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Waypa GB, Smith KA, Mungai PT, Dudley VJ, Helmin KA, Singer BD, Peek CB, Bass J, Beussink-Nelson L, Shah SJ, Ofman G, Wasserstrom JA, Muller WA, Misharin AV, Budinger GRS, Abdala-Valencia H, Chandel NS, Dokic D, Bartom ET, Zhang S, Tatekoshi Y, Mahmoodzadeh A, Ardehali H, Thorp EB, Schumacker PT. Mitochondria regulate proliferation in adult cardiac myocytes. J Clin Invest 2024:e165482. [PMID: 38722697 DOI: 10.1172/jci165482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024] Open
Abstract
Newborn mammalian cardiomyocytes quickly transition from a fetal to an adult phenotype that utilizes mitochondrial oxidative phosphorylation but loses mitotic capacity. We tested whether forced reversal of adult cardiomyocytes back to a fetal glycolytic phenotype would restore proliferative capacity. We deleted Uqcrfs1 (mitochondrial Rieske Iron-Sulfur protein, RISP) in hearts of adult mice. As RISP protein decreased, heart mitochondrial function declined, and glucose utilization increased. Simultaneously, they underwent hyperplastic remodeling during which cardiomyocyte number doubled without cellular hypertrophy. Cellular energy supply was preserved, AMPK activation was absent, and mTOR activation was evident. In ischemic hearts with RISP deletion, new cardiomyocytes migrated into the infarcted region, suggesting the potential for therapeutic cardiac regeneration. RNA-seq revealed upregulation of genes associated with cardiac development and proliferation. Metabolomic analysis revealed a decrease in alpha-ketoglutarate (required for TET-mediated demethylation) and an increase in S-adenosylmethionine (required for methyltransferase activity). Analysis revealed an increase in methylated CpGs near gene transcriptional start sites. Genes that were both differentially expressed and differentially methylated were linked to upregulated cardiac developmental pathways. We conclude that decreased mitochondrial function and increased glucose utilization can restore mitotic capacity in adult cardiomyocytes resulting in the generation of new heart cells, potentially through the modification of substrates that regulate epigenetic modification of genes required for proliferation.
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Affiliation(s)
- Gregory B Waypa
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Kimberly A Smith
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Paul T Mungai
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Vincent J Dudley
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Kathryn A Helmin
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Benjamin D Singer
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Clara Bien Peek
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Joseph Bass
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Lauren Beussink-Nelson
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Sanjiv J Shah
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Gaston Ofman
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - J Andrew Wasserstrom
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - William A Muller
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Alexander V Misharin
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - G R Scott Budinger
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Hiam Abdala-Valencia
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Navdeep S Chandel
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Danijela Dokic
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Shuang Zhang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Yuki Tatekoshi
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Amir Mahmoodzadeh
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Hossein Ardehali
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Edward B Thorp
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Paul T Schumacker
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, United States of America
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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 DOI: 10.1172/jci.insight.178859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Chaudhuri SM, Weinberg SE, Wang D, Yalom LK, Montauti E, Iyer R, Tang AY, Torres Acosta MA, Shen J, Mani NL, Wang S, Liu K, Lu W, Bui TM, Manzanares LD, Dehghani Z, Wai CM, Gao B, Wei J, Yue F, Cui W, Singer BD, Sumagin R, Zhang Y, Fang D. Mediator complex subunit 1 architects a tumorigenic Treg cell program independent of inflammation. Cell Rep Med 2024; 5:101441. [PMID: 38428427 PMCID: PMC10983042 DOI: 10.1016/j.xcrm.2024.101441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/18/2023] [Accepted: 02/01/2024] [Indexed: 03/03/2024]
Abstract
While immunotherapy has revolutionized cancer treatment, its safety has been hampered by immunotherapy-related adverse events. Unexpectedly, we show that Mediator complex subunit 1 (MED1) is required for T regulatory (Treg) cell function specifically in the tumor microenvironment. Treg cell-specific MED1 deletion does not predispose mice to autoimmunity or excessive inflammation. In contrast, MED1 is required for Treg cell promotion of tumor growth because MED1 is required for the terminal differentiation of effector Treg cells in the tumor. Suppression of these terminally differentiated Treg cells is sufficient for eliciting antitumor immunity. Both human and murine Treg cells experience divergent paths of differentiation in tumors and matched tissues with non-malignant inflammation. Collectively, we identify a pathway promoting the differentiation of a Treg cell effector subset specific to tumors and demonstrate that suppression of a subset of Treg cells is sufficient for promoting antitumor immunity in the absence of autoimmune consequences.
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Affiliation(s)
- Shuvam M Chaudhuri
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Samuel E Weinberg
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Dongmei Wang
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lenore K Yalom
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Elena Montauti
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Radhika Iyer
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Amy Y Tang
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Manuel A Torres Acosta
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Medical Scientist Training Program, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jian Shen
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Nikita L Mani
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Shengnan Wang
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kun Liu
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Weiyuan Lu
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Triet M Bui
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Laura D Manzanares
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Zeinab Dehghani
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ching Man Wai
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Beixue Gao
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Juncheng Wei
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Feng Yue
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Weiguo Cui
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ronen Sumagin
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Yana Zhang
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Deyu Fang
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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Titanji BK, Sereti I, Singer BD. Culturing the Future of Medicine: The Imperative of Strengthening the ID Physician-Scientist Pipeline. J Infect Dis 2024:jiae074. [PMID: 38365222 DOI: 10.1093/infdis/jiae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 02/09/2024] [Indexed: 02/18/2024] Open
Affiliation(s)
- Boghuma K Titanji
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Irini Sereti
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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5
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Michki NS, Singer BD, Perez JV, Thomas AJ, Natale V, Helmin KA, Wright J, Cheng L, Young LR, Lederman HM, McGrath-Morrow SA. Transcriptional profiling of peripheral blood mononuclear cells identifies inflammatory phenotypes in Ataxia Telangiectasia. Orphanet J Rare Dis 2024; 19:67. [PMID: 38360726 PMCID: PMC10870445 DOI: 10.1186/s13023-024-03073-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/03/2024] [Indexed: 02/17/2024] Open
Abstract
INTRODUCTION Ataxia telangiectasia (A-T) is an autosomal recessive neurodegenerative disease with widespread systemic manifestations and marked variability in clinical phenotypes. In this study, we sought to determine whether transcriptomic profiling of peripheral blood mononuclear cells (PBMCs) defines subsets of individuals with A-T beyond mild and classic phenotypes, enabling identification of novel features for disease classification and treatment response to therapy. METHODS Participants with classic A-T (n = 77), mild A-T (n = 13), and unaffected controls (n = 15) were recruited from two outpatient clinics. PBMCs were isolated and bulk RNAseq was performed. Plasma was also isolated in a subset of individuals. Affected individuals were designated mild or classic based on ATM mutations and clinical and laboratory features. RESULTS People with classic A-T were more likely to be younger and IgA deficient and to have higher alpha-fetoprotein levels and lower % forced vital capacity compared to individuals with mild A-T. In classic A-T, the expression of genes required for V(D)J recombination was lower, and the expression of genes required for inflammatory activity was higher. We assigned inflammatory scores to study participants and found that inflammatory scores were highly variable among people with classic A-T and that higher scores were associated with lower ATM mRNA levels. Using a cell type deconvolution approach, we inferred that CD4 + T cells and CD8 + T cells were lower in number in people with classic A-T. Finally, we showed that individuals with classic A-T exhibit higher SERPINE1 (PAI-1) mRNA and plasma protein levels, irrespective of age, and higher FLT4 (VEGFR3) and IL6ST (GP130) plasma protein levels compared with mild A-T and controls. CONCLUSION Using a transcriptomic approach, we identified novel features and developed an inflammatory score to identify subsets of individuals with different inflammatory phenotypes in A-T. Findings from this study could be used to help direct treatment and to track treatment response to therapy.
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Affiliation(s)
- Nigel S Michki
- Division of Pulmonary and Sleep Medicine, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Javier V Perez
- Division of Pulmonary and Sleep Medicine, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Aaron J Thomas
- Division of Pulmonary and Sleep Medicine, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Valerie Natale
- Forgotten Diseases Research Foundation, Santa Clara, CA, USA
| | - Kathryn A Helmin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Jennifer Wright
- Department of Immunology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Leon Cheng
- Department of Immunology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Lisa R Young
- Division of Pulmonary and Sleep Medicine, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Howard M Lederman
- Department of Immunology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Sharon A McGrath-Morrow
- Division of Pulmonary and Sleep Medicine, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA.
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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Mikacenic C, Fussner LA, Simpson AJ, Singer BD, Files DC. Reply: Research Bronchoscopy Standards and the Need for Noninvasive Sampling of the Failing Lungs. Ann Am Thorac Soc 2024; 21:184-185. [PMID: 37776284 PMCID: PMC10867905 DOI: 10.1513/annalsats.202309-811le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 09/29/2023] [Indexed: 10/02/2023] Open
Affiliation(s)
| | | | - A. John Simpson
- Newcastle UniversityNewcastle upon Tyne, United Kingdom
- Newcastle upon Tyne Hospitals National Health Service Foundation TrustNewcastle upon Tyne, United Kingdom
| | | | - D. Clark Files
- Wake Forest School of MedicineWinston-Salem, North Carolina
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8
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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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Torres Acosta MA, Mambetsariev N, Reyes Flores CP, Helmin KA, Liu Q, Joudi AM, Morales-Nebreda L, Gurkan J, Cheng K, Abdala-Valencia H, Weinberg SE, Singer BD. AMP-activated protein kinase is necessary for Treg cell functional adaptation to microenvironmental stress. bioRxiv 2023:2023.11.29.568904. [PMID: 38076988 PMCID: PMC10705412 DOI: 10.1101/2023.11.29.568904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
CD4+FOXP3+ regulatory T (Treg) cells maintain self-tolerance, suppress the immune response to cancer, and protect against tissue injury in the lung and other organs. Treg cells require mitochondrial metabolism to exert their function, but how Treg cells adapt their metabolic programs to sustain and optimize their function during an immune response occurring in a metabolically stressed microenvironment remains unclear. Here, we tested whether Treg cells require the energy homeostasis-maintaining enzyme AMP-activated protein kinase (AMPK) to adapt to metabolically aberrant microenvironments caused by malignancy or lung injury, finding that AMPK is dispensable for Treg cell immune-homeostatic function but is necessary for full Treg cell function in B16 melanoma tumors and during acute lung injury caused by influenza virus pneumonia. AMPK-deficient Treg cells had lower mitochondrial mass and exhibited an impaired ability to maximize aerobic respiration. Mechanistically, we found that AMPK regulates DNA methyltransferase 1 to promote transcriptional programs associated with mitochondrial function in the tumor microenvironment. In the lung during viral pneumonia, we found that AMPK sustains metabolic homeostasis and mitochondrial activity. Induction of DNA hypomethylation was sufficient to rescue mitochondrial mass in AMPK-deficient Treg cells, linking DNA methylation with AMPK function and mitochondrial metabolism. These results define AMPK as a determinant of Treg cell adaptation to metabolic stress and offer potential therapeutic targets in cancer and tissue injury.
