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Peronnet E, Terraz G, Cerrato E, Imhoff K, Blein S, Brengel-Pesce K, Bodinier M, Fleurie A, Rimmelé T, Lukaszewicz AC, Monneret G, Llitjos JF. Use of Immune Profiling Panel to assess the immune response of septic patients for prediction of worsening as a composite endpoint. Sci Rep 2024; 14:11305. [PMID: 38760488 PMCID: PMC11101454 DOI: 10.1038/s41598-024-62202-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: 12/22/2023] [Accepted: 05/14/2024] [Indexed: 05/19/2024] Open
Abstract
Sepsis induces intense, dynamic and heterogeneous host response modulations. Despite improvement of patient management, the risk of mortality and healthcare-associated infections remains high. Treatments to counterbalance immune response are under evaluation, but effective biomarkers are still lacking to perform patient stratification. The design of the present study was defined to alleviate the limitations of existing literature: we selected patients who survived the initial hyperinflammatory response and are still hospitalized at day 5-7 after ICU admission. Using the Immune Profiling Panel (IPP), a fully automated RT-qPCR multiplex prototype, we optimized a machine learning model combining the IPP gene expression levels for the identification of patients at high risk of worsening, a composite endpoint defined as death or secondary infection, within one week after sampling. This was done on 332 sepsis patients selected from two retrospective studies. The IPP model identified a high-risk group comprising 30% of patients, with a significant increased proportion of worsening events at day 28 compared to the low-risk group (49% vs. 28%, respectively). These preliminary results underline the potential clinical application of IPP for sepsis patient stratification in a personalized medicine perspective, that will be confirmed in a larger prospective multicenter study.
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Affiliation(s)
- 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.
| | - Gabriel Terraz
- Joint Research Unit HCL-bioMérieux, EA 7426 "Pathophysiology of Injury-Induced Immunosuppression" (Université Claude Bernard Lyon 1 - Hospices Civils de Lyon, bioMérieux), Lyon, France
- EFOR, Champagne-au-Mont-d'Or, 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
| | - Katia Imhoff
- Data Science, bioMérieux S.A., Marcy l'Etoile, France
| | - Sophie Blein
- Data Science, bioMérieux S.A., Marcy l'Etoile, 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
- Open Innovation and Partnerships (OI&P), bioMérieux S.A., Marcy-l'Etoile, France
| | - 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
| | - 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
| | - 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
| | - 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
| | - 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
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Grudzinski KM, Fenske S, Wunderink RG, Gao CA. Neutrophil percentages in bronchoalveolar lavage fluid: Implications for diagnosing bacterial pneumonia in patients with immunocompromise and neutropenia. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.04.24306709. [PMID: 38766045 PMCID: PMC11100846 DOI: 10.1101/2024.05.04.24306709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Background Pneumonia is the leading cause of infectious deaths and the most common infection identified in ICU patients. Assessment of bronchoalveolar lavage fluid (BALF) cellularity can aid in pneumonia diagnosis. Low percentages (<50%) of BALF neutrophils have a high negative predictive value for bacterial pneumonia in a general medical ICU population, but unclear operating characteristics in patients with immunocompromise and neutropenia remain unknown. Methods We analyzed a large cohort of BALF specimens obtained for routine care for suspected pneumonia in mechanically ventilated patients and enrolled in the single-center Successful Clinical Response In Pneumonia Therapy (SCRIPT) study. BALF neutrophils were reported as a percentage of leukocytes by the clinical laboratory. The etiology of each episode of suspected pneumonia was adjudicated by a committee of critical care physicians using a predefined protocol. Immunocompromise was defined using predetermined criteria by the study research team. Neutropenia was defined here as a peripheral ANC <1500 cells/μl. Data are expressed as median [Quartile (Q) 1, Q3] and compared using the Mann-Whitney U test. Results 688 mechanically ventilated patients with suspected pneumonia were included. 409 (59.4%) were male; median age was 62 [51,71]. 461 patients (67.0%) were immunocompetent, 149 (21.7%) were immunocompromised without neutropenia and 78 (11.3%) were neutropenic at some point during their admission. A total of 1746 BALs were performed. Fifty-seven BALs were obtained on a day where the patient's ANC<1500. Amongst pneumonia episodes classified as bacterial, no difference was found amongst BALF percent neutrophils taken patients who were immunocompetent and those who were immunocompromised but not neutropenic on day of sampling: 84.0% [69.0, 93.0] vs 87.0% [68.3, 93.0], p = 0.878 (Figure 1B). However, BALF percent neutrophils were significantly lower in patients neutropenic on day of sampling, with median BALF percent neutrophils of only 65.0% [22.3, 70.5] (p=0.016 compared with immunocompromised group, p=0.0096 compared with immunocompetent group). Conclusion Among patients with bacterial pneumonia, BALF neutrophil percentage was not significantly decreased by a spectrum of immunocompromise. However, the subset of patients who were acutely neutropenic at the time of BAL sampling had significantly lower BALF % neutrophils. A traditional approach using BALF<50% to suggest against bacterial pneumonia may be inaccurate in this particular population.
