus, 43205, OH, USA
| | - Mark W Hall
- Division of Critical Care Medicine, Nationwide Children's Hospital, Columbus, 43205, OH, USA; Department of Pediatrics, Ohio State University, Columbus, 43205, OH, USA
| | - L Nelson Sanchez-Pinto
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, 60611, IL, USA; Department of Health and Biomedical Informatics, Northwestern University Feinberg School of Medicine, Chicago, 60611, IL, USA
| | - Rishikesan Kamaleswaran
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, 30322, GA, United States; Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, 30322, GA, United States
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21
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Kim YT, Huh JW, Choi YH, Yoon HK, Nguyen TT, Chun E, Jeong G, Park S, Ahn S, Lee WK, Noh YW, Lee KS, Ahn HS, Lee C, Lee SM, Kim KS, Suh GJ, Jeon K, Kim S, Jin M. Highly secreted tryptophanyl tRNA synthetase 1 as a potential theranostic target for hypercytokinemic severe sepsis. EMBO Mol Med 2024; 16:40-63. [PMID: 38177528 PMCID: PMC10883277 DOI: 10.1038/s44321-023-00004-y] [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: 06/01/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 01/06/2024] Open
Abstract
Despite intensive clinical and scientific efforts, the mortality rate of sepsis remains high due to the lack of precise biomarkers for patient stratification and therapeutic guidance. Secreted human tryptophanyl-tRNA synthetase 1 (WARS1), an endogenous ligand for Toll-like receptor (TLR) 2 and TLR4 against infection, activates the genes that signify the hyperinflammatory sepsis phenotype. High plasma WARS1 levels stratified the early death of critically ill patients with sepsis, along with elevated levels of cytokines, chemokines, and lactate, as well as increased numbers of absolute neutrophils and monocytes, and higher Sequential Organ Failure Assessment (SOFA) scores. These symptoms were recapitulated in severely ill septic mice with hypercytokinemia. Further, injection of WARS1 into mildly septic mice worsened morbidity and mortality. We created an anti-human WARS1-neutralizing antibody that suppresses proinflammatory cytokine expression in marmosets with endotoxemia. Administration of this antibody into severe septic mice attenuated cytokine storm, organ failure, and early mortality. With antibiotics, the antibody almost completely prevented fatalities. These data imply that blood-circulating WARS1-guided anti-WARS1 therapy may provide a novel theranostic strategy for life-threatening systemic hyperinflammatory sepsis.
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Affiliation(s)
- Yoon Tae Kim
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon, Republic of Korea
| | - Jin Won Huh
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yun Hui Choi
- R&D Center, MirimGENE, Incheon, Republic of Korea
| | | | | | - Eunho Chun
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon, Republic of Korea
| | - Geunyeol Jeong
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon, Republic of Korea
| | - Sunyoung Park
- Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Republic of Korea
| | - Sungwoo Ahn
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - Won-Kyu Lee
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju, Republic of Korea
| | - Young-Woock Noh
- New Drug Development Center, Osong Medical Innovation Foundation, Cheongju, Republic of Korea
| | - Kyoung Sun Lee
- Non-Clinical Evaluation Center, Osong Medical Innovation Foundation, Cheongju, Republic of Korea
| | - Hee-Sung Ahn
- Convergence Medicine Research Center, Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
| | - Cheolju Lee
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Sang Min Lee
- Department of Internal Medicine, Gil Medical Center, College of Medicine, Gachon University, Incheon, Republic of Korea
| | - Kyung Su Kim
- Department of Emergency Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Gil Joon Suh
- Department of Emergency Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyeongman Jeon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, Institute for Artificial Intelligence and Biomedical Research, The interdisciplinary graduate program in integrative biotechnology, College of Pharmacy & College of Medicine, Gangnam Severance Hospital, Yonsei University, Incheon, Republic of Korea
| | - Mirim Jin
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon, Republic of Korea.
- R&D Center, MirimGENE, Incheon, Republic of Korea.
- Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Republic of Korea.
- Department of Microbiology, College of Medicine, Gachon University, Incheon, Republic of Korea.
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22
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Giamarellos-Bourboulis EJ, Aschenbrenner AC, Bauer M, Bock C, Calandra T, Gat-Viks I, Kyriazopoulou E, Lupse M, Monneret G, Pickkers P, Schultze JL, van der Poll T, van de Veerdonk FL, Vlaar APJ, Weis S, Wiersinga WJ, Netea MG. The pathophysiology of sepsis and precision-medicine-based immunotherapy. Nat Immunol 2024; 25:19-28. [PMID: 38168953 DOI: 10.1038/s41590-023-01660-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/21/2023] [Indexed: 01/05/2024]
Abstract
Sepsis remains a major cause of morbidity and mortality in both low- and high-income countries. Antibiotic therapy and supportive care have significantly improved survival following sepsis in the twentieth century, but further progress has been challenging. Immunotherapy trials for sepsis, mainly aimed at suppressing the immune response, from the 1990s and 2000s, have largely failed, in part owing to unresolved patient heterogeneity in the underlying immune disbalance. The past decade has brought the promise to break this blockade through technological developments based on omics-based technologies and systems medicine that can provide a much larger data space to describe in greater detail the immune endotypes in sepsis. Patient stratification opens new avenues towards precision medicine approaches that aim to apply immunotherapies to sepsis, on the basis of precise biomarkers and molecular mechanisms defining specific immune endotypes. This approach has the potential to lead to the establishment of immunotherapy as a successful pillar in the treatment of sepsis for future generations.
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Affiliation(s)
- Evangelos J Giamarellos-Bourboulis
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens Medical School, Athens, Greece
- Hellenic Institute for the Study of Sepsis, Athens, Greece
| | - Anna C Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Michael Bauer
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Friedrich-Schiller University, Jena, Germany
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Vienna, Austria
| | - Thierry Calandra
- Service of Immunology and Allergy and Center of Human Immunology Lausanne, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Irit Gat-Viks
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Evdoxia Kyriazopoulou
- 4th Department of Internal Medicine, National and Kapodistrian University of Athens Medical School, Athens, Greece
- Hellenic Institute for the Study of Sepsis, Athens, Greece
| | - Mihaela Lupse
- Infectious Diseases Hospital, University of Medicine and Pharmacy 'Iuliu Hatieganu', Cluj-Napoca, Romania
| | - Guillaume Monneret
- Joint Research Unit HCL-bioMérieux, EA 7426 'Pathophysiology of Injury-Induced Immunosuppression' (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, bioMérieux), Lyon, France
- Immunology Laboratory, Edouard Herriot Hospital - Hospices Civils de Lyon, Lyon, France
| | - Peter Pickkers
- Department of Intensive Care, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) and the University of Bonn, Bonn, Germany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Tom van der Poll
- Division of Infectious Diseases, Amsterdam University Medical Centers (Amsterdam UMC), Center for Experimental and Molecular Medicine (CEMM), University of Amsterdam, Amsterdam, The Netherlands
| | - Frank L van de Veerdonk
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alexander P J Vlaar
- Department of Intensive Care and Laboratory of Experimental Intensive Care and Anesthesiology L.E.C.A. Amsterdam Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Sebastian Weis
- Institute for Infectious Disease and Infection Control, Jena University Hospital, Friedrich-Schiller University, Jena, Germany
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute-HKI, Jena, Germany
| | - W Joost Wiersinga
- Division of Infectious Diseases, Amsterdam University Medical Centers (Amsterdam UMC), Center for Experimental and Molecular Medicine (CEMM), University of Amsterdam, Amsterdam, The Netherlands
| | - Mihai G Netea
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.
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23
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Yang JO, Zinter MS, Pellegrini M, Wong MY, Gala K, Markovic D, Nadel B, Peng K, Do N, Mangul S, Nadkarni VM, Karlsberg A, Deshpande D, Butte MJ, Asaro L, Agus M, Sapru A. Whole blood transcriptomics identifies subclasses of pediatric septic shock. Crit Care 2023; 27:486. [PMID: 38066613 PMCID: PMC10709863 DOI: 10.1186/s13054-023-04689-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/14/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Sepsis is a highly heterogeneous syndrome, which has hindered the development of effective therapies. This has prompted investigators to develop a precision medicine approach aimed at identifying biologically homogenous subgroups of patients with septic shock and critical illnesses. Transcriptomic analysis can identify subclasses derived from differences in underlying pathophysiological processes that may provide the basis for new targeted therapies. The goal of this study was to elucidate pathophysiological pathways and identify pediatric septic shock subclasses based on whole blood RNA expression profiles. METHODS The subjects were critically ill children with cardiopulmonary failure who were a part of a prospective randomized insulin titration trial to treat hyperglycemia. Genome-wide expression profiling was conducted using RNA sequencing from whole blood samples obtained from 46 children with septic shock and 52 mechanically ventilated noninfected controls without shock. Patients with septic shock were allocated to subclasses based on hierarchical clustering of gene expression profiles, and we then compared clinical characteristics, plasma inflammatory markers, cell compositions using GEDIT, and immune repertoires using Imrep between the two subclasses. RESULTS Patients with septic shock depicted alterations in innate and adaptive immune pathways. Among patients with septic shock, we identified two subtypes based on gene expression patterns. Compared with Subclass 2, Subclass 1 was characterized by upregulation of innate immunity pathways and downregulation of adaptive immunity pathways. Subclass 1 had significantly worse clinical outcomes despite the two classes having similar illness severity on initial clinical presentation. Subclass 1 had elevated levels of plasma inflammatory cytokines and endothelial injury biomarkers and demonstrated decreased percentages of CD4 T cells and B cells and less diverse T cell receptor repertoires. CONCLUSIONS Two subclasses of pediatric septic shock patients were discovered through genome-wide expression profiling based on whole blood RNA sequencing with major biological and clinical differences. Trial Registration This is a secondary analysis of data generated as part of the observational CAF-PINT ancillary of the HALF-PINT study (NCT01565941). Registered March 29, 2012.