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Affiliation(s)
- Manuel A. Torres Acosta
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
- Driskill Graduate Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Nurbek Mambetsariev
- Division of Allergy and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Carla P. Reyes Flores
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
- Driskill Graduate Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Kathryn A. Helmin
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Qianli Liu
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
- Driskill Graduate Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Anthony M. Joudi
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Luisa Morales-Nebreda
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Jonathan Gurkan
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
- Driskill Graduate Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Kathleen Cheng
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
- Driskill Graduate Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
- Department of Dermatology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Samuel E. Weinberg
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago IL 60611 USA
| | - Benjamin D. Singer
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
- Simpson Querrey Lung Institute for Translational Science (SQ LIFTS), Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
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10
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Morgan MA, Mohammad Parast S, Iwanaszko M, Aoi Y, Yoo D, Dumar ZJ, Howard BC, Helmin KA, Liu Q, Thakur WR, Zeidner JM, Singer BD, Eichler EE, Shilatifard A. ELOA3: A primate-specific RNA polymerase II elongation factor encoded by a tandem repeat gene cluster. Sci Adv 2023; 9:eadj1261. [PMID: 37992162 PMCID: PMC10664989 DOI: 10.1126/sciadv.adj1261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/19/2023] [Indexed: 11/24/2023]
Abstract
The biological role of the repetitive DNA sequences in the human genome remains an outstanding question. Recent long-read human genome assemblies have allowed us to identify a function for one of these repetitive regions. We have uncovered a tandem array of conserved primate-specific retrogenes encoding the protein Elongin A3 (ELOA3), a homolog of the RNA polymerase II (RNAPII) elongation factor Elongin A (ELOA). Our genomic analysis shows that the ELOA3 gene cluster is conserved among primates and the number of ELOA3 gene repeats is variable in the human population and across primate species. Moreover, the gene cluster has undergone concerted evolution and homogenization within primates. Our biochemical studies show that ELOA3 functions as a promoter-associated RNAPII pause-release elongation factor with distinct biochemical and functional features from its ancestral homolog, ELOA. We propose that the ELOA3 gene cluster has evolved to fulfil a transcriptional regulatory function unique to the primate lineage that can be targeted to regulate cellular hyperproliferation.
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Affiliation(s)
- Marc A. J. Morgan
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Saeid Mohammad Parast
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Marta Iwanaszko
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yuki Aoi
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - DongAhn Yoo
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA 98195, USA
| | - Zachary J. Dumar
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Benjamin C. Howard
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kathryn A. Helmin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Qianli Liu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - William R. Thakur
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jacob M. Zeidner
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Benjamin D. Singer
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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11
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Pickens CI, Singer BD. Finding Facts in Postacute Sequelae of COVID-19: Clinical, Radiographic, and Histopathologic Markers of Disease. Am J Respir Crit Care Med 2023; 208:521-523. [PMID: 37387599 PMCID: PMC10492246 DOI: 10.1164/rccm.202306-1043ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 06/29/2023] [Indexed: 07/01/2023] Open
Affiliation(s)
- Chiagozie I Pickens
- Division of Pulmonary and Critical Care Medicine Northwestern University Feinberg School of Medicine Chicago, Illinois
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine Northwestern University Feinberg School of Medicine Chicago, Illinois
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12
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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Jovisic M, Mambetsariev N, Singer BD, Morales-Nebreda L. Differential roles of regulatory T cells in acute respiratory infections. J Clin Invest 2023; 133:e170505. [PMID: 37463441 DOI: 10.1172/jci170505] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023] Open
Abstract
Acute respiratory infections trigger an inflammatory immune response with the goal of pathogen clearance; however, overexuberant inflammation causes tissue damage and impairs pulmonary function. CD4+FOXP3+ regulatory T cells (Tregs) interact with cells of both the innate and the adaptive immune system to limit acute pulmonary inflammation and promote its resolution. Tregs also provide tissue protection and coordinate lung tissue repair, facilitating a return to homeostatic pulmonary function. Here, we review Treg-mediated modulation of the host response to respiratory pathogens, focusing on mechanisms underlying how Tregs promote resolution of inflammation and repair of acute lung injury. We also discuss potential strategies to harness and optimize Tregs as a cellular therapy for patients with severe acute respiratory infection and discuss open questions in the field.
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Affiliation(s)
- Milica Jovisic
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
- Simpson Querrey Lung Institute for Translational Science
| | | | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
- Simpson Querrey Lung Institute for Translational Science
- Department of Biochemistry and Molecular Genetics, and
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Luisa Morales-Nebreda
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
- Simpson Querrey Lung Institute for Translational Science
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14
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Pickens CI, Gao CA, Bodner J, Walter JM, Kruser JM, Donnelly HK, Donayre A, Clepp K, Borkowski N, Wunderink RG, Singer BD. An Adjudication Protocol for Severe Pneumonia. Open Forum Infect Dis 2023; 10:ofad336. [PMID: 37520413 PMCID: PMC10372865 DOI: 10.1093/ofid/ofad336] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Background Clinical end points that constitute successful treatment in severe pneumonia are difficult to ascertain and vulnerable to bias. The utility of a protocolized adjudication procedure to determine meaningful end points in severe pneumonia has not been well described. Methods This was a single-center prospective cohort study of patients with severe pneumonia admitted to the medical intensive care unit. The objective was to develop an adjudication protocol for severe bacterial and/or viral pneumonia. Each episode of pneumonia was independently reviewed by 2 pulmonary and critical care physicians. If a discrepancy occurred between the 2 adjudicators, a third adjudicator reviewed the case. If a discrepancy remained after all 3 adjudications, consensus was achieved through committee review. Results Evaluation of 784 pneumonia episodes during 593 hospitalizations achieved only 48.1% interobserver agreement between the first 2 adjudicators and 78.8% when agreement was defined as concordance between 2 of 3 adjudicators. Multiple episodes of pneumonia and presence of bacterial/viral coinfection in the initial pneumonia episode were associated with lower interobserver agreement. For an initial episode of bacterial pneumonia, patients with an adjudicated day 7-8 clinical impression of cure (compared with alternative impressions) were more likely to be discharged alive (odds ratio, 6.3; 95% CI, 3.5-11.6). Conclusions A comprehensive adjudication protocol to identify clinical end points in severe pneumonia resulted in only moderate interobserver agreement. An adjudicated end point of clinical cure by day 7-8 was associated with more favorable hospital discharge dispositions, suggesting that clinical cure by day 7-8 may be a valid end point to use in adjudication protocols.
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Affiliation(s)
- Chiagozie I Pickens
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Catherine A Gao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Justin Bodner
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - James M Walter
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Jacqueline M Kruser
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Helen K Donnelly
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Alvaro Donayre
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Katie Clepp
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Nicole Borkowski
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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15
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Hassler L, Wysocki J, Ahrendsen JT, Ye M, Gelarden I, Nicolaescu V, Tomatsidou A, Gula H, Cianfarini C, Forster P, Khurram N, Singer BD, Randall G, Missiakas D, Henkin J, Batlle D. Intranasal soluble ACE2 improves survival and prevents brain SARS-CoV-2 infection. Life Sci Alliance 2023; 6:e202301969. [PMID: 37041017 PMCID: PMC10098141 DOI: 10.26508/lsa.202301969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/01/2023] [Accepted: 04/04/2023] [Indexed: 04/13/2023] Open
Abstract
A soluble ACE2 protein bioengineered for long duration of action and high affinity to SARS-CoV-2 was administered either intranasally (IN) or intraperitoneally (IP) to SARS-CoV-2-inoculated k18hACE2 mice. This decoy protein (ACE2 618-DDC-ABD) was given either IN or IP, pre- and post-inoculation, or IN, IP, or IN + IP but only post-inoculation. Survival by day 5 was 0% in untreated mice, 40% in the IP-pre, and 90% in the IN-pre group. In the IN-pre group, brain histopathology was essentially normal and lung histopathology significantly improved. Consistent with this, brain SARS-CoV-2 titers were undetectable and lung titers reduced in the IN-pre group. When ACE2 618-DDC-ABD was administered only post-inoculation, survival was 30% in the IN + IP, 20% in the IN, and 20% in the IP group. We conclude that ACE2 618-DDC-ABD results in markedly improved survival and provides organ protection when given intranasally as compared with when given either systemically or after viral inoculation, and that lowering brain titers is a critical determinant of survival and organ protection.