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Affiliation(s)
- Kevin M. Grudzinski
- Department of Internal Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Samuel Fenske
- Division of Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Richard G. Wunderink
- Division of Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Catherine A. Gao
- Division of Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, Chicago, IL
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3
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Salluh JIF, Póvoa P, Beane A, Kalil A, Sendagire C, Sweeney DA, Pilcher D, Polverino E, Tacconelli E, Estenssoro E, Frat JP, Ramirez J, Reyes LF, Roca O, Nseir S, Nobre V, Lisboa T, Martin-Loeches I. Challenges for a broad international implementation of the current severe community-acquired pneumonia guidelines. Intensive Care Med 2024; 50:526-538. [PMID: 38546855 DOI: 10.1007/s00134-024-07381-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: 10/09/2023] [Accepted: 02/29/2024] [Indexed: 04/16/2024]
Abstract
Severe community-acquired pneumonia (sCAP) remains one of the leading causes of admission to the intensive care unit, thus consuming a large share of resources and is associated with high mortality rates worldwide. The evidence generated by clinical studies in the last decade was translated into recommendations according to the first published guidelines focusing on severe community-acquired pneumonia. Despite the advances proposed by the present guidelines, several challenges preclude the prompt implementation of these diagnostic and therapeutic measures. The present article discusses the challenges for the broad implementation of the sCAP guidelines and proposes solutions when applicable.
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Affiliation(s)
- Jorge I F Salluh
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, RJ, Brazil.
- Postgraduate Program of Internal Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, UFRJ, Brazil.
| | - Pedro Póvoa
- NOVA Medical School, CHRC, New University of Lisbon, Lisbon, Portugal
- Research Unit of Clinical Epidemiology, Institute of Clinical Research, Odense University Hospital, University of Southern Denmark Centre for Clinical Epidemiology, Odense, Denmark
- Department of Intensive Care, Hospital de São Francisco Xavier, CHLO, Lisbon, Portugal
| | - Abi Beane
- Pandemic Science Hub and Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
- NICS-MORU, Colombo, Sri Lanka
| | - Andre Kalil
- Division of Infectious Diseases, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Cornelius Sendagire
- Anesthesia and Critical Care, Makerere University College of Health Sciences, P.O. Box 7072, Kampala, Uganda
| | - Daniel A Sweeney
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, La Jolla, San Diego, CA, USA
| | - David Pilcher
- Department of Intensive Care, Alfred Health, Commercial Road3004, Prahran, VIC, Australia
- The Australian and New Zealand Intensive Care Society (ANZICS) Centre for Outcome and Resource Evaluation, Camberwell, Australia
| | - Eva Polverino
- Pneumology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, CIBERES, Barcelona, Spain
| | - Evelina Tacconelli
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Elisa Estenssoro
- Hospital Interzonal de Agudos General San Martín, Servicio de Terapia Intensiva, Buenos Aires, Argentina
| | - Jean-Pierre Frat
- CHU de Poitiers, Médecine Intensive Réanimation, Poitiers, France
- INSERM, CIC-1402, IS-ALIVE, Faculté de Médecine Et de Pharmacie de Poitiers, Université de Poitiers, Poitiers, France
| | - Julio Ramirez
- Norton Infectious Diseases Institute, Norton Healthcare, Louisville, KY, USA
- University of Louisville, Louisville, KY, USA
| | - Luis Felipe Reyes