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Affiliation(s)
- Jamie O Yang
- UCLA Department of Internal Medicine, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Matt S Zinter
- UCSF Department of Pediatrics, San Francisco, CA, USA
| | - Matteo Pellegrini
- UCLA Department of Molecular, Cell, and Developmental Biology, Los Angeles, CA, USA
| | - Man Yee Wong
- Division of Pediatric Critical Care, UCLA Department of Pediatrics, UCLA Mattel Children's Hospital, Los Angeles, CA, USA
| | - Kinisha Gala
- Division of Pediatric Critical Care, UCLA Department of Pediatrics, UCLA Mattel Children's Hospital, Los Angeles, CA, USA
| | - Daniela Markovic
- UCLA Department of Medicine Statistics Core, Los Angeles, CA, USA
| | - Brian Nadel
- USC Department of Clinical Pharmacy, USC Alfred E Mann School of Pharmacy and Pharmaceutical Sciences, Los Angeles, CA, USA
| | - Kerui Peng
- USC Department of Clinical Pharmacy, USC Alfred E Mann School of Pharmacy and Pharmaceutical Sciences, Los Angeles, CA, USA
| | - Nguyen Do
- Division of Pediatric Critical Care, UCLA Department of Pediatrics, UCLA Mattel Children's Hospital, Los Angeles, CA, USA
| | - Serghei Mangul
- USC Department of Clinical Pharmacy, USC Alfred E Mann School of Pharmacy and Pharmaceutical Sciences, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, USA
| | - Vinay M Nadkarni
- Department of Anesthesiology and Critical Care Medicine, Children's Hospital of Philadelphia, and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aaron Karlsberg
- USC Department of Clinical Pharmacy, USC Alfred E Mann School of Pharmacy and Pharmaceutical Sciences, Los Angeles, CA, USA
| | - Dhrithi Deshpande
- USC Department of Clinical Pharmacy, USC Alfred E Mann School of Pharmacy and Pharmaceutical Sciences, Los Angeles, CA, USA
| | - Manish J Butte
- Division of Immunology, Allergy, and Rheumatology, UCLA Department of Pediatrics, Los Angeles, CA, USA
| | - Lisa Asaro
- Department of Pediatrics, Division of Medical Critical Care, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael Agus
- Department of Pediatrics, Division of Medical Critical Care, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anil Sapru
- Division of Pediatric Critical Care, UCLA Department of Pediatrics, UCLA Mattel Children's Hospital, Los Angeles, CA, USA.
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24
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Bode C, Weis S, Sauer A, Wendel-Garcia P, David S. Targeting the host response in sepsis: current approaches and future evidence. Crit Care 2023; 27:478. [PMID: 38057824 PMCID: PMC10698949 DOI: 10.1186/s13054-023-04762-6] [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: 09/13/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023] Open
Abstract
Sepsis, a dysregulated host response to infection characterized by organ failure, is one of the leading causes of death worldwide. Disbalances of the immune response play an important role in its pathophysiology. Patients may develop simultaneously or concomitantly states of systemic or local hyperinflammation and immunosuppression. Although a variety of effective immunomodulatory treatments are generally available, attempts to inhibit or stimulate the immune system in sepsis have failed so far to improve patients' outcome. The underlying reason is likely multifaceted including failure to identify responders to a specific immune intervention and the complex pathophysiology of organ dysfunction that is not exclusively caused by immunopathology but also includes dysfunction of the coagulation system, parenchymal organs, and the endothelium. Increasing evidence suggests that stratification of the heterogeneous population of septic patients with consideration of their host response might led to treatments that are more effective. The purpose of this review is to provide an overview of current studies aimed at optimizing the many facets of host response and to discuss future perspectives for precision medicine approaches in sepsis.
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Affiliation(s)
- Christian Bode
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Bonn, Venusberg-Campus 1, 53127, Bonn, Germany.
| | - Sebastian Weis
- Institute for Infectious Disease and Infection Control, University Hospital Jena, Friedrich-Schiller University Jena, Jena, Germany
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Jena, Friedrich-Schiller University Jena, Jena, Germany
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll Institute-HKI, Jena, Germany
| | - Andrea Sauer
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Pedro Wendel-Garcia
- Institute of Intensive Care Medicine, University Hospital Zurich, Zurich, Switzerland
| | - Sascha David
- Institute of Intensive Care Medicine, University Hospital Zurich, Zurich, Switzerland
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25
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Buckel M, Maclean P, Knight JC, Lawler PR, Proudfoot AG. Extending the 'host response' paradigm from sepsis to cardiogenic shock: evidence, limitations and opportunities. Crit Care 2023; 27:460. [PMID: 38012789 PMCID: PMC10683227 DOI: 10.1186/s13054-023-04752-8] [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: 09/18/2023] [Accepted: 11/20/2023] [Indexed: 11/29/2023] Open
Abstract
Recent clinical and research efforts in cardiogenic shock (CS) have largely focussed on the restoration of the low cardiac output state that is the conditio sine qua non of the clinical syndrome. This approach has failed to translate into improved outcomes, and mortality has remained static at 30-50%. There is an unmet need to better delineate the pathobiology of CS to understand the observed heterogeneity of presentation and treatment effect and to identify novel therapeutic targets. Despite data in other critical illness syndromes, specifically sepsis, the role of dysregulated inflammation and immunity is hitherto poorly described in CS. High-dimensional molecular profiling, particularly through leukocyte transcriptomics, may afford opportunity to better characterise subgroups of patients with shared mechanisms of immune dysregulation. In this state-of-the-art review, we outline the rationale for considering molecular subtypes of CS. We describe how high-dimensional molecular technologies can be used to identify these subtypes, and whether they share biological features with sepsis and other critical illness states. Finally, we propose how the identification of molecular subtypes of patients may enrich future clinical trial design and identification of novel therapies for CS.
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Affiliation(s)
- Marie Buckel
- Department of Perioperative Medicine, Bart's Heart Centre, St. Bartholomew's Hospital, London, UK
| | - Patrick Maclean
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Patrick R Lawler
- Peter Munk Cardiac Centre, University Health Network, University of Toronto, Toronto, ON, Canada
- McGill University Health Centre, McGill University, Montreal, QC, Canada
| | - Alastair G Proudfoot
- Department of Perioperative Medicine, Bart's Heart Centre, St. Bartholomew's Hospital, London, UK.
- Queen Mary University of London, London, UK.
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26
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Diao Y, Zhao Y, Li X, Li B, Huo R, Han X. A simplified machine learning model utilizing platelet-related genes for predicting poor prognosis in sepsis. Front Immunol 2023; 14:1286203. [PMID: 38054005 PMCID: PMC10694245 DOI: 10.3389/fimmu.2023.1286203] [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: 08/31/2023] [Accepted: 11/03/2023] [Indexed: 12/07/2023] Open
Abstract
Background Thrombocytopenia is a known prognostic factor in sepsis, yet the relationship between platelet-related genes and sepsis outcomes remains elusive. We developed a machine learning (ML) model based on platelet-related genes to predict poor prognosis in sepsis. The model underwent rigorous evaluation on six diverse platforms, ensuring reliable and versatile findings. Methods A retrospective analysis of platelet data from 365 sepsis patients confirmed the predictive role of platelet count in prognosis. We employed COX analysis, Least Absolute Shrinkage and Selection Operator (LASSO) and Support Vector Machine (SVM) techniques to identify platelet-related genes from the GSE65682 dataset. Subsequently, these genes were trained and validated on six distinct platforms comprising 719 patients, and compared against the Acute Physiology and Chronic Health Evaluation II (APACHE II) and Sequential Organ-Failure Assessment (SOFA) score. Results A PLT count <100×109/L independently increased the risk of death in sepsis patients (OR = 2.523; 95% CI: 1.084-5.872). The ML model, based on five platelet-related genes, demonstrated impressive area under the curve (AUC) values ranging from 0.5 to 0.795 across various validation platforms. On the GPL6947 platform, our ML model outperformed the APACHE II score with an AUC of 0.795 compared to 0.761. Additionally, by incorporating age, the model's performance was further improved to an AUC of 0.812. On the GPL4133 platform, the initial AUC of the machine learning model based on five platelet-related genes was 0.5. However, after including age, the AUC increased to 0.583. In comparison, the AUC of the APACHE II score was 0.604, and the AUC of the SOFA score was 0.542. Conclusion Our findings highlight the broad applicability of this ML model, based on platelet-related genes, in facilitating early treatment decisions for sepsis patients with poor outcomes. Our study paves the way for advancements in personalized medicine and improved patient care.
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Affiliation(s)
| | | | | | | | | | - Xiaoxu Han
- National Clinical Research Center for Laboratory Medicine, Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, China
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27
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Sinha P, Kerchberger VE, Willmore A, Chambers J, Zhuo H, Abbott J, Jones C, Wickersham N, Wu N, Neyton L, Langelier CR, Mick E, He J, Jauregui A, Churpek MM, Gomez AD, Hendrickson CM, Kangelaris KN, Sarma A, Leligdowicz A, Delucchi KL, Liu KD, Russell JA, Matthay MA, Walley KR, Ware LB, Calfee CS. Identifying molecular phenotypes in sepsis: an analysis of two prospective observational cohorts and secondary analysis of two randomised controlled trials. THE LANCET. RESPIRATORY MEDICINE 2023; 11:965-974. [PMID: 37633303 PMCID: PMC10841178 DOI: 10.1016/s2213-2600(23)00237-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 08/28/2023]
Abstract
BACKGROUND In sepsis and acute respiratory distress syndrome (ARDS), heterogeneity has contributed to difficulty identifying effective pharmacotherapies. In ARDS, two molecular phenotypes (hypoinflammatory and hyperinflammatory) have consistently been identified, with divergent outcomes and treatment responses. In this study, we sought to derive molecular phenotypes in critically ill adults with sepsis, determine their overlap with previous ARDS phenotypes, and evaluate whether they respond differently to treatment in completed sepsis trials. METHODS We used clinical data and plasma biomarkers from two prospective sepsis cohorts, the Validating Acute Lung Injury biomarkers for Diagnosis (VALID) study (N=1140) and the Early Assessment of Renal and Lung Injury (EARLI) study (N=818), in latent class analysis (LCA) to identify the optimal number of classes in each cohort independently. We used validated models trained to classify ARDS phenotypes to evaluate concordance of sepsis and ARDS phenotypes. We applied these models retrospectively to the previously published Prospective Recombinant Human Activated Protein C Worldwide Evaluation in Severe Sepsis and Septic Shock (PROWESS-SHOCK) trial and Vasopressin and Septic Shock Trial (VASST) to assign phenotypes and evaluate heterogeneity of treatment effect. FINDINGS A two-class model best fit both VALID and EARLI (p<0·0001). In VALID, 804 (70·5%) of the 1140 patients were classified as hypoinflammatory and 336 (29·5%) as hyperinflammatory; in EARLI, 530 (64·8%) of 818 were hypoinflammatory and 288 (35·2%) hyperinflammatory. We observed higher plasma pro-inflammatory cytokines, more vasopressor use, more bacteraemia, lower protein C, and higher mortality in the hyperinflammatory than in the hypoinflammatory phenotype (p<0·0001 for all). Classifier models indicated strong concordance between sepsis phenotypes and previously identified ARDS phenotypes (area under the curve 0·87-0·96, depending on the model). Findings were similar excluding participants with both sepsis and ARDS. In PROWESS-SHOCK, 1142 (68·0%) of 1680 patients had the hypoinflammatory phenotype and 538 (32·0%) had the hyperinflammatory phenotype, and response to activated protein C differed by phenotype (p=0·0043). In VASST, phenotype proportions were similar to other cohorts; however, no treatment interaction with the type of vasopressor was observed (p=0·72). INTERPRETATION Molecular phenotypes previously identified in ARDS are also identifiable in multiple sepsis cohorts and respond differently to activated protein C. Molecular phenotypes could represent a treatable trait in critical illness beyond the patient's syndromic diagnosis. FUNDING US National Institutes of Health.