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Affiliation(s)
- Luise Hassler
- Division of Nephrology/Hypertension, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Jan Wysocki
- Division of Nephrology/Hypertension, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Jared T Ahrendsen
- Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Minghao Ye
- Division of Nephrology/Hypertension, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Ian Gelarden
- Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Vlad Nicolaescu
- Department of Microbiology, University of Chicago, Chicago, IL, USA
- Ricketts Regional Biocontainment Laboratory, University of Chicago, Lemont, IL, USA
| | - Anastasia Tomatsidou
- Department of Microbiology, University of Chicago, Chicago, IL, USA
- Ricketts Regional Biocontainment Laboratory, University of Chicago, Lemont, IL, USA
| | - Haley Gula
- Department of Microbiology, University of Chicago, Chicago, IL, USA
- Ricketts Regional Biocontainment Laboratory, University of Chicago, Lemont, IL, USA
| | - Cosimo Cianfarini
- Division of Nephrology/Hypertension, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Peter Forster
- Division of Nephrology/Hypertension, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Nigar Khurram
- Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Glenn Randall
- Department of Microbiology, University of Chicago, Chicago, IL, USA
- Ricketts Regional Biocontainment Laboratory, University of Chicago, Lemont, IL, USA
| | - Dominique Missiakas
- Department of Microbiology, University of Chicago, Chicago, IL, USA
- Ricketts Regional Biocontainment Laboratory, University of Chicago, Lemont, IL, USA
| | - Jack Henkin
- Center for Developmental Therapeutics, Northwestern University, Evanston, IL, USA
| | - Daniel Batlle
- Division of Nephrology/Hypertension, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
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16
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Mikacenic C, Fussner LA, Bell J, Burnham EL, Chlan LL, Cook SK, Dickson RP, Almonor F, Luo F, Madan K, Morales-Nebreda L, Mould KJ, Simpson AJ, Singer BD, Stapleton RD, Wendt CH, Files DC. Research Bronchoscopies in Critically Ill Research Participants: An Official American Thoracic Society Workshop Report. Ann Am Thorac Soc 2023; 20:621-631. [PMID: 37125997 PMCID: PMC10174130 DOI: 10.1513/annalsats.202302-106st] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Bronchoscopy for research purposes is a valuable tool to understand lung-specific biology in human participants. Despite published reports and active research protocols using this procedure in critically ill patients, no recent document encapsulates the important safety considerations and downstream applications of this procedure in this setting. The objectives were to identify safe practices for patient selection and protection of hospital staff, provide recommendations for sample procurement to standardize studies, and give guidance on sample preparation for novel research technologies. Seventeen international experts in the management of critically ill patients, bronchoscopy in clinical and research settings, and experience in patient-oriented clinical or translational research convened for a workshop. Review of relevant literature, expert presentations, and discussion generated the findings presented herein. The committee concludes that research bronchoscopy with bronchoalveolar lavage in critically ill patients on mechanical ventilation is valuable and safe in appropriately selected patients. This report includes recommendations on standardization of this procedure and prioritizes the reporting of sample management to produce more reproducible results between laboratories. This document serves as a resource to the community of researchers who endeavor to include bronchoscopy as part of their research protocols and highlights key considerations for the inclusion and safety of research participants.
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17
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Gao CA, Markov NS, Stoeger T, Pawlowski AE, Kang M, Nannapaneni P, Grant RA, Pickens C, Walter JM, Kruser JM, Rasmussen LV, Schneider D, Starren J, Donnelly HK, Donayre A, Luo Y, Budinger GRS, Wunderink RG, Misharin AV, Singer BD. Machine learning links unresolving secondary pneumonia to mortality in patients with severe pneumonia, including COVID-19. J Clin Invest 2023:170682. [PMID: 37104035 DOI: 10.1172/jci170682] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Despite guidelines promoting the prevention and aggressive treatment of ventilator-associated pneumonia (VAP), the importance of VAP as a driver of outcomes in mechanically ventilated patients, including patients with severe COVID-19, remains unclear. We aimed to determine the contribution of unsuccessful treatment of VAP to mortality in patients with severe pneumonia. METHODS We performed a single-center prospective cohort study of 585 mechanically ventilated patients with severe pneumonia and respiratory failure, 190 of whom had COVID-19, who underwent at least one bronchoalveolar lavage. A panel of ICU physicians adjudicated pneumonia episodes and endpoints based on clinical and microbiologic data. Given the relatively long ICU length of stay among patients with COVID-19, we developed a machine learning approach called CarpeDiem, which groups similar ICU patient-days into clinical states based on electronic health record data. RESULTS CarpeDiem revealed that the long ICU length of stay among patients with COVID-19 is attributable to long stays in clinical states characterized primarily by respiratory failure. While VAP was not associated with mortality overall, mortality was higher in patients with one episode of unsuccessfully treated VAP compared with successfully treated VAP (76.4% versus 17.6%, P < 0.001). In all patients, including those with COVID-19, CarpeDiem demonstrated that unresolving VAP was associated with transitions to clinical states associated with higher mortality. CONCLUSIONS Unsuccessful treatment of VAP is associated with greater mortality. The relatively long length of stay among patients with COVID-19 is primarily due to prolonged respiratory failure, placing them at higher risk of VAP. FUNDING U19AI135964.
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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, United States of America
| | - Nikolay S Markov
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Thomas Stoeger
- Department of Chemical and Biological Engineering, Northwestern University, McCormick School of Engineering, Evanston, United States of America
| | - Anna E Pawlowski
- Northwestern Medicine Enterprise Data Warehouse, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Mengjia Kang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Prasanth Nannapaneni
- Northwestern Medicine Enterprise Data Warehouse, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Rogan A Grant
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Chiagozie Pickens
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - James M Walter
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Jacqueline M Kruser
- Division of Allergy, Pulmonary and Critical Care, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, United States of America
| | - Luke V Rasmussen
- Division of Health and Biomedical Informatics, Department of Preventive Med, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Daniel Schneider
- Northwestern Medicine Enterprise Data Warehouse, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Justin Starren
- Division of Health and Biomedical Informatics, Department of Preventive Med, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Helen K Donnelly
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Alvaro Donayre
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Yuan Luo
- Division of Health and Biomedical Informatics, Department of Preventive Med, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - G R Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, United States of America
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18
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Michki NS, Ndeh R, Helmin KA, Singer BD, McGrath-Morrow SA. DNA methyltransferase inhibition induces dynamic gene expression changes in lung CD4 + T cells of neonatal mice with E. coli pneumonia. Sci Rep 2023; 13:4283. [PMID: 36922640 PMCID: PMC10017701 DOI: 10.1038/s41598-023-31285-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
Bacterial pulmonary infections are a major cause of morbidity and mortality in neonates, with less severity in older children. Previous studies demonstrated that the DNA of CD4+ T cells in the mouse lung, whose primary responsibility is to coordinate the immune response to foreign pathogens, is differentially methylated in neonates compared with juveniles. Nevertheless, the effect of this differential DNA methylation on CD4+ T cell gene expression and response to infection remains unclear. Here we treated E. coli-infected neonatal (4-day-old) and juvenile (13-day-old) mice with decitabine (DAC), a DNA methyltransferase inhibitor with broad-spectrum DNA demethylating activity, and performed simultaneous genome-wide DNA methylation and transcriptional profiling on lung CD4+ T cells. We show that juvenile and neonatal mice experienced differential demethylation in response to DAC treatment, with larger methylation differences observed in neonates. By cross-filtering differentially expressed genes between juveniles and neonates with those sites that were demethylated in neonates, we find that interferon-responsive genes such as Ifit1 are the most down-regulated methylation-sensitive genes in neonatal mice. DAC treatment shifted neonatal lung CD4+ T cells toward a gene expression program similar to that of juveniles. Following lung infection with E. coli, lung CD4+ T cells in neonatal mice exhibit epigenetic repression of important host defense pathways, which are activated by inhibition of DNA methyltransferase activity to resemble a more mature profile.
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Affiliation(s)
- Nigel S Michki
- Children's Hospital of Philadelphia Division of Pulmonary and Sleep Medicine, Philadelphia, PA, 19104, USA.
- Children's Hospital of Philadelphia Division of Cardiology, Philadelphia, PA, 19104, USA.
| | - Roland Ndeh
- Eudowood Division of Pediatric Respiratory Sciences, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Kathryn A Helmin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine Chicago, Chicago, IL, 60611, USA
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine Chicago, Chicago, IL, 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Human Immunobiology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Sharon A McGrath-Morrow
- Children's Hospital of Philadelphia Division of Pulmonary and Sleep Medicine, Philadelphia, PA, 19104, USA
- Eudowood Division of Pediatric Respiratory Sciences, Johns Hopkins University, Baltimore, MD, 21287, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
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19
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Singer BD, Chotirmall SH, Leither LM, Meldrum OW, Joudi AM, Seam N, Brown SM, Çoruh B. Selected Bibliography of Recent Research in COVID-19. Am J Respir Crit Care Med 2022; 206:1548-1562. [PMID: 35442171 PMCID: PMC9757093 DOI: 10.1164/rccm.202202-0277up] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Benjamin D. Singer
- Department of Medicine, Division of Pulmonary and Critical Care Medicine,,Department of Biochemistry and Molecular Genetics,,Canning Thoracic Institute, and,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore;,Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Lindsay M. Leither
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Intermountain Medical Center, Murray, Utah;,Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah
| | - Oliver W. Meldrum
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Anthony M. Joudi
- Department of Medicine, Division of Pulmonary and Critical Care Medicine,,Canning Thoracic Institute, and
| | - Nitin Seam
- Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland; and
| | - Samuel M. Brown
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Intermountain Medical Center, Murray, Utah;,Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah
| | - Başak Çoruh
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington
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20
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Hassler L, Wysocki J, Ahrendsen JT, Ye M, Gelarden I, Nicolaescu V, Tomatsidou A, Gula H, Cianfarini C, Khurram N, Kanwar Y, Singer BD, Randall G, Missiakas D, Henkin J, Batlle D. Superiority of intranasal over systemic administration of bioengineered soluble ACE2 for survival and brain protection against SARS-CoV-2 infection. bioRxiv 2022:2022.12.05.519032. [PMID: 36523403 PMCID: PMC9753780 DOI: 10.1101/2022.12.05.519032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The present study was designed to investigate the effects of a soluble ACE2 protein termed ACE2 618-DDC-ABD, bioengineered to have long duration of action and high binding affinity to SARS-CoV-2, when administered either intranasally (IN) or intraperitoneally (IP) and before or after SARS-CoV-2 inoculation. K18hACE2 mice permissive for SARS-CoV-2 infection were inoculated with 2Ã-10 4 PFU wildtype SARS-CoV-2. In one protocol, ACE2 618-DDC-ABD was given either IN or IP, pre- and post-viral inoculation. In a second protocol, ACE2 618-DDC-ABD was given either IN, IP or IN+IP but only post-viral inoculation. In addition, A549 and Vero E6 cells were used to test neutralization of SARS-CoV-2 variants by ACE2 618-DDC-ABD at different concentrations. Survival by day 5 was 0% in infected untreated mice, and 40% in mice from the ACE2 618-DDC-ABD IP-pre treated group. By contrast, in the IN-pre group survival was 90%, histopathology of brain and kidney was essentially normal and markedly improved in the lungs. When ACE2 618-DDC-ABD was administered only post viral inoculation, survival was 30% in the IN+IP group, 20% in the IN and 0% in the IP group. Brain SARS-CoV-2 titers were high in all groups except for the IN-pre group where titers were undetectable in all mice. In cells permissive for SARS-CoV-2 infection, ACE2 618-DDC-ABD neutralized wildtype SARS-CoV-2 at high concentrations, whereas much lower concentrations neutralized omicron BA. 1. We conclude that ACE2 618-DDC-ABD provides much better survival and organ protection when administered intranasally than when given systemically or after viral inoculation and that lowering brain titers is a critical determinant of survival and organ protection.