- Unisabana Center for Translational Science, School of Medicine, Universidad de La Sabana, Chia, Colombia
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Oriol Roca
- Servei de Medicina Intensiva, Parc Taulí Hospital Universitari, Institut de Recerca Part Taulí - I3PT, Parc del Taulí 1, 08028, Sabadell, Spain
- Departament de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Saad Nseir
- Centre de Réanimation, CHU de Lille, 59000, Lille, France
- Team Fungal Associated Invasive and Inflammatory Diseases, Lille Inflammation Research International Center, Université de Lille, INSERM U995, Lille, France
| | - Vandack Nobre
- Department of Internal Medicine, Medical School and University Hospital, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Thiago Lisboa
- Critical Care Department, Programa de Pós-Graduação em Ciencias Pneumologicas, Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ignacio Martin-Loeches
- Department of Intensive Care Medicine, Multidisciplinary Intensive Care Research Organization, St. James's University Hospital, Trinity Centre for Health Sciences, Dublin, Ireland
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Grant RA, Poor TA, Sichizya L, Diaz E, Bailey JI, Soni S, Senkow KJ, Pérez-Leonor XG, Abdala-Valencia H, Lu Z, Donnelly HK, Simons LM, Ozer EA, Tighe RM, Lomasney JW, Wunderink RG, Singer BD, Misharin AV, Budinger GRS. Prolonged exposure to lung-derived cytokines is associated with activation of microglia in patients with COVID-19. JCI Insight 2024; 9:e178859. [PMID: 38502186 PMCID: PMC11141878 DOI: 10.1172/jci.insight.178859] [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: 12/27/2023] [Accepted: 03/13/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUNDSurvivors of pneumonia, including SARS-CoV-2 pneumonia, are at increased risk for cognitive dysfunction and dementia. In rodent models, cognitive dysfunction following pneumonia has been linked to the systemic release of lung-derived pro-inflammatory cytokines. Microglia are poised to respond to inflammatory signals from the circulation, and their dysfunction has been linked to cognitive impairment in murine models of dementia and in humans.METHODSWe measured levels of 55 cytokines and chemokines in bronchoalveolar lavage fluid and plasma from 341 patients with respiratory failure and 13 healthy controls, including 93 unvaccinated patients with COVID-19 and 203 patients with other causes of pneumonia. We used flow cytometry to sort neuroimmune cells from postmortem brain tissue from 5 patients who died from COVID-19 and 3 patients who died from other causes for single-cell RNA-sequencing.RESULTSMicroglia from patients with COVID-19 exhibited a transcriptomic signature suggestive of their activation by circulating pro-inflammatory cytokines. Peak levels of pro-inflammatory cytokines were similar in patients with pneumonia irrespective of etiology, but cumulative cytokine exposure was higher in patients with COVID-19. Treatment with corticosteroids reduced expression of COVID-19-specific cytokines.CONCLUSIONProlonged lung inflammation results in sustained elevations in circulating cytokines in patients with SARS-CoV-2 pneumonia compared with those with pneumonia secondary to other pathogens. Microglia from patients with COVID-19 exhibit transcriptional responses to inflammatory cytokines. These findings support data from rodent models causally linking systemic inflammation with cognitive dysfunction in pneumonia and support further investigation into the role of microglia in pneumonia-related cognitive dysfunction.FUNDINGSCRIPT U19AI135964, UL1TR001422, P01AG049665, P01HL154998, R01HL149883, R01LM013337, R01HL153122, R01HL147290, R01HL147575, R01HL158139, R01ES034350, R01ES027574, I01CX001777, U01TR003528, R21AG075423, T32AG020506, F31AG071225, T32HL076139.