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Affiliation(s)
- Pratik Sinha
- Division of Clinical and Translational Research, Division of Critical Care, Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA.
| | - V Eric Kerchberger
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Andrew Willmore
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Julia Chambers
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Hanjing Zhuo
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Jason Abbott
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Chayse Jones
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Nancy Wickersham
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nelson Wu
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Lucile Neyton
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Charles R Langelier
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Eran Mick
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - June He
- Division of Clinical and Translational Research, Division of Critical Care, Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Alejandra Jauregui
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Matthew M Churpek
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Antonio D Gomez
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Zuckerberg San Francisco General Hospital and Trauma Center, San Francisco, CA, USA
| | | | - Kirsten N Kangelaris
- Division of Hospital Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Aartik Sarma
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Aleksandra Leligdowicz
- Department of Medicine, Division of Critical Care Medicine, Robarts Research Institute, University of Western Ontario, London, ON, Canada
| | - Kevin L Delucchi
- Department of Psychiatry, University of California San Francisco, San Francisco, CA, USA
| | - Kathleen D Liu
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Division of Nephrology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - James A Russell
- Division of Critical Care Medicine, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada; Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
| | - Michael A Matthay
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Department of Anesthesia, University of California San Francisco, San Francisco, CA, USA
| | - Keith R Walley
- Division of Critical Care Medicine, St Paul's Hospital, University of British Columbia, Vancouver, BC, Canada; Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
| | - Lorraine B Ware
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Carolyn S Calfee
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Department of Anesthesia, University of California San Francisco, San Francisco, CA, USA
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28
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Dong J, Wang S, Hu Z, Gong L. Extracellular proteins as potential biomarkers in Sepsis-related cerebral injury. Front Immunol 2023; 14:1128476. [PMID: 37901226 PMCID: PMC10611492 DOI: 10.3389/fimmu.2023.1128476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 09/13/2023] [Indexed: 10/31/2023] Open
Abstract
Background Sepsis can cause brain damage known as septic encephalopathy (SAE), which is linked to higher mortality and poorer outcomes. Objective clinical markers for SAE diagnosis and prognosis are lacking. This study aimed to identify biomarkers of SAE by investigating genes and extracellular proteins involved in sepsis-induced brain injury. Methods Extracellular protein differentially expressed genes (EP-DEGs) from sepsis patients' brain tissue (GSE135838) were obtained from Gene Expression Omnibus (GEO) and evaluated by protein annotation database. The function and pathways of EP-DEGs were examined using GO and KEGG. Protein-protein interaction (PPI) networks were built and crucial EP-DEGs were screened using STRING, Cytoscape, MCODE, and Cytohubba. The diagnostic and prognostic accuracy of key EP-DEGs was assessed in 31 sepsis patients' blood samples and a rat cecal ligation and puncture (CLP)-induced sepsis model. Cognitive and spatial memory impairment was evaluated 7-11 days post-CLP using behavioral tests. Blood and cerebrospinal fluid from 26 rats (SHAM n=14, CLP n=12) were collected 6 days after CLP to analyze key EP-DEGs. Results Thirty-one EP-DEGs from DEGs were examined. Bone marrow leukocytes, neutrophil movement, leukocyte migration, and reactions to molecules with bacterial origin were all enhanced in EP-DEGs. In comparison to the sham-operated group, sepsis rats had higher levels of MMP8 and S100A8 proteins in their venous blood (both p<0.05) and cerebrospinal fluid (p=0.0506, p<0.0001, respectively). Four important extracellular proteins, MMP8, CSF3, IL-6, and S100A8, were identified in clinical peripheral blood samples. MMP8 and S100A8 levels in the peripheral blood of sepsis patients were higher in SAE than in non-SAE. In comparison to MMP8, S100A8 had a higher area under the curve (AUC: 0.962, p<0.05) and a higher sensitivity and specificity (80% and 100%, respectively) than MMP8 (AUC: 0.790, p<0.05). High levels of S100A8 strongly correlated with 28-day mortality and the Glasgow Coma Scale (GCS) scores. Conclusion The extracellular proteins MMP8, CSF3, IL-6, and S100A8 may be crucial in the pathophysiology of SAE. S100A8 and MMP8 are possible biomarkers for SAE's onset and progression. This research may help to clarify the pathogenesis of SAE and improve the diagnosis and prognosis of the disease.
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Affiliation(s)
| | | | - Zhonghua Hu
- Department of Anesthesiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Li Gong
- Department of Anesthesiology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
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29
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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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Yao H, Zhou Y, Li T, Li Y, Li F, Zhang G, Fu X, Kang Y, Wu Q. Bioinformatic identification and experiment validation revealed that ACTG1 is a promising prognostic signature and therapeutic target for sepsis. J Leukoc Biol 2023; 114:325-334. [PMID: 37368839 DOI: 10.1093/jleuko/qiad072] [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: 12/16/2022] [Revised: 05/24/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
In the intensive care unit, sepsis is a prevalent clinical syndrome (i.e. the final pathway to death from most infections). Peripheral blood gene expression profiling is becoming more and more accepted as a potential diagnostic or prognostic tool. This work aimed to recognize genes related to sepsis, providing potential translational therapeutic targets. RNA sequencing was performed on peripheral blood mononuclear cells from 20 healthy control subjects and 51 sepsis patients. Weighted gene coexpression network analysis was employed to pick out sepsis-related and immunocyte-related gene modules. Genes in the yellow module are primarily involved in excessive inflammation and immune suppression. STRING and Cytoscape were combined to identify ACTG1 and IQGAP1 as hub genes with highest connective degree, and prognostic predication value of ACTG1 was confirmed. Both univariate and multivariate logistic regression analyses were carried out. ACTG1 messenger RNA expression was increased in animal and in cell-related sepsis models. Small interfering RNA revealed decreasing ACTG1 can reduce the in vitro sepsis model apoptosis. We have authenticated ACTG1 as a reliable signature of a poor outcome of sepsis and promising therapeutic targets for sepsis.
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Affiliation(s)
- Hua Yao
- Department of Critical Care Medicine, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Yue Zhou
- Department of Critical Care Medicine, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Tingting Li
- Department of Critical Care Medicine, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Yao Li
- Department of Critical Care Medicine, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Fan Li
- Department of Critical Care Medicine, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Geng Zhang
- Department of Critical Care Medicine, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Xin Fu
- Department of Critical Care Medicine, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Yan Kang
- Department of Critical Care Medicine, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu, 610041, Sichuan, China
| | - Qin Wu
- Department of Critical Care Medicine, West China Hospital, Sichuan University, No.37 Guoxue Alley, Wuhou District, Chengdu, 610041, Sichuan, China
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Zhang T, Lian G, Fang W, Tian L, Ma W, Zhang J, Meng Z, Yang H, Wang C, Wei C, Chen M. Comprehensive single-cell analysis reveals novel anergic antigen-presenting cell subtypes in human sepsis. Front Immunol 2023; 14:1257572. [PMID: 37781404 PMCID: PMC10538568 DOI: 10.3389/fimmu.2023.1257572] [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: 07/12/2023] [Accepted: 08/21/2023] [Indexed: 10/03/2023] Open
Abstract
Background Sepsis is a life-threatening condition with high mortality. A few studies have emerged utilizing single-cell RNA sequencing (scRNA-seq) to analyze gene expression at the single-cell resolution in sepsis, but a comprehensive high-resolution analysis of blood antigen-presenting cells has not been conducted. Methods All published human scRNA-seq data were downloaded from the single cell portal database. After manually curating the dataset, we extracted all antigen-presenting cells, including dendritic cells (DCs) and monocytes, for identification of cell subpopulations and their gene profiling and intercellular interactions between septic patients and healthy controls. Finally, we further validated the findings by performing deconvolution analysis on bulk RNA sequencing (RNA-seq) data and flow cytometry. Results Within the traditional DC populations, we discovered novel anergic DC subtypes characterized by low major histocompatibility complex class II expression. Notably, these anergic DC subtypes showed a significant increase in septic patients. Additionally, we found that a previously reported immunosuppressive monocyte subtype, Mono1, exhibited a similar gene expression profile to these anergic DCs. The consistency of our findings was confirmed through validation using bulk RNA-seq and flow cytometry, ensuring accurate identification of cell subtypes and gene expression patterns. Conclusions This study represents the first comprehensive single-cell analysis of antigen-presenting cells in human sepsis, revealing novel disease-associated anergic DC subtypes. These findings provide new insights into the cellular mechanisms of immune dysregulation in bacterial sepsis.
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Affiliation(s)
- Tuo Zhang
- Department of Critical Care Medicine, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Guodong Lian
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Wei Fang
- Department of Critical Care Medicine, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Critical Care Medicine, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, China
| | - Lei Tian
- Department of Critical Care Medicine, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, China
| | - Wenhao Ma
- Department of Critical Care Medicine, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, China
| | - Jicheng Zhang
- Department of Critical Care Medicine, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Critical Care Medicine, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, China
| | - Zhaoli Meng
- Department of Critical Care Medicine, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Critical Care Medicine, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, China
| | - Hongna Yang
- Department of Critical Care Medicine, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Critical Care Medicine, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, China
| | - Chunting Wang
- Department of Critical Care Medicine, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Critical Care Medicine, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, China
| | - Chengguo Wei
- Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Man Chen
- Department of Critical Care Medicine, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Critical Care Medicine, Shandong Provincial Hospital affiliated to Shandong First Medical University, Jinan, China
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Tuerxun K, Eklund D, Wallgren U, Dannenberg K, Repsilber D, Kruse R, Särndahl E, Kurland L. Predicting sepsis using a combination of clinical information and molecular immune markers sampled in the ambulance. Sci Rep 2023; 13:14917. [PMID: 37691028 PMCID: PMC10493220 DOI: 10.1038/s41598-023-42081-6] [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: 06/16/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023] Open
Abstract
Sepsis is a time dependent condition. Screening tools based on clinical parameters have been shown to increase the identification of sepsis. The aim of current study was to evaluate the additional predictive value of immunological molecular markers to our previously developed prehospital screening tools. This is a prospective cohort study of 551 adult patients with suspected infection in the ambulance setting of Stockholm, Sweden between 2017 and 2018. Initially, 74 molecules and 15 genes related to inflammation were evaluated in a screening cohort of 46 patients with outcome sepsis and 50 patients with outcome infection no sepsis. Next, 12 selected molecules, as potentially synergistic predictors, were evaluated in combination with our previously developed screening tools based on clinical parameters in a prediction cohort (n = 455). Seven different algorithms with nested cross-validation were used in the machine learning of the prediction models. Model performances were compared using posterior distributions of average area under the receiver operating characteristic (ROC) curve (AUC) and difference in AUCs. Model variable importance was assessed by permutation of variable values, scoring loss of classification as metric and with model-specific weights when applicable. When comparing the screening tools with and without added molecular variables, and their interactions, the molecules per se did not increase the predictive values. Prediction models based on the molecular variables alone showed a performance in terms of AUCs between 0.65 and 0.70. Among the molecular variables, IL-1Ra, IL-17A, CCL19, CX3CL1 and TNF were significantly higher in septic patients compared to the infection non-sepsis group. Combing immunological molecular markers with clinical parameters did not increase the predictive values of the screening tools, most likely due to the high multicollinearity of temperature and some of the markers. A group of sepsis patients was consistently miss-classified in our prediction models, due to milder symptoms as well as lower expression levels of the investigated immune mediators. This indicates a need of stratifying septic patients with a priori knowledge of certain clinical and molecular parameters in order to improve prediction for early sepsis diagnosis.Trial registration: NCT03249597. Registered 15 August 2017.