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21
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Stoeger T, Grant RA, McQuattie-Pimentel AC, Anekalla KR, Liu SS, Tejedor-Navarro H, Singer BD, Abdala-Valencia H, Schwake M, Tetreault MP, Perlman H, Balch WE, Chandel NS, Ridge KM, Sznajder JI, Morimoto RI, Misharin AV, Budinger GRS, Nunes Amaral LA. Aging is associated with a systemic length-associated transcriptome imbalance. Nat Aging 2022; 2:1191-1206. [PMID: 37118543 PMCID: PMC10154227 DOI: 10.1038/s43587-022-00317-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 10/21/2022] [Indexed: 12/14/2022]
Abstract
Aging is among the most important risk factors for morbidity and mortality. To contribute toward a molecular understanding of aging, we analyzed age-resolved transcriptomic data from multiple studies. Here, we show that transcript length alone explains most transcriptional changes observed with aging in mice and humans. We present three lines of evidence supporting the biological importance of the uncovered transcriptome imbalance. First, in vertebrates the length association primarily displays a lower relative abundance of long transcripts in aging. Second, eight antiaging interventions of the Interventions Testing Program of the National Institute on Aging can counter this length association. Third, we find that in humans and mice the genes with the longest transcripts enrich for genes reported to extend lifespan, whereas those with the shortest transcripts enrich for genes reported to shorten lifespan. Our study opens fundamental questions on aging and the organization of transcriptomes.
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Affiliation(s)
- Thomas Stoeger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL, USA.
- Center for Genetic Medicine, Northwestern University, Evanston, IL, USA.
| | - Rogan A Grant
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
| | | | - Kishore R Anekalla
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
| | - Sophia S Liu
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | | | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University, Evanston, IL, USA
| | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
| | - Michael Schwake
- Department of Neurology, Northwestern University, Evanston, IL, USA
- Faculty of Chemistry, University of Bielefeld, Bielefeld, Germany
| | - Marie-Pier Tetreault
- Division of Gastroenterology and Hepatology, Northwestern University, Evanston, IL, USA
| | - Harris Perlman
- Division of Rheumatology, Northwestern University, Evanston, IL, USA
| | | | - Navdeep S Chandel
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA
| | - Karen M Ridge
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA
| | - Jacob I Sznajder
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA
| | - Richard I Morimoto
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
- Rice Institute for Biomedical Research, Northwestern University, Evanston, IL, USA.
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA.
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA.
| | - G R Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Evanston, IL, USA.
- Simpson Querrey Lung Institute for Translational Science at Northwestern University (SQLIFTSNU), Evanston, IL, USA.
| | - Luis A Nunes Amaral
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL, USA.
- Department of Physics and Astronomy, Northwestern University, Evanston, IL, USA.
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22
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Rahimi RA, Cho JL, Jakubzick CV, Khader SA, Lambrecht BN, Lloyd CM, Molofsky AB, Talbot S, Bonham CA, Drake WP, Sperling AI, Singer BD. Advancing Lung Immunology Research: An Official American Thoracic Society Workshop Report. Am J Respir Cell Mol Biol 2022; 67:e1-18. [PMID: 35776495 PMCID: PMC9273224 DOI: 10.1165/rcmb.2022-0167st] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The mammalian airways and lungs are exposed to a myriad of inhaled particulate matter, allergens, and pathogens. The immune system plays an essential role in protecting the host from respiratory pathogens, but a dysregulated immune response during respiratory infection can impair pathogen clearance and lead to immunopathology. Furthermore, inappropriate immunity to inhaled antigens can lead to pulmonary diseases. A complex network of epithelial, neural, stromal, and immune cells has evolved to sense and respond to inhaled antigens, including the decision to promote tolerance versus a rapid, robust, and targeted immune response. Although there has been great progress in understanding the mechanisms governing immunity to respiratory pathogens and aeroantigens, we are only beginning to develop an integrated understanding of the cellular networks governing tissue immunity within the lungs and how it changes after inflammation and over the human life course. An integrated model of airway and lung immunity will be necessary to improve mucosal vaccine design as well as prevent and treat acute and chronic inflammatory pulmonary diseases. Given the importance of immunology in pulmonary research, the American Thoracic Society convened a working group to highlight central areas of investigation to advance the science of lung immunology and improve human health.
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23
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McElroy GS, Chakrabarty RP, D'Alessandro KB, Hu YS, Vasan K, Tan J, Stoolman JS, Weinberg SE, Steinert EM, Reyfman PA, Singer BD, Ladiges WC, Gao L, Lopéz-Barneo J, Ridge K, Budinger GRS, Chandel NS. Author Correction: Reduced expression of mitochondrial complex I subunit Ndufs2 does not impact healthspan in mice. Sci Rep 2022; 12:8191. [PMID: 35581238 PMCID: PMC9113994 DOI: 10.1038/s41598-022-12069-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Gregory S McElroy
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ram P Chakrabarty
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Karis B D'Alessandro
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yuan-Shih Hu
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Karthik Vasan
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jerica Tan
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Joshua S Stoolman
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Samuel E Weinberg
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Elizabeth M Steinert
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Paul A Reyfman
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Benjamin D Singer
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Warren C Ladiges
- Department of Comparative Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Lin Gao
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío, CSIC, Universidad de Sevilla, Seville, Spain.,Departamento de Fisiología Médica Y Biofísica, Facultad de Medicina, Universidad de Sevilla, Seville, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - José Lopéz-Barneo
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío, CSIC, Universidad de Sevilla, Seville, Spain.,Departamento de Fisiología Médica Y Biofísica, Facultad de Medicina, Universidad de Sevilla, Seville, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Karen Ridge
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - G R Scott Budinger
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Navdeep S Chandel
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. .,Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
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24
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McElroy GS, Chakrabarty RP, D'Alessandro KB, Hu YS, Vasan K, Tan J, Stoolman JS, Weinberg SE, Steinert EM, Reyfman PA, Singer BD, Ladiges WC, Gao L, Lopéz-Barneo J, Ridge K, Budinger GRS, Chandel NS. Reduced expression of mitochondrial complex I subunit Ndufs2 does not impact healthspan in mice. Sci Rep 2022; 12:5196. [PMID: 35338200 PMCID: PMC8956724 DOI: 10.1038/s41598-022-09074-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/16/2022] [Indexed: 01/01/2023] Open
Abstract
Aging in mammals leads to reduction in genes encoding the 45-subunit mitochondrial electron transport chain complex I. It has been hypothesized that normal aging and age-related diseases such as Parkinson’s disease are in part due to modest decrease in expression of mitochondrial complex I subunits. By contrast, diminishing expression of mitochondrial complex I genes in lower organisms increases lifespan. Furthermore, metformin, a putative complex I inhibitor, increases healthspan in mice and humans. In the present study, we investigated whether loss of one allele of Ndufs2, the catalytic subunit of mitochondrial complex I, impacts healthspan and lifespan in mice. Our results indicate that Ndufs2 hemizygous mice (Ndufs2+/−) show no overt impairment in aging-related motor function, learning, tissue histology, organismal metabolism, or sensitivity to metformin in a C57BL6/J background. Despite a significant reduction of Ndufs2 mRNA, the mice do not demonstrate a significant decrease in complex I function. However, there are detectable transcriptomic changes in individual cell types and tissues due to loss of one allele of Ndufs2. Our data indicate that a 50% decline in mRNA of the core mitochondrial complex I subunit Ndufs2 is neither beneficial nor detrimental to healthspan.
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Affiliation(s)
- Gregory S McElroy
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ram P Chakrabarty
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Karis B D'Alessandro
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yuan-Shih Hu
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Karthik Vasan
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jerica Tan
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Joshua S Stoolman
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Samuel E Weinberg
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Elizabeth M Steinert
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Paul A Reyfman
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Benjamin D Singer
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Warren C Ladiges
- Department of Comparative Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Lin Gao
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío, CSIC, Universidad de Sevilla, Seville, Spain.,Departamento de Fisiología Médica y Biofísica, Facultad de Medicina, Universidad de Sevilla, Seville, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - José Lopéz-Barneo
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío, CSIC, Universidad de Sevilla, Seville, Spain.,Departamento de Fisiología Médica y Biofísica, Facultad de Medicina, Universidad de Sevilla, Seville, Spain.,Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Karen Ridge
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - G R Scott Budinger
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Navdeep S Chandel
- Department of Medicine Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. .,Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
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25
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Joudi AM, Reyes Flores CP, Singer BD. Epigenetic Control of Regulatory T Cell Stability and Function: Implications for Translation. Front Immunol 2022; 13:861607. [PMID: 35309306 PMCID: PMC8924620 DOI: 10.3389/fimmu.2022.861607] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/14/2022] [Indexed: 12/13/2022] Open
Abstract
FoxP3+ regulatory T (Treg) cells maintain immune homeostasis, promote self-tolerance, and have an emerging role in resolving acute inflammation, providing tissue protection, and repairing tissue damage. Some data suggest that FoxP3+ T cells are plastic, exhibiting susceptibility to losing their function in inflammatory cytokine-rich microenvironments and paradoxically contributing to inflammatory pathology. As a result, plasticity may represent a barrier to Treg cell immunotherapy. Here, we discuss controversies surrounding Treg cell plasticity and explore determinants of Treg cell stability in inflammatory microenvironments, focusing on epigenetic mechanisms that clinical protocols could leverage to enhance efficacy and limit toxicity of Treg cell-based therapeutics.
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Affiliation(s)
- Anthony M. Joudi
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Canning Thoracic Institute, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Carla P. Reyes Flores
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Canning Thoracic Institute, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Benjamin D. Singer
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Canning Thoracic Institute, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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26
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Weinberg SE, Singer BD. Toward a Paradigm to Distinguish Distinct Functions of FOXP3 + Regulatory T Cells. Immunohorizons 2021; 5:944-952. [PMID: 34893512 DOI: 10.4049/immunohorizons.2100046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 11/22/2021] [Indexed: 12/13/2022] Open
Abstract
FOXP3+ regulatory T (Treg) cells are a unique subset of CD4+ T cells that classically function as master regulators of immune homeostasis. Besides this canonical suppressive role, which is required to maintain self-tolerance, a growing body of literature has identified Treg cells as critical orchestrators of tissue protection during acute stress and as effector cells that drive repair following tissue injury. Despite substantial interest in these distinct roles, the field has struggled to disentangle Treg cell suppressive functions from those that promote tissue defense and repair. In this article, we will examine the literature in the context of specific physiologic settings, contrasting the suppressive function of Treg cells with their emerging roles in promoting tissue homeostasis and tissue repair. Further, we will discuss a new paradigm differentiating tissue defense from tissue repair-a paradigm needed to translate Treg cell-based therapies to the clinic.