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Affiliation(s)
- Rogan A Grant
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
| | - Taylor A Poor
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
| | - Lango Sichizya
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
| | - Estefani Diaz
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
| | - Joseph I Bailey
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
| | - Sahil Soni
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
| | - Karolina J Senkow
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
| | | | | | - Ziyan Lu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
| | - Helen K Donnelly
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
| | - Lacy M Simons
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Pathogen Genomics and Microbial Evolution, Robert J. Havey, MD Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Egon A Ozer
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Center for Pathogen Genomics and Microbial Evolution, Robert J. Havey, MD Institute for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Robert M Tighe
- Division of Pulmonary, Allergy, and Critical Care Medicine, Duke University School of Medicine, Duke University, Durham, North Carolina, USA
| | | | - Richard G Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
- Department of Biochemistry and Molecular Genetics, and Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | | | - G R Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Department of Medicine; and
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5
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Gao CA, Markov NS, Pickens C, Pawlowski A, Kang M, Walter JM, Singer BD, Wunderink RG. An observational cohort study of bronchoalveolar lavage fluid galactomannan and Aspergillus culture positivity in patients requiring mechanical ventilation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.07.24302392. [PMID: 38370841 PMCID: PMC10871379 DOI: 10.1101/2024.02.07.24302392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Rationale Critically ill patients who develop invasive pulmonary aspergillosis (IPA) have high mortality rates despite antifungal therapy. Diagnosis is difficult in these patients. Bronchoalveolar lavage (BAL) fluid galactomannan (GM) is a helpful marker of infection, although the optimal cutoff for IPA is unclear. We aimed to evaluate the BAL fluid GM and fungal culture results, demographics, and outcomes among a large cohort of mechanically ventilated patients with suspected pneumonia. Methods A single-center cohort study of patients enrolled in the Successful Clinical Response in Pneumonia Therapy (SCRIPT) study from June 2018 to March 2023. Demographics, BAL results, and outcomes data were extracted from the electronic health record and compared between groups of patients who grew Aspergillus on a BAL fluid culture, those who had elevated BAL fluid GM levels (defined as >0.5 or >0.8) but did not grow Aspergillus on BAL fluid culture, and those with neither. Results Of over 1700 BAL samples from 688 patients, only 18 BAL samples grew Aspergillus. Patients who had a BAL sample grow Aspergillus (n=15) were older (median 71 vs 62 years, p=0.023), had more days intubated (29 vs 11, p=0.002), and more ICU days (34 vs 15, p=0.002) than patients whose BAL fluid culture was negative for Aspergillus (n=672). The BAL fluid galactomannan level was higher from samples that grew Aspergillus on culture than those that did not (median ODI 7.08 vs 0.11, p<0.001), though the elevation of BAL fluid GM varied across BAL samples for patients who had serial sampling. Patients who grew Aspergillus had a similar proportion of underlying immunocompromise compared with the patients who did not, and while no statistically significant difference in overall unfavorable outcome, had longer duration of ventilation and longer ICU stays. Conclusions In this large cohort of critically ill patients with a high number of BAL samples with GM levels, we found a relatively low rate of Aspergillus growth. Patients who eventually grew Aspergillus had inconsistently elevated BAL fluid GM, and many patients with elevated BAL fluid GM did not grow Aspergillus. These data suggest that the pre-test probability of invasive pulmonary aspergillosis should be considered low in a general ICU population undergoing BAL evaluation to define the etiology of pneumonia. Improved scoring systems are needed to enhance pre-test probability for diagnostic test stewardship purposes.
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Affiliation(s)
- Catherine A. Gao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Nikolay S. Markov
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chiagozie Pickens
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Anna Pawlowski
- Northwestern Medicine Enterprise Data Warehouse, Chicago, IL, USA
| | - Mengjia Kang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - James M. Walter
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Benjamin D. Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Richard G. Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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6
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Markov NS, Ren Z, Senkow KJ, Grant RA, Gao CA, Malsin ES, Sichizya L, Kihshen H, Helmin KA, Jovisic M, Arnold JM, Pérez-Leonor XG, Abdala-Valencia H, Swaminathan S, Nwaezeapu J, Kang M, Rasmussen L, Ozer EA, Lorenzo-Redondo R, Hultquist JF, Simons LM, Rios-Guzman E, Misharin AV, Wunderink RG, Budinger GS, Singer BD, Morales-Nebreda L. A distinctive evolution of alveolar T cell responses is associated with clinical outcomes in unvaccinated patients with SARS-CoV-2 pneumonia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571479. [PMID: 38168346 PMCID: PMC10760069 DOI: 10.1101/2023.12.13.571479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Pathogen clearance and resolution of inflammation in patients with pneumonia require an effective local T cell response. Nevertheless, local T cell activation may drive lung injury, particularly during prolonged episodes of respiratory failure characteristic of severe SARS-CoV-2 pneumonia. While T cell responses in the peripheral blood are well described, the evolution of T cell phenotypes and molecular signatures in the distal lung of patients with severe pneumonia caused by SARS-CoV-2 or other pathogens is understudied. Accordingly, we serially obtained 432 bronchoalveolar lavage fluid samples from 273 patients with severe pneumonia and respiratory failure, including 74 unvaccinated patients with COVID-19, and performed flow cytometry, transcriptional, and T cell receptor profiling on sorted CD8+ and CD4+ T cell subsets. In patients with COVID-19 but not pneumonia secondary to other pathogens, we found that early and persistent enrichment in CD8+ and CD4+ T cell subsets correlated with survival to hospital discharge. Activation of interferon signaling pathways early after intubation for COVID-19 was associated with favorable outcomes, while activation of NF-κB-driven programs late in disease was associated with poor outcomes. Patients with SARS-CoV-2 pneumonia whose alveolar T cells preferentially targeted the Spike and Nucleocapsid proteins tended to experience more favorable outcomes than patients whose T cells predominantly targeted the ORF1ab polyprotein complex. These results suggest that in patients with severe SARS-CoV-2 pneumonia, alveolar T cell interferon responses targeting structural SARS-CoV-2 proteins characterize patients who recover, yet these responses progress to NF-κB activation against non-structural proteins in patients who go on to experience poor clinical outcomes.