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Affiliation(s)
- Kedeye Tuerxun
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
- Inflammatory Response and Infection Susceptibility Centre, (iRiSC), Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
| | - Daniel Eklund
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Inflammatory Response and Infection Susceptibility Centre, (iRiSC), Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | - Katharina Dannenberg
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Dirk Repsilber
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Robert Kruse
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Inflammatory Response and Infection Susceptibility Centre, (iRiSC), Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Department of Clinical Research Laboratory, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Eva Särndahl
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Inflammatory Response and Infection Susceptibility Centre, (iRiSC), Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Lisa Kurland
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Inflammatory Response and Infection Susceptibility Centre, (iRiSC), Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Department of Emergency Medicine, Örebro University Hospital, Örebro, Sweden
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Yang JO, Zinter MS, Pellegrini M, Wong MY, Gala K, Markovic D, Nadel B, Peng K, Do N, Mangul S, Nadkarni VM, Karlsberg A, Deshpande D, Butte MJ, Asaro L, Agus M, Sapru A. Whole Blood Transcriptomics Identifies Subclasses of Pediatric Septic Shock. RESEARCH SQUARE 2023:rs.3.rs-3267057. [PMID: 37693502 PMCID: PMC10491329 DOI: 10.21203/rs.3.rs-3267057/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Background Sepsis is a highly heterogeneous syndrome, that has hindered the development of effective therapies. This has prompted investigators to develop a precision medicine approach aimed at identifying biologically homogenous subgroups of patients with septic shock and critical illnesses. Transcriptomic analysis can identify subclasses derived from differences in underlying pathophysiological processes that may provide the basis for new targeted therapies. The goal of this study was to elucidate pathophysiological pathways and identify pediatric septic shock subclasses based on whole blood RNA expression profiles. Methods The subjects were critically ill children with cardiopulmonary failure who were a part of a prospective randomized insulin titration trial to treat hyperglycemia. Genome-wide expression profiling was conducted using RNA-sequencing from whole blood samples obtained from 46 children with septic shock and 52 mechanically ventilated noninfected controls without shock. Patients with septic shock were allocated to subclasses based on hierarchical clustering of gene expression profiles, and we then compared clinical characteristics, plasma inflammatory markers, cell compositions using GEDIT, and immune repertoires using Imrep between the two subclasses. Results Patients with septic shock depicted alterations in innate and adaptive immune pathways. Among patients with septic shock, we identified two subtypes based on gene expression patterns. Compared with Subclass 2, Subclass 1 was characterized by upregulation of innate immunity pathways and downregulation of adaptive immunity pathways. Subclass 1 had significantly worse clinical outcomes despite the two classes having similar illness severity on initial clinical presentation. Subclass 1 had elevated levels of plasma inflammatory cytokines and endothelial injury biomarkers and demonstrated decreased percentages of CD4 T cells and B cells, and less diverse T-Cell receptor repertoires. Conclusions Two subclasses of pediatric septic shock patients were discovered through genome-wide expression profiling based on whole blood RNA sequencing with major biological and clinical differences. Trial Registration This is a secondary analysis of data generated as part of the observational CAF PINT ancillary of the HALF PINT study (NCT01565941). Registered 29 March 2012.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Nguyen Do
- University of California, Los Angeles
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Schertz AR, Eisner AE, Smith SA, Lenoir KM, Thomas KW. Clinical Phenotypes of Sepsis in a Cohort of Hospitalized Patients According to Infection Site. Crit Care Explor 2023; 5:e0955. [PMID: 37614801 PMCID: PMC10443761 DOI: 10.1097/cce.0000000000000955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023] Open
Abstract
OBJECTIVES Clinical sepsis phenotypes may be defined by a wide range of characteristics such as site of infection, organ dysfunction patterns, laboratory values, and demographics. There is a paucity of literature regarding the impact of site of infection on the timing and pattern of clinical sepsis markers. This study hypothesizes that important phenotypic variation in clinical markers and outcomes of sepsis exists when stratified by infection site. DESIGN Retrospective cohort study. SETTING Five hospitals within the Wake Forest Health System from June 2019 to December 2019. PATIENTS Six thousand seven hundred fifty-three hospitalized adults with a discharge International Classification of Diseases, 10th Revision code for acute infection who met systemic inflammatory response syndrome (SIRS), quick Sepsis-related Organ Failure Assessment (qSOFA), or Sequential Organ Failure Assessment (SOFA) criteria during the index hospitalization. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS The primary outcome of interest was a composite of 30-day mortality or shock. Infection site was determined by a two-reviewer process. Significant demographic, vital sign, and laboratory result differences were seen across all infection sites. For the composite outcome of shock or 30-day mortality, unknown or unspecified infections had the highest proportion (21.34%) and CNS infections had the lowest proportion (8.11%). Respiratory, vascular, and unknown or unspecified infection sites showed a significantly increased adjusted and unadjusted odds of the composite outcome as compared with the other infection sites except CNS. Hospital time prior to SIRS positivity was shortest in unknown or unspecified infections at a median of 0.88 hours (interquartile range [IQR], 0.22-5.05 hr), and hospital time prior to qSOFA and SOFA positivity was shortest in respiratory infections at a median of 54.83 hours (IQR, 9.55-104.67 hr) and 1.88 hours (IQR, 0.47-17.40 hr), respectively. CONCLUSIONS Phenotypic variation in illness severity and mortality exists when stratified by infection site. There is a significantly higher adjusted and unadjusted odds of the composite outcome of 30-day mortality or shock in respiratory, vascular, and unknown or unspecified infections as compared with other sites.
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Affiliation(s)
- Adam R Schertz
- Department of Internal Medicine, Section of Pulmonology, Critical Care, Allergy & Immunologic Diseases, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Ashley E Eisner
- Department of Internal Medicine, Section of Pulmonology, Critical Care, Allergy & Immunologic Diseases, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Sydney A Smith
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Kristin M Lenoir
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Karl W Thomas
- Department of Internal Medicine, Section of Pulmonology, Critical Care, Allergy & Immunologic Diseases, Wake Forest University School of Medicine, Winston-Salem, NC
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Balch JA, Chen UI, Liesenfeld O, Starostik P, Loftus TJ, Efron PA, Brakenridge SC, Sweeney TE, Moldawer LL. Defining critical illness using immunological endotypes in patients with and without sepsis: a cohort study. Crit Care 2023; 27:292. [PMID: 37474944 PMCID: PMC10360294 DOI: 10.1186/s13054-023-04571-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/07/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND Sepsis is a heterogenous syndrome with limited therapeutic options. Identifying immunological endotypes through gene expression patterns in septic patients may lead to targeted interventions. We investigated whether patients admitted to a surgical intensive care unit (ICU) with sepsis and with high risk of mortality express similar endotypes to non-septic, but still critically ill patients using two multiplex transcriptomic metrics obtained both on admission to a surgical ICU and at set intervals. METHODS We analyzed transcriptomic data from 522 patients in two single-site, prospective, observational cohorts admitted to surgical ICUs over a 5-year period ending in July 2020. Using an FDA-cleared analytical platform (nCounter FLEX®, NanoString, Inc.), we assessed a previously validated 29-messenger RNA transcriptomic classifier for likelihood of 30-day mortality (IMX-SEV-3) and a 33-messenger RNA transcriptomic endotype classifier. Clinical outcomes included all-cause mortality, development of chronic critical illness, and secondary infections. Univariate and multivariate analyses were performed to assess for true effect and confounding. RESULTS Sepsis was associated with a significantly higher predicted and actual hospital mortality. At enrollment, the predominant endotype for both septic and non-septic patients was adaptive, though with significantly different distributions. Inflammopathic and coagulopathic septic patients, as well as inflammopathic non-septic patients, showed significantly higher frequencies of secondary infections compared to those with adaptive endotypes (p < 0.01). Endotypes changed during ICU hospitalization in 57.5% of patients. Patients who remained adaptive had overall better prognosis, while those who remained inflammopathic or coagulopathic had worse overall outcomes. For severity metrics, patients admitted with sepsis and a high predicted likelihood of mortality showed an inflammopathic (49.6%) endotype and had higher rates of cumulative adverse outcomes (67.4%). Patients at low mortality risk, whether septic or non-septic, almost uniformly presented with an adaptive endotype (100% and 93.4%, respectively). CONCLUSION Critically ill surgical patients express different and evolving immunological endotypes depending upon both their sepsis status and severity of their clinical course. Future studies will elucidate whether endotyping critically ill, septic patients can identify individuals for targeted therapeutic interventions to improve patient management and outcomes.
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Affiliation(s)
- Jeremy A Balch
- Sepsis and Critical Illness Research Center, Department of Surgery, Shands Hospital, University of Florida College of Medicine, Room 6116, 1600 SW Archer Road, P. O. Box 100019, Gainesville, FL, 32610-0019, USA
| | - Uan-I Chen
- Inflammatix, Inc., Sunnyvale, CA, 94085, USA
| | | | - Petr Starostik
- UF Health Medical Laboratory at Rocky Point, Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, 32610, USA
| | - Tyler J Loftus
- Sepsis and Critical Illness Research Center, Department of Surgery, Shands Hospital, University of Florida College of Medicine, Room 6116, 1600 SW Archer Road, P. O. Box 100019, Gainesville, FL, 32610-0019, USA
| | - Philip A Efron
- Sepsis and Critical Illness Research Center, Department of Surgery, Shands Hospital, University of Florida College of Medicine, Room 6116, 1600 SW Archer Road, P. O. Box 100019, Gainesville, FL, 32610-0019, USA
| | - Scott C Brakenridge
- Sepsis and Critical Illness Research Center, Department of Surgery, Shands Hospital, University of Florida College of Medicine, Room 6116, 1600 SW Archer Road, P. O. Box 100019, Gainesville, FL, 32610-0019, USA
- Department of Surgery, Harborview Medical Center, University of Washington School of Medicine, Seattle, WA, 63110, USA
| | | | - Lyle L Moldawer
- Sepsis and Critical Illness Research Center, Department of Surgery, Shands Hospital, University of Florida College of Medicine, Room 6116, 1600 SW Archer Road, P. O. Box 100019, Gainesville, FL, 32610-0019, USA.