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Affiliation(s)
- Samuel E Weinberg
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL.,Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL; .,Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL; and.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL
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27
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Koch CM, Prigge AD, Anekalla KR, Shukla A, Do Umehara HC, Setar L, Chavez J, Abdala-Valencia H, Politanska Y, Markov NS, Hahn GR, Heald-Sargent T, Sanchez-Pinto LN, Muller WJ, Singer BD, Misharin AV, Ridge KM, Coates BM. Age-related Differences in the Nasal Mucosal Immune Response to SARS-CoV-2. Am J Respir Cell Mol Biol 2021; 66:206-222. [PMID: 34731594 PMCID: PMC8845137 DOI: 10.1165/rcmb.2021-0292oc] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected more than 180 million people since the onset of the pandemic. Despite similar viral load and infectivity rates between children and adults, children rarely develop severe illness. Differences in the host response to the virus at the primary infection site are among the mechanisms proposed to account for this disparity. Our objective was to investigate the host response to SARS-CoV-2 in the nasal mucosa in children and adults and compare it with the host response to respiratory syncytial virus (RSV) and influenza virus. We analyzed clinical outcomes and gene expression in the nasal mucosa of 36 children with SARS-CoV-2, 24 children with RSV, 9 children with influenza virus, 16 adults with SARS-CoV-2, and 7 healthy pediatric and 13 healthy adult controls. In both children and adults, infection with SARS-CoV-2 led to an IFN response in the nasal mucosa. The magnitude of the IFN response correlated with the abundance of viral reads, not the severity of illness, and was comparable between children and adults infected with SARS-CoV-2 and children with severe RSV infection. Expression of ACE2 and TMPRSS2 did not correlate with age or presence of viral infection. SARS-CoV-2–infected adults had increased expression of genes involved in neutrophil activation and T-cell receptor signaling pathways compared with SARS-CoV-2–infected children, despite similar severity of illness and viral reads. Age-related differences in the immune response to SARS-CoV-2 may place adults at increased risk of developing severe illness.
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Affiliation(s)
- Clarissa M Koch
- Northwestern University, Medicine , Chicago, Illinois, United States
| | - Andrew D Prigge
- Ann and Robert H Lurie Children's Hospital of Chicago, 2429, Pediatrics, Chicago, Illinois, United States
| | - Kishore R Anekalla
- Northwestern University Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, Chicago, Illinois, United States
| | - Avani Shukla
- Ann and Robert H Lurie Children's Hospital of Chicago, 2429, Chicago, Illinois, United States
| | | | - Leah Setar
- Ann and Robert H Lurie Children's Hospital of Chicago, 2429, Pediatrics, Chicago, Illinois, United States
| | - Jairo Chavez
- Ann and Robert H Lurie Children's Hospital of Chicago, 2429, Chicago, Illinois, United States
| | - Hiam Abdala-Valencia
- Northwestern University Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, Chicago, Illinois, United States
| | - Yuliya Politanska
- Northwestern University, Medicine , Chicago, Illinois, United States
| | - Nikolay S Markov
- Northwestern University, Medicine , Chicago, Illinois, United States
| | - Grant R Hahn
- Ann and Robert H Lurie Children's Hospital of Chicago, 2429, Pediatrics, Chicago, Illinois, United States
| | - Taylor Heald-Sargent
- Ann and Robert H Lurie Children's Hospital of Chicago, 2429, Pediatrics, Chicago, Illinois, United States
| | - L Nelson Sanchez-Pinto
- Ann and Robert H Lurie Children's Hospital of Chicago, 2429, Critical Care Medicine, Chicago, Illinois, United States.,Northwestern University Feinberg School of Medicine, 12244, Pediatrics, Chicago, Illinois, United States
| | - William J Muller
- Ann and Robert H Lurie Children's Hospital of Chicago, 2429, Pediatrics, Chicago, Illinois, United States
| | - Benjamin D Singer
- Northwestern University Feinberg School of Medicine, 12244, Medicine and Biochemistry & Molecular Genetics, Chicago, Illinois, United States
| | - Alexander V Misharin
- Northwestern University, Rheumatology/Medicine, Chicago, Illinois, United States
| | - Karen M Ridge
- Northwestern University, Pulmonary and Critical Care, Chicago, Illinois, United States
| | - Bria M Coates
- Northwestern University, Division of Pulmonary and Critical Care Medicine, Chicago, Illinois, United States;
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28
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Pickens CO, Gao CA, Cuttica MJ, Smith SB, Pesce LL, Grant RA, Kang M, Morales-Nebreda L, Bavishi AA, Arnold JM, Pawlowski A, Qi C, Budinger GRS, Singer BD, Wunderink RG. Bacterial Superinfection Pneumonia in Patients Mechanically Ventilated for COVID-19 Pneumonia. Am J Respir Crit Care Med 2021; 204:921-932. [PMID: 34409924 PMCID: PMC8534629 DOI: 10.1164/rccm.202106-1354oc] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Rationale: Current guidelines recommend patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia receive empirical antibiotics for suspected bacterial superinfection on the basis of weak evidence. Rates of ventilator-associated pneumonia (VAP) in clinical trials of patients with SARS-CoV-2 pneumonia are unexpectedly low. Objectives: We conducted an observational single-center study to determine the prevalence and etiology of bacterial superinfection at the time of initial intubation and the incidence and etiology of subsequent bacterial VAP in patients with severe SARS-CoV-2 pneumonia. Methods: Bronchoscopic BAL fluid samples from all patients with SARS-CoV-2 pneumonia requiring mechanical ventilation were analyzed using quantitative cultures and a multiplex PCR panel. Actual antibiotic use was compared with guideline-recommended therapy. Measurements and Main Results: We analyzed 386 BAL samples from 179 patients with SARS-CoV-2 pneumonia requiring mechanical ventilation. Bacterial superinfection within 48 hours of intubation was detected in 21% of patients. Seventy-two patients (44.4%) developed at least one VAP episode (VAP incidence rate = 45.2/1,000 ventilator days); 15 (20.8%) initial VAPs were caused by difficult-to-treat pathogens. The clinical criteria did not distinguish between patients with or without bacterial superinfection. BAL-based management was associated with significantly reduced antibiotic use compared with guideline recommendations. Conclusions: In patients with SARS-CoV-2 pneumonia requiring mechanical ventilation, bacterial superinfection at the time of intubation occurs in <25% of patients. Guideline-based empirical antibiotic management at the time of intubation results in antibiotic overuse. Bacterial VAP developed in 44% of patients and could not be accurately identified in the absence of microbiologic analysis of BAL fluid.
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Affiliation(s)
| | - Catherine A Gao
- Division of Pulmonary and Critical Care, Department of Medicine
| | | | - Sean B Smith
- Division of Pulmonary and Critical Care, Department of Medicine
| | | | - Rogan A Grant
- Division of Pulmonary and Critical Care, Department of Medicine
| | - Mengjia Kang
- Division of Pulmonary and Critical Care, Department of Medicine
| | | | - Avni A Bavishi
- Division of Pulmonary and Critical Care, Department of Medicine
| | - Jason M Arnold
- Division of Pulmonary and Critical Care, Department of Medicine
| | | | - Chao Qi
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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29
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Zhao Z, Szczepanski AP, Tsuboyama N, Abdala-Valencia H, Goo YA, Singer BD, Bartom ET, Yue F, Wang L. PAX9 Determines Epigenetic State Transition and Cell Fate in Cancer. Cancer Res 2021; 81:4696-4708. [PMID: 34341073 PMCID: PMC8448979 DOI: 10.1158/0008-5472.can-21-1114] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/01/2021] [Accepted: 07/28/2021] [Indexed: 01/07/2023]
Abstract
Abnormalities in genetic and epigenetic modifications can lead to drastic changes in gene expression profiles that are associated with various cancer types. Small cell lung cancer (SCLC) is an aggressive and deadly form of lung cancer with limited effective therapies currently available. By utilizing a genome-wide CRISPR-Cas9 dropout screen in SCLC cells, we identified paired box protein 9 (PAX9) as an essential factor that is overexpressed in human malignant SCLC tumor samples and is transcriptionally driven by the BAP1/ASXL3/BRD4 epigenetic axis. Genome-wide studies revealed that PAX9 occupies distal enhancer elements and represses gene expression by restricting enhancer activity. In multiple SCLC cell lines, genetic depletion of PAX9 led to significant induction of a primed-active enhancer transition, resulting in increased expression of a large number of neural differentiation and tumor-suppressive genes. Mechanistically, PAX9 interacted and cofunctioned with the nucleosome remodeling and deacetylase (NuRD) complex at enhancers to repress nearby gene expression, which was reversed by pharmacologic HDAC inhibition. Overall, this study provides mechanistic insight into the oncogenic function of the PAX9/NuRD complex epigenetic axis in human SCLC and suggests that reactivation of primed enhancers may have potential therapeutic efficacy in treating SCLC expressing high levels of PAX9. SIGNIFICANCE: A genome-wide screen in small cell lung cancer reveals PAX9/NuRD-mediated epigenetic enhancer silencing and tumor progression, supporting the development of novel personalized therapeutic approaches targeting the PAX9-regulated network.
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Affiliation(s)
- Zibo Zhao
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Aileen P. Szczepanski
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Natsumi Tsuboyama
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Young Ah Goo
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Proteomics Center of Excellence, Northwestern University, Evanston, Illinois
| | - Benjamin D. Singer
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Elizabeth T. Bartom
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Lu Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Corresponding Author: Lu Wang, Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611. E-mail:
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30
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Alser M, Rotman J, Deshpande D, Taraszka K, Shi H, Baykal PI, Yang HT, Xue V, Knyazev S, Singer BD, Balliu B, Koslicki D, Skums P, Zelikovsky A, Alkan C, Mutlu O, Mangul S. Technology dictates algorithms: recent developments in read alignment. Genome Biol 2021; 22:249. [PMID: 34446078 PMCID: PMC8390189 DOI: 10.1186/s13059-021-02443-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 07/28/2021] [Indexed: 01/08/2023] Open
Abstract
Aligning sequencing reads onto a reference is an essential step of the majority of genomic analysis pipelines. Computational algorithms for read alignment have evolved in accordance with technological advances, leading to today's diverse array of alignment methods. We provide a systematic survey of algorithmic foundations and methodologies across 107 alignment methods, for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. We discuss how general alignment algorithms have been tailored to the specific needs of various domains in biology.