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Affiliation(s)
- Nikolay S. Markov
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Ziyou Ren
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Karolina J. Senkow
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Rogan A. Grant
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Catherine A. Gao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Elizabeth S. Malsin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Lango Sichizya
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Hermon Kihshen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Kathryn A. Helmin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Milica Jovisic
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Jason M. Arnold
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | | | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Suchitra Swaminathan
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Julu Nwaezeapu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Mengjia Kang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Luke Rasmussen
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Egon A. Ozer
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Ramon Lorenzo-Redondo
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Lacy M. Simons
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Estefany Rios-Guzman
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Alexander V. Misharin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Richard G. Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - G.R. Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Benjamin D. Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | - Luisa Morales-Nebreda
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL USA
- Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL USA
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7
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Grant RA, Poor TA, Sichizya L, Diaz E, Bailey JI, Soni S, Senkow KJ, Pérez-Leonor XG, Abdala-Valencia H, Lu Z, Donnelly HK, Tighe RM, Lomasney JW, Wunderink RG, Singer BD, Misharin AV, Budinger GS. Prolonged exposure to lung-derived cytokines is associated with inflammatory activation of microglia in patients with COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.550765. [PMID: 37546860 PMCID: PMC10402123 DOI: 10.1101/2023.07.28.550765] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Neurological impairment is the most common finding in patients with post-acute sequelae of COVID-19. Furthermore, survivors of pneumonia from any cause have an elevated risk of dementia1-4. Dysfunction in microglia, the primary immune cell in the brain, has been linked to cognitive impairment in murine models of dementia and in humans5. Here, we report a transcriptional response in human microglia collected from patients who died following COVID-19 suggestive of their activation by TNF-α and other circulating pro-inflammatory cytokines. Consistent with these findings, the levels of 55 alveolar and plasma cytokines were elevated in a cohort of 341 patients with respiratory failure, including 93 unvaccinated patients with COVID-19 and 203 patients with other causes of pneumonia. While peak levels of pro-inflammatory cytokines were similar in patients with pneumonia irrespective of etiology, cumulative cytokine exposure was higher in patients with COVID-19. Corticosteroid treatment, which has been shown to be beneficial in patients with COVID-196, was associated with lower levels of CXCL10, CCL8, and CCL2-molecules that sustain inflammatory circuits between alveolar macrophages harboring SARS-CoV-2 and activated T cells7. These findings suggest that corticosteroids may break this cycle and decrease systemic exposure to lung-derived cytokines and inflammatory activation of microglia in patients with COVID-19.
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Affiliation(s)
- Rogan A Grant
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Taylor A Poor
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Lango Sichizya
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Estefani Diaz
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Joseph I Bailey
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Sahil Soni
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Karolina J Senkow
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Xochítl G Pérez-Leonor
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ziyan Lu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Helen K Donnelly
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Robert M Tighe
- Division of Pulmonary, Allergy, and Critical Care Medicine, Duke University School of Medicine, Duke University, Durham, NC, USA
| | - Jon W Lomasney
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Biochemistry and Molecular Genetics, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Gr Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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