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Novak T, Crawford JC, Hahn G, Hall MW, Thair SA, Newhams MM, Chou J, Mourani PM, Tarquinio KM, Markovitz B, Loftis LL, Weiss SL, Higgerson R, Schwarz AJ, Pinto NP, Thomas NJ, Gedeit RG, Sanders RC, Mahapatra S, Coates BM, Cvijanovich NZ, Ackerman KG, Tellez DW, McQuillen P, Kurachek SC, Shein SL, Lange C, Thomas PG, Randolph AG. Transcriptomic profiles of multiple organ dysfunction syndrome phenotypes in pediatric critical influenza. Front Immunol 2023; 14:1220028. [PMID: 37533854 PMCID: PMC10390830 DOI: 10.3389/fimmu.2023.1220028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/19/2023] [Indexed: 08/04/2023] Open
Abstract
Background Influenza virus is responsible for a large global burden of disease, especially in children. Multiple Organ Dysfunction Syndrome (MODS) is a life-threatening and fatal complication of severe influenza infection. Methods We measured RNA expression of 469 biologically plausible candidate genes in children admitted to North American pediatric intensive care units with severe influenza virus infection with and without MODS. Whole blood samples from 191 influenza-infected children (median age 6.4 years, IQR: 2.2, 11) were collected a median of 27 hours following admission; for 45 children a second blood sample was collected approximately seven days later. Extracted RNA was hybridized to NanoString mRNA probes, counts normalized, and analyzed using linear models controlling for age and bacterial co-infections (FDR q<0.05). Results Comparing pediatric samples collected near admission, children with Prolonged MODS for ≥7 days (n=38; 9 deaths) had significant upregulation of nine mRNA transcripts associated with neutrophil degranulation (RETN, TCN1, OLFM4, MMP8, LCN2, BPI, LTF, S100A12, GUSB) compared to those who recovered more rapidly from MODS (n=27). These neutrophil transcripts present in early samples predicted Prolonged MODS or death when compared to patients who recovered, however in paired longitudinal samples, they were not differentially expressed over time. Instead, five genes involved in protein metabolism and/or adaptive immunity signaling pathways (RPL3, MRPL3, HLA-DMB, EEF1G, CD8A) were associated with MODS recovery within a week. Conclusion Thus, early increased expression of neutrophil degranulation genes indicated worse clinical outcomes in children with influenza infection, consistent with reports in adult cohorts with influenza, sepsis, and acute respiratory distress syndrome.
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Affiliation(s)
- Tanya Novak
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, MA, United States
- Department of Anaesthesia, Harvard Medical School, Boston, MA, United States
- National Institute of Allergy and Infectious Diseases (NIAID), Centers of Excellence for Influenza Research and Response (CEIRR), Center for Influenza Disease and Emergence Response (CIDER), Athens, GA, United States
| | - Jeremy Chase Crawford
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, MA, United States
- National Institute of Allergy and Infectious Diseases (NIAID), Centers of Excellence for Influenza Research and Response (CEIRR), St. Jude Children's Research Hospital, Memphis, TN, United States
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN, United States
| | - Georg Hahn
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Mark W. Hall
- Division of Critical Care Medicine, Department of Pediatrics, Nationwide Children’s Hospital, Columbus, OH, United States
| | - Simone A. Thair
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, MA, United States
- Division of Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Margaret M. Newhams
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, MA, United States
- National Institute of Allergy and Infectious Diseases (NIAID), Centers of Excellence for Influenza Research and Response (CEIRR), Center for Influenza Disease and Emergence Response (CIDER), Athens, GA, United States
| | - Janet Chou
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Peter M. Mourani
- Department of Pediatrics, Section of Critical Care Medicine, University of Arkansas for Medical Sciences and Arkansas Children’s Research Institute, Little Rock, AR, United States
| | - Keiko M. Tarquinio
- Division of Critical Care Medicine, Department of Pediatrics, Emory University School of Medicine, Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Barry Markovitz
- Department of Anesthesiology Critical Care Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Laura L. Loftis
- Division of Critical Care Medicine, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Scott L. Weiss
- Nemours Children’s Hospital Delaware, Critical Care Medicine, Wilmington, DE, United States
| | - Renee Higgerson
- Pediatric Critical Care Medicine, St. David’s Children’s Hospital, Austin, TX, United States
| | - Adam J. Schwarz
- Department of Pediatrics, Children’s Hospital of Orange County, Orange, CA, United States
| | - Neethi P. Pinto
- Department of Anesthesiology and Critical Care Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Neal J. Thomas
- Department of Pediatrics, Penn State Health Children’s Hospital, Penn State University College of Medicine, Hershey, PA, United States
| | - Rainer G. Gedeit
- Pediatric Critical Care, Milwaukee Hospital-Children’s Wisconsin, Milwaukee, WI, United States
| | - Ronald C. Sanders
- Section of Pediatric Critical Care, Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children’s Research Institute, Little Rock, AR, United States
| | - Sidharth Mahapatra
- Pediatric Critical Care Medicine, Children’s Hospital & Medical Center Omaha, University of Nebraska Medical Center, Omaha, NE, United States
| | - Bria M. Coates
- Division of Critical Care Medicine, Department of Pediatrics, Northwestern University Feinberg School of Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, United States
| | - Natalie Z. Cvijanovich
- Division of Critical Care Medicine, UCSF Benioff Children’s Hospital, Oakland, CA, United States
| | - Kate G. Ackerman
- Department of Pediatrics, University of Rochester/UR Medicine Golisano Children’s Hospital, Rochester, NY, United States
| | - David W. Tellez
- Pediatric Critical Care Medicine, Phoenix Children’s Hospital, Phoenix, AZ, United States
| | - Patrick McQuillen
- Department of Pediatrics, Benioff Children’s Hospital, University of California, San Francisco, San Francisco, CA, United States
| | - Stephen C. Kurachek
- Department of Critical Care, Children’s Specialty Center, Children’s Minnesota, Minneapolis, MN, United States
| | - Steven L. Shein
- Division of Pediatric Critical Care Medicine, University Hospitals Rainbow Babies and Children’s Hospital, Cleveland, OH, United States
| | - Christoph Lange
- Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA, United States
| | - Paul G. Thomas
- National Institute of Allergy and Infectious Diseases (NIAID), Centers of Excellence for Influenza Research and Response (CEIRR), St. Jude Children's Research Hospital, Memphis, TN, United States
- Department of Immunology, St Jude Children’s Research Hospital, Memphis, TN, United States
| | - Adrienne G. Randolph
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children’s Hospital, Boston, MA, United States
- Department of Anaesthesia, Harvard Medical School, Boston, MA, United States
- National Institute of Allergy and Infectious Diseases (NIAID), Centers of Excellence for Influenza Research and Response (CEIRR), Center for Influenza Disease and Emergence Response (CIDER), Athens, GA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
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Kraven LM, Taylor AR, Molyneaux PL, Maher TM, McDonough JE, Mura M, Yang IV, Schwartz DA, Huang Y, Noth I, Ma SF, Yeo AJ, Fahy WA, Jenkins RG, Wain LV. Cluster analysis of transcriptomic datasets to identify endotypes of idiopathic pulmonary fibrosis. Thorax 2023; 78:551-558. [PMID: 35534152 PMCID: PMC9643664 DOI: 10.1136/thoraxjnl-2021-218563] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/14/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Considerable clinical heterogeneity in idiopathic pulmonary fibrosis (IPF) suggests the existence of multiple disease endotypes. Identifying these endotypes would improve our understanding of the pathogenesis of IPF and could allow for a biomarker-driven personalised medicine approach. We aimed to identify clinically distinct groups of patients with IPF that could represent distinct disease endotypes. METHODS We co-normalised, pooled and clustered three publicly available blood transcriptomic datasets (total 220 IPF cases). We compared clinical traits across clusters and used gene enrichment analysis to identify biological pathways and processes that were over-represented among the genes that were differentially expressed across clusters. A gene-based classifier was developed and validated using three additional independent datasets (total 194 IPF cases). FINDINGS We identified three clusters of patients with IPF with statistically significant differences in lung function (p=0.009) and mortality (p=0.009) between groups. Gene enrichment analysis implicated mitochondrial homeostasis, apoptosis, cell cycle and innate and adaptive immunity in the pathogenesis underlying these groups. We developed and validated a 13-gene cluster classifier that predicted mortality in IPF (high-risk clusters vs low-risk cluster: HR 4.25, 95% CI 2.14 to 8.46, p=3.7×10-5). INTERPRETATION We have identified blood gene expression signatures capable of discerning groups of patients with IPF with significant differences in survival. These clusters could be representative of distinct pathophysiological states, which would support the theory of multiple endotypes of IPF. Although more work must be done to confirm the existence of these endotypes, our classifier could be a useful tool in patient stratification and outcome prediction in IPF.
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Affiliation(s)
- Luke M Kraven
- Department of Health Sciences, University of Leicester, Leicester, UK
- Research & Development, GlaxoSmithKline, Stevenage, UK
| | - Adam R Taylor
- Research & Development, GlaxoSmithKline, Stevenage, UK
| | - Philip L Molyneaux
- Guy's and St Thomas' NHS Foundation Trust, Royal Brompton and Harefield Hospitals, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Toby M Maher
- Guy's and St Thomas' NHS Foundation Trust, Royal Brompton and Harefield Hospitals, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - John E McDonough
- Division of Pulmonary, Critical Care & Sleep Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Marco Mura
- Division of Respirology, Western University, London, Ontario, Canada
| | - Ivana V Yang
- Department of Medicine, University of Colorado, Denver, Colorado, USA
| | - David A Schwartz
- Department of Medicine, University of Colorado, Denver, Colorado, USA
| | - Yong Huang
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Imre Noth
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Shwu Fan Ma
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Astrid J Yeo
- Research & Development, GlaxoSmithKline, Stevenage, UK
| | | | - R Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, UK
- National Institute for Health Research Respiratory Clinical Research Facility, Royal Brompton Hospital, London, UK
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Glenfield Hospital, Leicester, UK
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Balch JA, Chen UI, Liesenfeld O, Starostik P, Loftus TJ, Efron PA, Brakenridge SC, Sweeney TE, Moldawer LL. Defining critical illness using immunological endotypes in patients with and without of sepsis: A cohort study. RESEARCH SQUARE 2023:rs.3.rs-2874506. [PMID: 37214996 PMCID: PMC10197751 DOI: 10.21203/rs.3.rs-2874506/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background: Sepsis is a heterogenous syndrome with limited therapeutic options. Identifying characteristic gene expression patterns, or endotypes, in septic patients may lead to targeted interventions. We investigated whether patients admitted to a surgical ICU with sepsis and with high risk of mortality express similar endotypes to non-septic, but still critically ill patients using two multiplex transcriptomic metrics obtained both on admission to a surgical intensive care unit (ICU) and at set intervals. Methods: We analyzed transcriptomic data from 522 patients in two single-site, prospective, observational cohorts admitted to surgical ICUs over a 5-year period ending in July 2020 . Using an FDA-cleared analytical platform (nCounter FLEX ® , NanoString, Inc.), we assessed a previously validated 29-messenger RNA transcriptomic classifier for likelihood of 30-day mortality (IMX-SEV-3) and a 33-messenger RNA transcriptomic endotype classifier. Clinical outcomes included all-cause (in-hospital, 30-, 90-day) mortality, development of chronic critical illness (CCI), and secondary infections. Univariate and multivariate analyses were performed to assess for true effect and confounding. Results: Sepsis was associated with a significantly higher predicted and actual hospital mortality. At enrollment, the predominant endotype for both septic and non-septic patients was adaptive , though with significantly different distributions. Inflammopathic and coagulopathic septic patients, as well as inflammopathic non-septic patients, showed significantly higher frequencies of secondary infections compared to those with adaptive endotypes (p<0.01). Endotypes changed during ICU hospitalization in 57.5% of patients. Patients who remained adaptive had overall better prognosis, while those who remained inflammopathic or coagulopathic had worse overall outcomes. For severity metrics, patients admitted with sepsis and a high predicted likelihood of mortality showed an inflammopathic (49.6%) endotype and had higher rates of cumulative adverse outcomes (67.4%). Patients at low mortality risk, whether septic or non-septic, almost uniformly presented with an adaptive endotype (100% and 93.4%, respectively). Conclusion : Critically ill surgical patients express different and evolving immunological endotypes depending upon both their sepsis status and severity of their clinical course. Future studies will elucidate whether endotyping critically ill, septic patients can identify individuals for targeted therapeutic interventions to improve patient management and outcomes.