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Affiliation(s)
- Mohammed Alser
- Computer Science Department, ETH Zürich, 8092, Zürich, Switzerland
- Computer Engineering Department, Bilkent University, 06800 Bilkent, Ankara, Turkey
- Information Technology and Electrical Engineering Department, ETH Zürich, Zürich, 8092, Switzerland
| | - Jeremy Rotman
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Dhrithi Deshpande
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
| | - Kodi Taraszka
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Huwenbo Shi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Pelin Icer Baykal
- Department of Computer Science, Georgia State University, Atlanta, GA, 30302, USA
| | - Harry Taegyun Yang
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Bioinformatics Interdepartmental Ph.D. Program, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Victor Xue
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Sergey Knyazev
- Department of Computer Science, Georgia State University, Atlanta, GA, 30302, USA
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Department of Biochemistry & Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Brunilda Balliu
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - David Koslicki
- Computer Science and Engineering, Pennsylvania State University, University Park, PA, 16801, USA
- Biology Department, Pennsylvania State University, University Park, PA, 16801, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16801, USA
| | - Pavel Skums
- Department of Computer Science, Georgia State University, Atlanta, GA, 30302, USA
| | - Alex Zelikovsky
- Department of Computer Science, Georgia State University, Atlanta, GA, 30302, USA
- The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Can Alkan
- Computer Engineering Department, Bilkent University, 06800 Bilkent, Ankara, Turkey
- Bilkent-Hacettepe Health Sciences and Technologies Program, Ankara, Turkey
| | - Onur Mutlu
- Computer Science Department, ETH Zürich, 8092, Zürich, Switzerland
- Computer Engineering Department, Bilkent University, 06800 Bilkent, Ankara, Turkey
- Information Technology and Electrical Engineering Department, ETH Zürich, Zürich, 8092, Switzerland
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA.
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31
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Abstract
The coronavirus disease 2019 (COVID-19) pandemic is among the most important public health crises of our generation. Despite the promise of prevention offered by effective vaccines, patients with severe COVID-19 will continue to populate hospitals and intensive care units for the foreseeable future. The most common clinical presentation of severe COVID-19 is hypoxemia and respiratory failure, typical of the acute respiratory distress syndrome (ARDS). Whether the clinical features and pathobiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia differ from those of pneumonia secondary to other pathogens is unclear. This uncertainty has created variability in the application of historically proven therapies for ARDS to patients with COVID-19. We review the available literature and find many similarities between patients with ARDS from pneumonia attributable to SARS-CoV-2 versus other respiratory pathogens. A notable exception is the long duration of illness among patients with COVID-19, which could result from its unique pathobiology. Available data support the use of care pathways and therapies proven effective for patients with ARDS, while pointing to unique features that might be therapeutically targeted for patients with severe SARS-CoV-2 pneumonia.
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32
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Affiliation(s)
- Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Lindsay M Leither
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Intermountain Medical Center, Murray, Utah.,Department of Medicine, School of Medicine, University of Utah, Salt Lake City, Utah
| | - Başak Çoruh
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington
| | - Louisa L Y Chan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Anthony M Joudi
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - Samuel M Brown
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Intermountain Medical Center, Murray, Utah.,Department of Medicine, School of Medicine, University of Utah, Salt Lake City, Utah
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine.,Department of Biochemistry and Molecular Genetics, and.,Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois; and
| | - Nitin Seam
- Critical Care Medicine Department, NIH, Bethesda, Maryland
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33
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Villa E, Sahu U, O'Hara BP, Ali ES, Helmin KA, Asara JM, Gao P, Singer BD, Ben-Sahra I. mTORC1 stimulates cell growth through SAM synthesis and m 6A mRNA-dependent control of protein synthesis. Mol Cell 2021; 81:2076-2093.e9. [PMID: 33756106 PMCID: PMC8141029 DOI: 10.1016/j.molcel.2021.03.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 01/21/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022]
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) regulates metabolism and cell growth in response to nutrient, growth, and oncogenic signals. We found that mTORC1 stimulates the synthesis of the major methyl donor, S-adenosylmethionine (SAM), through the control of methionine adenosyltransferase 2 alpha (MAT2A) expression. The transcription factor c-MYC, downstream of mTORC1, directly binds to intron 1 of MAT2A and promotes its expression. Furthermore, mTORC1 increases the protein abundance of Wilms' tumor 1-associating protein (WTAP), the positive regulatory subunit of the human N6-methyladenosine (m6A) RNA methyltransferase complex. Through the control of MAT2A and WTAP levels, mTORC1 signaling stimulates m6A RNA modification to promote protein synthesis and cell growth. A decline in intracellular SAM levels upon MAT2A inhibition decreases m6A RNA modification, protein synthesis rate, and tumor growth. Thus, mTORC1 adjusts m6A RNA modification through the control of SAM and WTAP levels to prime the translation machinery for anabolic cell growth.
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Affiliation(s)
- Elodie Villa
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Umakant Sahu
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Brendan P O'Hara
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Eunus S Ali
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Kathryn A Helmin
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - John M Asara
- Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Peng Gao
- Metabolomics Core Facility, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Benjamin D Singer
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Issam Ben-Sahra
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA.
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34
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Morales-Nebreda L, Helmin KA, Torres Acosta MA, Markov NS, Hu JYS, Joudi AM, Piseaux-Aillon R, Abdala-Valencia H, Politanska Y, Singer BD. Aging imparts cell-autonomous dysfunction to regulatory T cells during recovery from influenza pneumonia. JCI Insight 2021; 6:141690. [PMID: 33600379 PMCID: PMC8026188 DOI: 10.1172/jci.insight.141690] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 02/17/2021] [Indexed: 01/05/2023] Open
Abstract
Regulatory T (Treg) cells orchestrate resolution and repair of acute lung inflammation and injury after viral pneumonia. Compared with younger patients, older individuals experience impaired recovery and worse clinical outcomes after severe viral infections, including influenza and SARS coronavirus 2 (SARS-CoV-2). Whether age is a key determinant of Treg cell prorepair function after lung injury remains unknown. Here, we showed that aging results in a cell-autonomous impairment of reparative Treg cell function after experimental influenza pneumonia. Transcriptional and DNA methylation profiling of sorted Treg cells provided insight into the mechanisms underlying their age-related dysfunction, with Treg cells from aged mice demonstrating both loss of reparative programs and gain of maladaptive programs. Strategies to restore youthful Treg cell functional programs could be leveraged as therapies to improve outcomes among older individuals with severe viral pneumonia.
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MESH Headings
- Age Factors
- Aging/metabolism
- Aging/physiology
- Animals
- COVID-19/complications
- COVID-19/metabolism
- COVID-19/pathology
- COVID-19/virology
- Humans
- Influenza A virus
- Influenza, Human/complications
- Influenza, Human/metabolism
- Influenza, Human/pathology
- Influenza, Human/virology
- Lung/metabolism
- Lung/pathology
- Mice, Inbred C57BL
- Pneumonia, Viral/etiology
- Pneumonia, Viral/metabolism
- Pneumonia, Viral/pathology
- Pneumonia, Viral/virology
- SARS-CoV-2
- T-Lymphocytes, Regulatory/metabolism
- T-Lymphocytes, Regulatory/pathology
- Mice
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Affiliation(s)
| | - Kathryn A. Helmin
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | | | - Nikolay S. Markov
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | | | - Anthony M. Joudi
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | | | | | - Yuliya Politanska
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | - Benjamin D. Singer
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
- Department of Biochemistry and Molecular Genetics, and
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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35
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Helmin KA, Morales-Nebreda L, Torres Acosta MA, Anekalla KR, Chen SY, Abdala-Valencia H, Politanska Y, Cheresh P, Akbarpour M, Steinert EM, Weinberg SE, Singer BD. Maintenance DNA methylation is essential for regulatory T cell development and stability of suppressive function. J Clin Invest 2021; 130:6571-6587. [PMID: 32897881 DOI: 10.1172/jci137712] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 09/02/2020] [Indexed: 12/22/2022] Open
Abstract
Tregs require Foxp3 expression and induction of a specific DNA hypomethylation signature during development, after which Tregs persist as a self-renewing population that regulates immune system activation. Whether maintenance DNA methylation is required for Treg lineage development and stability and how methylation patterns are maintained during lineage self-renewal remain unclear. Here, we demonstrate that the epigenetic regulator ubiquitin-like with plant homeodomain and RING finger domains 1 (Uhrf1) is essential for maintenance of methyl-DNA marks that stabilize Treg cellular identity by repressing effector T cell transcriptional programs. Constitutive and induced deficiency of Uhrf1 within Foxp3+ cells resulted in global yet nonuniform loss of DNA methylation, derepression of inflammatory transcriptional programs, destabilization of the Treg lineage, and spontaneous inflammation. These findings support a paradigm in which maintenance DNA methylation is required in distinct regions of the Treg genome for both lineage establishment and stability of identity and suppressive function.
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Affiliation(s)
- Kathryn A Helmin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | | | | | - Kishore R Anekalla
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - Shang-Yang Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | | | - Yuliya Politanska
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - Paul Cheresh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | | | | | - Samuel E Weinberg
- Division of Pulmonary and Critical Care Medicine, Department of Medicine.,Department of Pathology
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine.,Department of Biochemistry and Molecular Genetics.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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36
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McQuattie-Pimentel AC, Ren Z, Joshi N, Watanabe S, Stoeger T, Chi M, Lu Z, Sichizya L, Aillon RP, Chen CI, Soberanes S, Chen Z, Reyfman PA, Walter JM, Anekalla KR, Davis JM, Helmin KA, Runyan CE, Abdala-Valencia H, Nam K, Meliton AY, Winter DR, Morimoto RI, Mutlu GM, Bharat A, Perlman H, Gottardi CJ, Ridge KM, Chandel NS, Sznajder JI, Balch WE, Singer BD, Misharin AV, Budinger GS. The lung microenvironment shapes a dysfunctional response of alveolar macrophages in aging. J Clin Invest 2021; 131:140299. [PMID: 33586677 PMCID: PMC7919859 DOI: 10.1172/jci140299] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022] Open
Abstract
Alveolar macrophages orchestrate the response to viral infections. Age-related changes in these cells may underlie the differential severity of pneumonia in older patients. We performed an integrated analysis of single-cell RNA-Seq data that revealed homogenous age-related changes in the alveolar macrophage transcriptome in humans and mice. Using genetic lineage tracing with sequential injury, heterochronic adoptive transfer, and parabiosis, we found that the lung microenvironment drove an age-related resistance of alveolar macrophages to proliferation that persisted during influenza A viral infection. Ligand-receptor pair analysis localized these changes to the extracellular matrix, where hyaluronan was increased in aged animals and altered the proliferative response of bone marrow-derived macrophages to granulocyte macrophage colony-stimulating factor (GM-CSF). Our findings suggest that strategies targeting the aging lung microenvironment will be necessary to restore alveolar macrophage function in aging.