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Garduno A, Cusack R, Leone M, Einav S, Martin-Loeches I. Multi-Omics Endotypes in ICU Sepsis-Induced Immunosuppression. Microorganisms 2023; 11:1119. [PMID: 37317092 DOI: 10.3390/microorganisms11051119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/03/2023] [Accepted: 04/21/2023] [Indexed: 06/16/2023] Open
Abstract
It is evident that the admission of some patients with sepsis and septic shock to hospitals is occurring late in their illness, which has contributed to the increase in poor outcomes and high fatalities worldwide across age groups. The current diagnostic and monitoring procedure relies on an inaccurate and often delayed identification by the clinician, who then decides the treatment upon interaction with the patient. Initiation of sepsis is accompanied by immune system paralysis following "cytokine storm". The unique immunological response of each patient is important to define in terms of subtyping for therapy. The immune system becomes activated in sepsis to produce interleukins, and endothelial cells express higher levels of adhesion molecules. The proportions of circulating immune cells change, reducing regulatory cells and increasing memory cells and killer cells, having long-term effects on the phenotype of CD8 T cells, HLA-DR, and dysregulation of microRNA. The current narrative review seeks to highlight the potential application of multi-omics data integration and immunological profiling at the single-cell level to define endotypes in sepsis and septic shock. The review will consider the parallels and immunoregulatory axis between cancer and immunosuppression, sepsis-induced cardiomyopathy, and endothelial damage. Second, the added value of transcriptomic-driven endotypes will be assessed through inferring regulatory interactions in recent clinical trials and studies reporting gene modular features that inform continuous metrics measuring clinical response in ICU, which can support the use of immunomodulating agents.
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Affiliation(s)
- Alexis Garduno
- Department of Clinical Medicine, Trinity College, University of Dublin, D02 PN40 Dublin, Ireland
| | - Rachael Cusack
- Department of Intensive Care Medicine, St. James's Hospital, James's Street, D08 NHY1 Dublin, Ireland
| | - Marc Leone
- Department of Anesthesia, Intensive Care and Trauma Center, Nord University Hospital, Aix Marseille University, APHM, 13015 Marseille, France
| | - Sharon Einav
- General Intensive Care Unit, Shaare Zedek Medical Center, Jerusalem 23456, Israel
- Faculty of Medicine, Hebrew University, Jerusalem 23456, Israel
| | - Ignacio Martin-Loeches
- Department of Clinical Medicine, Trinity College, University of Dublin, D02 PN40 Dublin, Ireland
- Department of Intensive Care Medicine, St. James's Hospital, James's Street, D08 NHY1 Dublin, Ireland
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Kwok AJ, Allcock A, Ferreira RC, Cano-Gamez E, Smee M, Burnham KL, Zurke YX, McKechnie S, Mentzer AJ, Monaco C, Udalova IA, Hinds CJ, Todd JA, Davenport EE, Knight JC. Neutrophils and emergency granulopoiesis drive immune suppression and an extreme response endotype during sepsis. Nat Immunol 2023; 24:767-779. [PMID: 37095375 DOI: 10.1038/s41590-023-01490-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 03/13/2023] [Indexed: 04/26/2023]
Abstract
Sepsis arises from diverse and incompletely understood dysregulated host response processes following infection that leads to life-threatening organ dysfunction. Here we showed that neutrophils and emergency granulopoiesis drove a maladaptive response during sepsis. We generated a whole-blood single-cell multiomic atlas (272,993 cells, n = 39 individuals) of the sepsis immune response that identified populations of immunosuppressive mature and immature neutrophils. In co-culture, CD66b+ sepsis neutrophils inhibited proliferation and activation of CD4+ T cells. Single-cell multiomic mapping of circulating hematopoietic stem and progenitor cells (HSPCs) (29,366 cells, n = 27) indicated altered granulopoiesis in patients with sepsis. These features were enriched in a patient subset with poor outcome and a specific sepsis response signature that displayed higher frequencies of IL1R2+ immature neutrophils, epigenetic and transcriptomic signatures of emergency granulopoiesis in HSPCs and STAT3-mediated gene regulation across different infectious etiologies and syndromes. Our findings offer potential therapeutic targets and opportunities for stratified medicine in severe infection.
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Affiliation(s)
- Andrew J Kwok
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alice Allcock
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ricardo C Ferreira
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Eddie Cano-Gamez
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Madeleine Smee
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Katie L Burnham
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Stuart McKechnie
- John Radcliffe Hospital, Oxford Universities Hospitals NHS Foundation Trust, Oxford, UK
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- John Radcliffe Hospital, Oxford Universities Hospitals NHS Foundation Trust, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Claudia Monaco
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Irina A Udalova
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Charles J Hinds
- William Harvey Research Institute, Faculty of Medicine and Dentistry, Queen Mary University, London, UK
| | - John A Todd
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Emma E Davenport
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- John Radcliffe Hospital, Oxford Universities Hospitals NHS Foundation Trust, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, Oxford, UK.
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK.
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Bodinier M, Monneret G, Casimir M, Fleurie A, Conti F, Venet F, Cazalis MA, Cerrato E, Peronnet E, Rimmelé T, Lukaszewicz AC, Brengel-Pesce K, Llitjos JF. Identification of a sub-group of critically ill patients with high risk of intensive care unit-acquired infections and poor clinical course using a transcriptomic score. Crit Care 2023; 27:158. [PMID: 37085849 PMCID: PMC10119529 DOI: 10.1186/s13054-023-04436-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/08/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND The development of stratification tools based on the assessment of circulating mRNA of genes involved in the immune response is constrained by the heterogeneity of septic patients. The aim of this study is to develop a transcriptomic score based on a pragmatic combination of immune-related genes detected with a prototype multiplex PCR tool. METHODS As training cohort, we used the gene expression dataset obtained from 176 critically ill patients enrolled in the REALISM study (NCT02638779) with various etiologies and still hospitalized in intensive care unit (ICU) at day 5-7. Based on the performances of each gene taken independently to identify patients developing ICU-acquired infections (ICU-AI) after day 5-7, we built an unweighted score assuming the independence of each gene. We then determined the performances of this score to identify a subgroup of patients at high risk to develop ICU-AI, and both longer ICU length of stay and mortality of this high-risk group were assessed. Finally, we validated the effectiveness of this score in a retrospective cohort of 257 septic patients. RESULTS This transcriptomic score (TScore) enabled the identification of a high-risk group of patients (49%) with an increased rate of ICU-AI when compared to the low-risk group (49% vs. 4%, respectively), with longer ICU length of stay (13 days [95% CI 8-30] vs. 7 days [95% CI 6-9], p < 0.001) and higher ICU mortality (15% vs. 2%). High-risk patients exhibited biological features of immune suppression with low monocytic HLA-DR levels, higher immature neutrophils rates and higher IL10 concentrations. Using the TScore, we identified 160 high-risk patients (62%) in the validation cohort, with 30% of ICU-AI (vs. 18% in the low-risk group, p = 0.06), and significantly higher mortality and longer ICU length of stay. CONCLUSIONS The transcriptomic score provides a useful and reliable companion diagnostic tool to further develop immune modulating drugs in sepsis in the context of personalized medicine.
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Affiliation(s)
- Maxime Bodinier
- Joint Research Unit HCL-bioMérieux, EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, bioMérieux), Lyon, France
- Open Innovation and Partnerships (OI&P), bioMérieux S.A., Marcy L'Etoile, France
| | - Guillaume Monneret
- Joint Research Unit HCL-bioMérieux, EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, bioMérieux), Lyon, France
- Immunology Laboratory, Edouard Herriot Hospital - Hospices Civils de Lyon, Lyon, France
| | - Marie Casimir
- Joint Research Unit HCL-bioMérieux, EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, bioMérieux), Lyon, France
- Open Innovation and Partnerships (OI&P), bioMérieux S.A., Marcy L'Etoile, France
| | - Aurore Fleurie
- Joint Research Unit HCL-bioMérieux, EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, bioMérieux), Lyon, France
- Open Innovation and Partnerships (OI&P), bioMérieux S.A., Marcy L'Etoile, France
| | - Filippo Conti
- Joint Research Unit HCL-bioMérieux, EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, bioMérieux), Lyon, France
| | - Fabienne Venet
- Immunology Laboratory, Edouard Herriot Hospital - Hospices Civils de Lyon, Lyon, France
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard-Lyon 1, Lyon, France
| | - Marie-Angélique Cazalis
- Joint Research Unit HCL-bioMérieux, EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, bioMérieux), Lyon, France
- Open Innovation and Partnerships (OI&P), bioMérieux S.A., Marcy L'Etoile, France
| | - Elisabeth Cerrato
- Joint Research Unit HCL-bioMérieux, EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, bioMérieux), Lyon, France
- Open Innovation and Partnerships (OI&P), bioMérieux S.A., Marcy L'Etoile, France
| | - Estelle Peronnet
- Joint Research Unit HCL-bioMérieux, EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, bioMérieux), Lyon, France
- Open Innovation and Partnerships (OI&P), bioMérieux S.A., Marcy L'Etoile, France
| | - Thomas Rimmelé
- Joint Research Unit HCL-bioMérieux, EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, bioMérieux), Lyon, France
- Anaesthesia and Critical Care Medicine Department, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France
| | - Anne-Claire Lukaszewicz
- Joint Research Unit HCL-bioMérieux, EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, bioMérieux), Lyon, France
- Anaesthesia and Critical Care Medicine Department, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France
| | - Karen Brengel-Pesce
- Joint Research Unit HCL-bioMérieux, EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, bioMérieux), Lyon, France
| | - Jean-François Llitjos
- Joint Research Unit HCL-bioMérieux, EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, bioMérieux), Lyon, France.
- Open Innovation and Partnerships (OI&P), bioMérieux S.A., Marcy L'Etoile, France.
- Anaesthesia and Critical Care Medicine Department, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France.
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Jennaro TS, Puskarich MA, Evans CR, Karnovsky A, Flott TL, McLellan LA, Jones AE, Stringer KA. Sustained Perturbation of Metabolism and Metabolic Subphenotypes Are Associated With Mortality and Protein Markers of the Host Response. Crit Care Explor 2023; 5:e0881. [PMID: 36998529 PMCID: PMC10047616 DOI: 10.1097/cce.0000000000000881] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Perturbed host metabolism is increasingly recognized as a pillar of sepsis pathogenesis, yet the dynamic alterations in metabolism and its relationship to other components of the host response remain incompletely understood. We sought to identify the early host-metabolic response in patients with septic shock and to explore biophysiological phenotyping and differences in clinical outcomes among metabolic subgroups. DESIGN We measured serum metabolites and proteins reflective of the host-immune and endothelial response in patients with septic shock. SETTING We considered patients from the placebo arm of a completed phase II, randomized controlled trial conducted at 16 U.S. medical centers. Serum was collected at baseline (within 24 hr of the identification of septic shock), 24-hour, and 48-hour postenrollment. Linear mixed models were built to assess the early trajectory of protein analytes and metabolites stratified by 28-day mortality status. Unsupervised clustering of baseline metabolomics data was conducted to identify subgroups of patients. PATIENTS Patients with vasopressor-dependent septic shock and moderate organ dysfunction that were enrolled in the placebo arm of a clinical trial. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS Fifty-one metabolites and 10 protein analytes were measured longitudinally in 72 patients with septic shock. In the 30 patients (41.7%) who died prior to 28 days, systemic concentrations of acylcarnitines and interleukin (IL)-8 were elevated at baseline and persisted at T24 and T48 throughout early resuscitation. Concentrations of pyruvate, IL-6, tumor necrosis factor-α, and angiopoietin-2 decreased at a slower rate in patients who died. Two groups emerged from clustering of baseline metabolites. Group 1 was characterized by higher levels of acylcarnitines, greater organ dysfunction at baseline and postresuscitation (p < 0.05), and greater mortality over 1 year (p < 0.001). CONCLUSIONS Among patients with septic shock, nonsurvivors exhibited a more profound and persistent dysregulation in protein analytes attributable to neutrophil activation and disruption of mitochondrial-related metabolism than survivors.
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Affiliation(s)
- Theodore S Jennaro
- The NMR Metabolomics Laboratory and the Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI
| | - Michael A Puskarich
- Department of Emergency Medicine, University of Minnesota, Minneapolis, MN
- Department of Emergency Medicine, Hennepin County Medical Center, Minneapolis, MN
| | - Charles R Evans
- Department of Emergency Medicine and the Weil Institute of Critical Care Medicine, School of Medicine, University of Michigan, Ann Arbor, MI
- Michigan Regional Comprehensive Metabolomics Resource Core ([MRC]), Division of Metabolism, Endocrinology and Diabetes, Department of Internal Medicine, School of Medicine, University of Michigan, Ann Arbor, MI
| | - Alla Karnovsky
- Michigan Regional Comprehensive Metabolomics Resource Core ([MRC]), Division of Metabolism, Endocrinology and Diabetes, Department of Internal Medicine, School of Medicine, University of Michigan, Ann Arbor, MI
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI
| | - Thomas L Flott
- The NMR Metabolomics Laboratory and the Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI
| | - Laura A McLellan
- The NMR Metabolomics Laboratory and the Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI
| | - Alan E Jones
- Department of Emergency Medicine, University of Mississippi Medical Center, Jackson, MS
| | - Kathleen A Stringer
- The NMR Metabolomics Laboratory and the Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI
- Department of Emergency Medicine and the Weil Institute of Critical Care Medicine, School of Medicine, University of Michigan, Ann Arbor, MI
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, School of Medicine, University of Michigan, Ann Arbor, MI
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Hu W, Chen H, Wang H, Peng Q, Wang J, Huang W, Liu A, Xu J, Li Q, Pan C, Xie J, Huang Y. Identifying high-risk phenotypes and associated harms of delayed time-to-antibiotics in patients with ICU onset sepsis: A retrospective cohort study. J Crit Care 2023; 74:154221. [PMID: 36565649 DOI: 10.1016/j.jcrc.2022.154221] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/19/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE To identify phenotypes of Intensive Care Unit (ICU) onset sepsis and its associated harms of delayed time-to-antibiotics. MATERIALS AND METHODS The Medical Information Mart for Intensive Care IV (MIMIC-IV) database was employed to identify patients with ICU onset sepsis. The primary exposure was time-to-antibiotics, as measured from sepsis recognition to first antibiotic administered. Latent profile analysis (LPA) was used to identify phenotypes of sepsis based on individual organ failure score derived from Sequential Organ Failure Assessment (SOFA). Interactions between phenotypes and time-to-antibiotics on 28-day mortality were explored. RESULTS 6246 patients were enrolled in final analysis. The overall 28-day mortality was 12.7%. Delayed time-to-antibiotics was associated with increased 28-day mortality in patients with ICU onset sepsis (HR 1.12, 95% CI 1.08-1.18). Four phenotypes of sepsis were identified: phenotype 1 was characterized by respiratory dysfunction, phenotype 2 was characterized by cardiovascular dysfunction, phenotype 3 was characterized by multiple organ dysfunction, and phenotype 4 was characterized by neurological dysfunction. The adjusted HR of 28-day mortality was 1.16 (95% CI 1.08-1.25) in phenotype 1, and 1.06 (95% CI 1.00-1.13) in phenotype 2, while no significant interaction was observed. CONCLUSIONS Septic patients with respiratory or cardiovascular dysfunction were associated with harms of delayed time-to-antibiotics.
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Affiliation(s)
- Wenhan Hu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, No. 87, Dingjiaqiao Road, Gulou District, Nanjing 210009, PR China
| | - Hui Chen
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, No. 87, Dingjiaqiao Road, Gulou District, Nanjing 210009, PR China
| | - Haofei Wang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, No. 87, Dingjiaqiao Road, Gulou District, Nanjing 210009, PR China
| | - Qingyun Peng
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, No. 87, Dingjiaqiao Road, Gulou District, Nanjing 210009, PR China
| | - Jinlong Wang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, No. 87, Dingjiaqiao Road, Gulou District, Nanjing 210009, PR China
| | - Wei Huang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, No. 87, Dingjiaqiao Road, Gulou District, Nanjing 210009, PR China.
| | - Airan Liu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, No. 87, Dingjiaqiao Road, Gulou District, Nanjing 210009, PR China
| | - Jingyuan Xu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, No. 87, Dingjiaqiao Road, Gulou District, Nanjing 210009, PR China
| | - Qing Li
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, No. 87, Dingjiaqiao Road, Gulou District, Nanjing 210009, PR China
| | - Chun Pan
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, No. 87, Dingjiaqiao Road, Gulou District, Nanjing 210009, PR China
| | - Jianfeng Xie
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, No. 87, Dingjiaqiao Road, Gulou District, Nanjing 210009, PR China
| | - Yingzi Huang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, No. 87, Dingjiaqiao Road, Gulou District, Nanjing 210009, PR China.
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Oruganti S, Rodrigues PRS, White D, Watkins WJ, Shapey S, Barrow A, Al Samsam R, Ali S, Gajraj M, Skone R, Jardine M, Evans J, Struik S, Song JE, Abood L, Paquete B, Foulkes S, Saunders B, Strang A, Kotecha SJ, Phillips B, Evans A, Buchanan I, Bowes S, Ali B, Gore M, Thomas-Turner R, Andrews R, Zaher S, Sharma S, Chakraborty M, Parkinson E, Liberatore F, Woolley T, Edkins S, Davies LC, Moet L, McLaren JE, Watson GL, O'Donnell V, Hood K, Ghazal P. Immune and metabolic markers for identifying and investigating severe Coronavirus disease and Sepsis in children and young people (pSeP/COVID ChYP study): protocol for a prospective cohort study. BMJ Open 2023; 13:e067002. [PMID: 36972964 PMCID: PMC10069273 DOI: 10.1136/bmjopen-2022-067002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
INTRODUCTION Early recognition and appropriate management of paediatric sepsis are known to improve outcomes. A previous system's biology investigation of the systemic immune response in neonates to sepsis identified immune and metabolic markers that showed high accuracy for detecting bacterial infection. Further gene expression markers have also been reported previously in the paediatric age group for discriminating sepsis from control cases. More recently, specific gene signatures were identified to discriminate between COVID-19 and its associated inflammatory sequelae. Through the current prospective cohort study, we aim to evaluate immune and metabolic blood markers which discriminate between sepses (including COVID-19) from other acute illnesses in critically unwell children and young persons, up to 18 years of age. METHODS AND ANALYSIS We describe a prospective cohort study for comparing the immune and metabolic whole-blood markers in patients with sepsis, COVID-19 and other illnesses. Clinical phenotyping and blood culture test results will provide a reference standard to evaluate the performance of blood markers from the research sample analysis. Serial sampling of whole blood (50 μL each) will be collected from children admitted to intensive care and with an acute illness to follow time dependent changes in biomarkers. An integrated lipidomics and RNASeq transcriptomics analyses will be conducted to evaluate immune-metabolic networks that discriminate sepsis and COVID-19 from other acute illnesses. This study received approval for deferred consent. ETHICS AND DISSEMINATION The study has received research ethics committee approval from the Yorkshire and Humber Leeds West Research Ethics Committee 2 (reference 20/YH/0214; IRAS reference 250612). Submission of study results for publication will involve making available all anonymised primary and processed data on public repository sites. TRIAL REGISTRATION NUMBER NCT04904523.