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Affiliation(s)
| | - Ziyou Ren
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Nikita Joshi
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Satoshi Watanabe
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Thomas Stoeger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois, USA
| | - Monica Chi
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Ziyan Lu
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Lango Sichizya
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Raul Piseaux Aillon
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Ching-I Chen
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Saul Soberanes
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Zhangying Chen
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Paul A. Reyfman
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - James M. Walter
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Kishore R. Anekalla
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Jennifer M. Davis
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Kathryn A. Helmin
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Constance E. Runyan
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Hiam Abdala-Valencia
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Kiwon Nam
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Angelo Y. Meliton
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Chicago Hospitals, Chicago, Illinois, USA
| | - Deborah R. Winter
- Department of Medicine, Division of Rheumatology, Northwestern University, Chicago, Illinois, USA
| | - Richard I. Morimoto
- Department of Biochemistry and Molecular Genetics, Northwestern University, Evanston, Illinois, USA
| | - Gökhan M. Mutlu
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Chicago Hospitals, Chicago, Illinois, USA
| | - Ankit Bharat
- Department of Surgery, Division of Thoracic Surgery, Northwestern University, Chicago, Illinois, USA
| | - Harris Perlman
- Department of Medicine, Division of Rheumatology, Northwestern University, Chicago, Illinois, USA
| | - Cara J. Gottardi
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Karen M. Ridge
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Navdeep S. Chandel
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - Jacob I. Sznajder
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - William E. Balch
- The Scripps Research Institute Department of Chemical Physiology, La Jolla, California, USA
| | - Benjamin D. Singer
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University, Evanston, Illinois, USA
| | - Alexander V. Misharin
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
| | - G.R. Scott Budinger
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois, USA
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37
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Pickens CO, Gao CA, Cuttica M, Smith SB, Pesce L, Grant R, Kang M, Morales-Nebreda L, Bavishi AA, Arnold J, Pawlowski A, Qi C, Budinger GS, Singer BD, Wunderink RG. Bacterial superinfection pneumonia in SARS-CoV-2 respiratory failure. medRxiv 2021. [PMID: 33469593 DOI: 10.1101/2021.01.12.20248588] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Background Severe community-acquired pneumonia secondary to SARS-CoV-2 is a leading cause of death. Current guidelines recommend patients with SARS-CoV-2 pneumonia receive empirical antibiotic therapy for suspected bacterial superinfection, but little evidence supports these recommendations. Methods We obtained bronchoscopic bronchoalveolar lavage (BAL) samples from patients with SARS-CoV-2 pneumonia requiring mechanical ventilation. We analyzed BAL samples with multiplex PCR and quantitative culture to determine the prevalence of superinfecting pathogens at the time of intubation and identify episodes of ventilator-associated pneumonia (VAP) over the course of mechanical ventilation. We compared antibiotic use with guideline-recommended care. Results The 179 ventilated patients with severe SARS-CoV-2 pneumonia discharged from our hospital by June 30, 2020 were analyzed. 162 (90.5%) patients had at least one BAL procedure; 133 (74.3%) within 48 hours after intubation and 112 (62.6%) had at least one subsequent BAL during their hospitalization. A superinfecting pathogen was identified within 48 hours of intubation in 28/133 (21%) patients, most commonly methicillin-sensitive Staphylococcus aureus or Streptococcus species (21/28, 75%). BAL-based treatment reduced antibiotic use compared with guideline-recommended care. 72 patients (44.4%) developed at least one VAP episode. Only 15/72 (20.8%) of initial VAPs were attributable to multidrug-resistant pathogens. The incidence rate of VAP was 45.2/1000 ventilator days. Conclusions With use of sensitive diagnostic tools, bacterial superinfection at the time of intubation is infrequent in patients with severe SARS-CoV-2 pneumonia. Treatment based on current guidelines would result in substantial antibiotic overuse. The incidence rate of VAP in ventilated patients with SARS-CoV-2 pneumonia are higher than historically reported.
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38
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Abstract
Respiratory infections from influenza A virus (IAV) cause substantial morbidity and mortality in children relative to adults. T cells play a critical role in the host response to IAV by supporting the innate and humoral responses, mediating cytotoxic activity, and promoting recovery. There are age-dependent differences in the number, subsets, and localization of T cells, which impact the host response to pathogens. In this article, we first review how T cells recognize IAV and examine differences in the resting T-cell populations between juveniles and adults. Next, we describe how the juvenile CD4+, CD8+, and regulatory T-cell responses compare with those in adults and discuss the potential physiologic and clinical consequences of the differences. Finally, we explore the roles of two unconventional T-cell types in the juvenile response to influenza, natural-killer T cells and γδ T cells. A clear understanding of age-dependent differences in the T-cell response is essential to developing therapies to prevent or reverse the deleterious effects of IAV in children.
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Affiliation(s)
- Andrew D Prigge
- Division of Critical Care Medicine, Department of Pediatrics.,Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Ruihua Ma
- Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - Bria M Coates
- Division of Critical Care Medicine, Department of Pediatrics.,Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine.,Department of Biochemistry and Molecular Genetics.,Simpson Querrey Center for Epigenetics, and
| | - Karen M Ridge
- Division of Pulmonary and Critical Care Medicine, Department of Medicine.,Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Northwestern University, Chicago, Illinois; and
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Torres Acosta MA, Singer BD. Pathogenesis of COVID-19-induced ARDS: implications for an ageing population. Eur Respir J 2020; 56:13993003.02049-2020. [PMID: 32747391 PMCID: PMC7397945 DOI: 10.1183/13993003.02049-2020] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/23/2020] [Indexed: 01/08/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has elicited a swift response by the scientific community to elucidate the pathogenesis of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2)-induced lung injury and develop effective therapeutics. Clinical data indicate that severe COVID-19 most commonly manifests as viral pneumonia-induced acute respiratory distress syndrome (ARDS), a clinical entity mechanistically understood best in the context of influenza A virus-induced pneumonia. Similar to influenza, advanced age has emerged as the leading host risk factor for developing severe COVID-19. In this review we connect the current understanding of the SARS-CoV-2 replication cycle and host response to the clinical presentation of COVID-19, borrowing concepts from influenza A virus-induced ARDS pathogenesis and discussing how these ideas inform our evolving understanding of COVID-19-induced ARDS. We also consider important differences between COVID-19 and influenza, mainly the protean clinical presentation and associated lymphopenia of COVID-19, the contrasting role of interferon-γ in mediating the host immune response to these viruses, and the tropism for vascular endothelial cells of SARS-CoV-2, commenting on the potential limitations of influenza as a model for COVID-19. Finally, we explore hallmarks of ageing that could explain the association between advanced age and susceptibility to severe COVID-19. Review of viral ARDS pathogenesis, how it informs evolving models of COVID-19, and how hallmarks of ageing explain the age-related morbidity and mortality of severe COVID-19https://bit.ly/39Ca0c0
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Affiliation(s)
- Manuel A Torres Acosta
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA .,Dept of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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40
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Fang C, Wang Z, Han C, Safgren SL, Helmin KA, Adelman ER, Serafin V, Basso G, Eagen KP, Gaspar-Maia A, Figueroa ME, Singer BD, Ratan A, Ntziachristos P, Zang C. Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation. Genome Biol 2020; 21:247. [PMID: 32933554 PMCID: PMC7493976 DOI: 10.1186/s13059-020-02152-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The three-dimensional genome organization is critical for gene regulation and can malfunction in diseases like cancer. As a key regulator of genome organization, CCCTC-binding factor (CTCF) has been characterized as a DNA-binding protein with important functions in maintaining the topological structure of chromatin and inducing DNA looping. Among the prolific binding sites in the genome, several events with altered CTCF occupancy have been reported as associated with effects in physiology or disease. However, hitherto there is no comprehensive survey of genome-wide CTCF binding patterns across different human cancers. RESULTS To dissect functions of CTCF binding, we systematically analyze over 700 CTCF ChIP-seq profiles across human tissues and cancers and identify cancer-specific CTCF binding patterns in six cancer types. We show that cancer-specific lost and gained CTCF binding events are associated with altered chromatin interactions, partially with DNA methylation changes, and rarely with sequence mutations. While lost bindings primarily occur near gene promoters, most gained CTCF binding events exhibit enhancer activities and are induced by oncogenic transcription factors. We validate these findings in T cell acute lymphoblastic leukemia cell lines and patient samples and show that oncogenic NOTCH1 induces specific CTCF binding and they cooperatively activate expression of target genes, indicating transcriptional condensation phenomena. CONCLUSIONS Specific CTCF binding events occur in human cancers. Cancer-specific CTCF binding can be induced by other transcription factors to regulate oncogenic gene expression. Our results substantiate CTCF binding alteration as a functional epigenomic signature of cancer.
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Affiliation(s)
- Celestia Fang
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Zhenjia Wang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Cuijuan Han
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Stephanie L Safgren
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kathryn A Helmin
- Department of Medicine, Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Emmalee R Adelman
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Valentina Serafin
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Giuseppe Basso
- Oncohematology Laboratory, Department of Women's and Children's Health, University of Padova, Padova, Italy
- Italian Institute for Genomic Medicine, 10060, Torino, Italy
| | - Kyle P Eagen
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alexandre Gaspar-Maia
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Maria E Figueroa
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Benjamin D Singer
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Medicine, Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
- UVA Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA.
- Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
| | - Chongzhi Zang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA.
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA.
- UVA Cancer Center, University of Virginia, Charlottesville, VA, USA.