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Affiliation(s)
- Sivakumar Oruganti
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | | | - Daniel White
- School of Medicine, Cardiff University, Cardiff, UK
| | - William John Watkins
- Cochrane Institute of Primary Care and Public Health, Cardiff University, Cardiff, UK
| | - Selyf Shapey
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Anna Barrow
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Rim Al Samsam
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Sara Ali
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Malcolm Gajraj
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Richard Skone
- Department of Paediatric Intensive Care, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Michelle Jardine
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Jennifer Evans
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Siske Struik
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Jong Eun Song
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | | | - Barbara Paquete
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Sian Foulkes
- Paediatric Critical Care Unit, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | - Benjamin Saunders
- Infectious Diseases services for Wales, Noah's Ark Children's Hospital for Wales, Cardiff, UK
| | | | | | - Bethan Phillips
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | - Awen Evans
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | - Iona Buchanan
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | - Susan Bowes
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | - Begum Ali
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | - Maya Gore
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | - Rhian Thomas-Turner
- Children's and Young Adults Research Unit, University Hospital of Wales, Cardiff, UK
| | | | - Summia Zaher
- Department of Obstetrics and Gynaecology, University Hospital of Wales, Cardiff, UK
| | - Simran Sharma
- Infection and Immunity, Cardiff University, Cardiff, UK
- Women's Unit, Cardiff and Vale NHS Trust, Cardiff, UK
| | | | | | | | | | - Sarah Edkins
- School of Medicine, Cardiff University, Cardiff, UK
| | | | - Linda Moet
- School of Medicine, Cardiff University, Cardiff, UK
| | | | | | - Valerie O'Donnell
- Centre for Trials Research, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Kerry Hood
- Centre for Trials Research, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
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Tsakiroglou M, Evans A, Pirmohamed M. Leveraging transcriptomics for precision diagnosis: Lessons learned from cancer and sepsis. Front Genet 2023; 14:1100352. [PMID: 36968610 PMCID: PMC10036914 DOI: 10.3389/fgene.2023.1100352] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/20/2023] [Indexed: 03/12/2023] Open
Abstract
Diagnostics require precision and predictive ability to be clinically useful. Integration of multi-omic with clinical data is crucial to our understanding of disease pathogenesis and diagnosis. However, interpretation of overwhelming amounts of information at the individual level requires sophisticated computational tools for extraction of clinically meaningful outputs. Moreover, evolution of technical and analytical methods often outpaces standardisation strategies. RNA is the most dynamic component of all -omics technologies carrying an abundance of regulatory information that is least harnessed for use in clinical diagnostics. Gene expression-based tests capture genetic and non-genetic heterogeneity and have been implemented in certain diseases. For example patients with early breast cancer are spared toxic unnecessary treatments with scores based on the expression of a set of genes (e.g., Oncotype DX). The ability of transcriptomics to portray the transcriptional status at a moment in time has also been used in diagnosis of dynamic diseases such as sepsis. Gene expression profiles identify endotypes in sepsis patients with prognostic value and a potential to discriminate between viral and bacterial infection. The application of transcriptomics for patient stratification in clinical environments and clinical trials thus holds promise. In this review, we discuss the current clinical application in the fields of cancer and infection. We use these paradigms to highlight the impediments in identifying useful diagnostic and prognostic biomarkers and propose approaches to overcome them and aid efforts towards clinical implementation.
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Affiliation(s)
- Maria Tsakiroglou
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- *Correspondence: Maria Tsakiroglou,
| | - Anthony Evans
- Computational Biology Facility, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Munir Pirmohamed
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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46
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Chen IC, Chen HH, Jiang YH, Hsiao TH, Ko TM, Chao WC. Whole transcriptome analysis to explore the impaired immunological features in critically ill elderly patients with sepsis. J Transl Med 2023; 21:141. [PMID: 36823620 PMCID: PMC9951485 DOI: 10.1186/s12967-023-04002-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Sepsis is a frequent complication in critically ill patients, is highly heterogeneous and is associated with high morbidity and mortality rates, especially in the elderly population. Utilizing RNA sequencing (RNA-Seq) to analyze biological pathways is widely used in clinical and molecular genetic studies, but studies in elderly patients with sepsis are still lacking. Hence, we investigated the mortality-relevant biological features and transcriptomic features in elderly patients who were admitted to the intensive care unit (ICU) for sepsis. METHODS We enrolled 37 elderly patients with sepsis from the ICU at Taichung Veterans General Hospital. On day-1 and day-8, clinical and laboratory data, as well as blood samples, were collected for RNA-Seq analysis. We identified the dynamic transcriptome and enriched pathways of differentially expressed genes between day-8 and day-1 through DVID enrichment analysis and Gene Set Enrichment Analysis. Then, the diversity of the T cell repertoire was analyzed with MiXCR. RESULTS Overall, 37 patients had sepsis, and responders and non-responders were grouped through principal component analysis. Significantly higher SOFA scores at day-7, longer ventilator days, ICU lengths of stay and hospital mortality were found in the non-responder group, than in the responder group. On day-8 in elderly ICU patients with sepsis, genes related to innate immunity and inflammation, such as ZDHCC19, ALOX15, FCER1A, HDC, PRSS33, and PCSK9, were upregulated. The differentially expressed genes (DEGs) were enriched in the regulation of transcription, adaptive immune response, immunoglobulin production, negative regulation of transcription, and immune response. Moreover, there was a higher diversity of T-cell receptors on day-8 in the responder group, than on day-1, indicating that they had better regulated recovery from sepsis compared with the non-response patients. CONCLUSION Sepsis mortality and incidence were both high in elderly individuals. We identified mortality-relevant biological features and transcriptomic features with functional pathway and MiXCR analyses based on RNA-Seq data; and found that the responder group had upregulated innate immunity and increased T cell diversity; compared with the non-responder group. RNA-Seq may be able to offer additional complementary information for the accurate and early prediction of treatment outcome.
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Affiliation(s)
- I-Chieh Chen
- grid.410764.00000 0004 0573 0731Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Hsin-Hua Chen
- grid.410764.00000 0004 0573 0731Division of General Internal Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan ,grid.260542.70000 0004 0532 3749Big Data Center, National Chung Hsing University, Taichung, Taiwan ,grid.265231.10000 0004 0532 1428Department of Industrial Engineering and Enterprise Information, Tunghai University, Taichung, Taiwan ,grid.260542.70000 0004 0532 3749Institute of Biomedical Science and Rong Hsing Research Centre for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Han Jiang
- grid.410764.00000 0004 0573 0731Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Tzu-Hung Hsiao
- grid.410764.00000 0004 0573 0731Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan ,grid.256105.50000 0004 1937 1063Department of Public Health, Fu Jen Catholic University, New Taipei City, Taiwan ,grid.260542.70000 0004 0532 3749Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
| | - Tai-Ming Ko
- grid.260539.b0000 0001 2059 7017Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan ,grid.260539.b0000 0001 2059 7017Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan ,grid.28665.3f0000 0001 2287 1366Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Wen-Cheng Chao
- Big Data Center, National Chung Hsing University, Taichung, Taiwan. .,Department of Critical Care Medicine, Taichung Veterans General Hospital, No. 1650 Taiwan Boulevard, Section 4, Xitun District, Taichung City, 40705, Taiwan. .,Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan. .,Department of Automatic Control Engineering, Feng Chia University, Taichung, Taiwan.
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Ferrada P, Cannon JW, Kozar RA, Bulger EM, Sugrue M, Napolitano LM, Tisherman SA, Coopersmith CM, Efron PA, Dries DJ, Dunn TB, Kaplan LJ. Surgical Science and the Evolution of Critical Care Medicine. Crit Care Med 2023; 51:182-211. [PMID: 36661448 DOI: 10.1097/ccm.0000000000005708] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Surgical science has driven innovation and inquiry across adult and pediatric disciplines that provide critical care regardless of location. Surgically originated but broadly applicable knowledge has been globally shared within the pages Critical Care Medicine over the last 50 years.
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Affiliation(s)
- Paula Ferrada
- Division of Trauma and Acute Care Surgery, Department of Surgery, Inova Fairfax Hospital, Falls Church, VA
| | - Jeremy W Cannon
- Division of Trauma, Surgical Critical Care and Emergency Surgery, Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Rosemary A Kozar
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD
| | - Eileen M Bulger
- Division of Trauma, Burn and Critical Care Surgery, Department of Surgery, University of Washington at Seattle, Harborview, Seattle, WA
| | - Michael Sugrue
- Department of Surgery, Letterkenny University Hospital, County of Donegal, Ireland
| | - Lena M Napolitano
- Division of Acute Care Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI
| | - Samuel A Tisherman
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD
| | - Craig M Coopersmith
- Division of General Surgery, Department of Surgery, Emory University, Emory Critical Care Center, Atlanta, GA
| | - Phil A Efron
- Department of Surgery, Division of Critical Care, University of Florida, Gainesville, FL
| | - David J Dries
- Department of Surgery, University of Minnesota, Regions Healthcare, St. Paul, MN
| | - Ty B Dunn
- Division of Transplant Surgery, Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Lewis J Kaplan
- Division of Trauma, Surgical Critical Care and Emergency Surgery, Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Corporal Michael J. Crescenz VA Medical Center, Section of Surgical Critical Care, Surgical Services, Philadelphia, PA
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Langston JC, Yang Q, Kiani MF, Kilpatrick LE. LEUKOCYTE PHENOTYPING IN SEPSIS USING OMICS, FUNCTIONAL ANALYSIS, AND IN SILICO MODELING. Shock 2023; 59:224-231. [PMID: 36377365 PMCID: PMC9957940 DOI: 10.1097/shk.0000000000002047] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
ABSTRACT Sepsis is a major health issue and a leading cause of death in hospitals globally. The treatment of sepsis is largely supportive, and there are no therapeutics available that target the underlying pathophysiology of the disease. The development of therapeutics for the treatment of sepsis is hindered by the heterogeneous nature of the disease. The presence of multiple, distinct immune phenotypes ranging from hyperimmune to immunosuppressed can significantly impact the host response to infection. Recently, omics, biomarkers, cell surface protein expression, and immune cell profiles have been used to classify immune status of sepsis patients. However, there has been limited studies of immune cell function during sepsis and even fewer correlating omics and biomarker alterations to functional consequences. In this review, we will discuss how the heterogeneity of sepsis and associated immune cell phenotypes result from changes in the omic makeup of cells and its correlation with leukocyte dysfunction. We will also discuss how emerging techniques such as in silico modeling and machine learning can help in phenotyping sepsis patients leading to precision medicine.
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Affiliation(s)
- Jordan C. Langston
- Department of Bioengineering, Temple University, Philadelphia, PA, 19122
| | - Qingliang Yang
- Department of Mechanical Engineering, Temple University, Philadelphia, PA, 19122
| | - Mohammad F. Kiani
- Department of Bioengineering, Temple University, Philadelphia, PA, 19122
- Department of Mechanical Engineering, Temple University, Philadelphia, PA, 19122
| | - Laurie E. Kilpatrick
- Center for Inflammation and Lung Research, Department of Microbiology, Immunology and Inflammation, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140
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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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Distinct subsets of neutrophils crosstalk with cytokines and metabolites in patients with sepsis. iScience 2023; 26:105948. [PMID: 36756375 PMCID: PMC9900520 DOI: 10.1016/j.isci.2023.105948] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/04/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023] Open
Abstract
Sepsis is a life-threatening condition caused by a dysregulated host response to infection. Despite continued efforts to understand the pathophysiology of sepsis, no effective therapies are currently available. While singular components of the aberrant immune response have been investigated, comprehensive studies linking different data layers are lacking. Using an integrated systems immunology approach, we evaluated neutrophil phenotypes and concomitant changes in cytokines and metabolites in patients with sepsis. Our findings identify differentially expressed mature and immature neutrophil subsets in patients with sepsis. These subsets correlate with various proteins, metabolites, and lipids, including pentraxin-3, angiopoietin-2, and lysophosphatidylcholines, in patients with sepsis. These results enabled the construction of a statistical model based on weighted multi-omics linear regression analysis for sepsis biomarker identification. These findings could help inform early patient stratification and treatment options, and facilitate further mechanistic studies targeting the trifecta of surface marker expression, cytokines, and metabolites.
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