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41
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Grant RA, Morales-Nebreda L, Markov NS, Swaminathan S, Guzman ER, Abbott DA, Donnelly HK, Donayre A, Goldberg IA, Klug ZM, Borkowski N, Lu Z, Kihshen H, Politanska Y, Sichizya L, Kang M, Shilatifard A, Qi C, Argento AC, Kruser JM, Malsin ES, Pickens CO, Smith S, Walter JM, Pawlowski AE, Schneider D, Nannapaneni P, Abdala-Valencia H, Bharat A, Gottardi CJ, Budinger GRS, Misharin AV, Singer BD, Wunderink RG. Alveolitis in severe SARS-CoV-2 pneumonia is driven by self-sustaining circuits between infected alveolar macrophages and T cells. bioRxiv 2020:2020.08.05.238188. [PMID: 34013276 PMCID: PMC8132268 DOI: 10.1101/2020.08.05.238188] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Some patients infected with Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) develop severe pneumonia and the acute respiratory distress syndrome (ARDS) [1]. Distinct clinical features in these patients have led to speculation that the immune response to virus in the SARS-CoV-2-infected alveolus differs from other types of pneumonia [2]. We collected bronchoalveolar lavage fluid samples from 86 patients with SARS-CoV-2-induced respiratory failure and 252 patients with known or suspected pneumonia from other pathogens and subjected them to flow cytometry and bulk transcriptomic profiling. We performed single cell RNA-Seq in 5 bronchoalveolar lavage fluid samples collected from patients with severe COVID-19 within 48 hours of intubation. In the majority of patients with SARS-CoV-2 infection at the onset of mechanical ventilation, the alveolar space is persistently enriched in alveolar macrophages and T cells without neutrophilia. Bulk and single cell transcriptomic profiling suggest SARS-CoV-2 infects alveolar macrophages that respond by recruiting T cells. These T cells release interferon-gamma to induce inflammatory cytokine release from alveolar macrophages and further promote T cell recruitment. Our results suggest SARS-CoV-2 causes a slowly unfolding, spatially-limited alveolitis in which alveolar macrophages harboring SARS-CoV-2 transcripts and T cells form a positive feedback loop that drives progressive alveolar inflammation. This manuscript is accompanied by an online resource: https://www.nupulmonary.org/covid-19/. ONE SENTENCE SUMMARY SARS-CoV-2-infected alveolar macrophages form positive feedback loops with T cells in patients with severe COVID-19.
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42
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Affiliation(s)
| | - Manu Jain
- Northwestern University Feinberg School of MedicineChicago, Illinois
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43
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Affiliation(s)
- Benjamin D Singer
- Division of Pulmonary and Critical Care, Department of Medicine, Department of Biochemistry and Molecular Genetics, Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Simpson Querrey, 5th Floor, Chicago, IL 60611, USA.
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McGrath-Morrow SA, Ndeh R, Helmin KA, Khuder B, Rothblum-Oviatt C, Collaco JM, Wright J, Reyfman PA, Lederman HM, Singer BD. DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype. Sci Rep 2020; 10:7479. [PMID: 32366930 PMCID: PMC7198504 DOI: 10.1038/s41598-020-64514-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/13/2020] [Indexed: 12/19/2022] Open
Abstract
People with ataxia-telangiectasia (A-T) display phenotypic variability with regard to progression of immunodeficiency, sino-pulmonary disease, and neurologic decline. To determine the association between differential gene expression, epigenetic state, and phenotypic variation among people with A-T, we performed transcriptional and genome-wide DNA methylation profiling in patients with mild and classic A-T progression as well as healthy controls. RNA and genomic DNA were isolated from peripheral blood mononuclear cells for transcriptional and DNA methylation profiling with RNA-sequencing and modified reduced representation bisulfite sequencing, respectively. We identified 555 genes that were differentially expressed among the control, mild A-T, and classic A-T groups. Genome-wide DNA methylation profiling revealed differential promoter methylation in cis with 146 of these differentially expressed genes. Functional enrichment analysis identified significant enrichment in immune, growth, and apoptotic pathways among the methylation-regulated genes. Regardless of clinical phenotype, all A-T participants exhibited downregulation of critical genes involved in B cell function (PAX5, CD79A, CD22, and FCRL1) and upregulation of several genes associated with senescence and malignancy, including SERPINE1. These findings indicate that gene expression differences may be associated with phenotypic variability and suggest that DNA methylation regulates expression of critical immune response genes in people with A-T.
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Affiliation(s)
- Sharon A McGrath-Morrow
- Eudowood Division of Pediatric Respiratory Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| | - Roland Ndeh
- Eudowood Division of Pediatric Respiratory Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kathryn A Helmin
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Basil Khuder
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Joseph M Collaco
- Eudowood Division of Pediatric Respiratory Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jennifer Wright
- Eudowood Division of Pediatric, Allergy and Immunology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Paul A Reyfman
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Howard M Lederman
- Eudowood Division of Pediatric, Allergy and Immunology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, 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 Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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45
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Abstract
DNA methylation represents a fundamental epigenetic mark that is associated with transcriptional repression during development, maintenance of homeostasis, and disease. In addition to methylation-sensitive PCR and targeted deep-amplicon bisulfite sequencing to measure DNA methylation at defined genomic loci, numerous unsupervised techniques exist to quantify DNA methylation on a genome-wide scale, including affinity enrichment strategies and methods involving bisulfite conversion. Both affinity-enriched and bisulfite-converted DNA can serve as input material for array hybridization or sequencing using next-generation technologies. In this practical guide to the measurement and analysis of DNA methylation, the goal is to convey basic concepts in DNA methylation biology and explore genome-scale bisulfite sequencing as the current gold standard for assessment of DNA methylation. Bisulfite conversion chemistry and library preparation are discussed in addition to a bioinformatics approach to quality assessment, trimming, alignment, and methylation calling of individual cytosine residues. Bisulfite-converted DNA presents challenges for standard next-generation sequencing library preparation protocols and data-processing pipelines, but these challenges can be met with elegant solutions that leverage the power of high-performance computing systems. Quantification of DNA methylation, data visualization, statistical approaches to compare DNA methylation between sample groups, and examples of integrating DNA methylation data with other -omics data sets are also discussed. The reader is encouraged to use this article as a foundation to pursue advanced topics in DNA methylation measurement and data analysis, particularly the application of bioinformatics and computational biology principles to generate a deeper understanding of mechanisms linking DNA methylation to cellular function.
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Affiliation(s)
- Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Department of Biochemistry and Molecular Genetics, and Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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46
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Abstract
Tregs require specific epigenetic signatures to induce and maintain their suppressive function in the context of inflammation and cancer surveillance. In this issue of the JCI, Xiong and colleagues identify a critical role for the epigenetic repressor REST corepressor 1 (CoREST) in promoting Treg suppressive transcriptional and functional programs. Pharmacologic inhibition and genetic loss of CoREST in Tregs impaired organ allograft tolerance and unleashed antitumor immunity via epigenetic activation of effector T cell programs. We propose that exploiting epigenetic control mechanisms will further the translation of Treg-based therapeutics to target inflammatory and malignant disorders.
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Affiliation(s)
| | | | - Benjamin D. Singer
- Division of Pulmonary and Critical Care Medicine
- Department of Biochemistry and Molecular Genetics, and
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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47
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Affiliation(s)
- Benjamin D Singer
- Corresponding Author: Benjamin D. Singer, MD; E-mail: ; Telephone: 312-503-4494
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48
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Abstract
Invasive mechanical ventilation is a potentially lifesaving intervention for acutely ill patients. The goal of this review is to provide a concise, clinically focused overview of basic invasive mechanical ventilation for the many clinicians who care for mechanically ventilated patients. Attention is given to how common ventilator modes differ in delivering a mechanical breath, evaluation of respiratory system mechanics, how to approach acute changes in airway pressure, and the diagnosis of auto-positive end-expiratory pressure. Waveform interpretation is emphasized throughout the review.
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Affiliation(s)
- James M Walter
- From the Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Thomas C Corbridge
- From the Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Benjamin D Singer
- From the Department of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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Tighe RM, Redente EF, Yu YR, Herold S, Sperling AI, Curtis JL, Duggan R, Swaminathan S, Nakano H, Zacharias WJ, Janssen WJ, Freeman CM, Brinkman RR, Singer BD, Jakubzick CV, Misharin AV. Improving the Quality and Reproducibility of Flow Cytometry in the Lung. An Official American Thoracic Society Workshop Report. Am J Respir Cell Mol Biol 2019; 61:150-161. [PMID: 31368812 PMCID: PMC6670040 DOI: 10.1165/rcmb.2019-0191st] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Defining responses of the structural and immune cells in biologic systems is critically important to understanding disease states and responses to injury. This requires accurate and sensitive methods to define cell types in organ systems. The principal method to delineate the cell populations involved in these processes is flow cytometry. Although researchers increasingly use flow cytometry, technical challenges can affect its accuracy and reproducibility, thus significantly limiting scientific advancements. This challenge is particularly critical to lung immunology, as the lung is readily accessible and therefore used in preclinical and clinical studies to define potential therapeutics. Given the importance of flow cytometry in pulmonary research, the American Thoracic Society convened a working group to highlight issues and technical challenges to the performance of high-quality pulmonary flow cytometry, with a goal of improving its quality and reproducibility.
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Piunti A, Smith ER, Morgan MAJ, Ugarenko M, Khaltyan N, Helmin KA, Ryan CA, Murray DC, Rickels RA, Yilmaz BD, Rendleman EJ, Savas JN, Singer BD, Bulun SE, Shilatifard A. CATACOMB: An endogenous inducible gene that antagonizes H3K27 methylation activity of Polycomb repressive complex 2 via an H3K27M-like mechanism. Sci Adv 2019; 5:eaax2887. [PMID: 31281901 PMCID: PMC6609211 DOI: 10.1126/sciadv.aax2887] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 05/28/2019] [Indexed: 05/16/2023]
Abstract
Using biochemical characterization of fusion proteins associated with endometrial stromal sarcoma, we identified JAZF1 as a new subunit of the NuA4 acetyltransferase complex and CXORF67 as a subunit of the Polycomb Repressive Complex 2 (PRC2). Since CXORF67's interaction with PRC2 leads to decreased PRC2-dependent H3K27me2/3 deposition, we propose a new name for this gene: CATACOMB (catalytic antagonist of Polycomb; official gene name: EZHIP ). We map CATACOMB's inhibitory function to a short highly conserved region and identify a single methionine residue essential for diminution of H3K27me2/3 levels. Remarkably, the amino acid sequence surrounding this critical methionine resembles the oncogenic histone H3 Lys27-to-methionine (H3K27M) mutation found in high-grade pediatric gliomas. As CATACOMB expression is regulated through DNA methylation/demethylation, we propose CATACOMB as the potential interlocutor between DNA methylation and PRC2 activity. We raise the possibility that similar regulatory mechanisms could exist for other methyltransferase complexes such as Trithorax/COMPASS.
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Affiliation(s)
- Andrea Piunti
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Edwin R. Smith
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Marc A. J. Morgan
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Michal Ugarenko
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Natalia Khaltyan
- Department of Neurology, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Kathryn A. Helmin
- Division of Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Caila A. Ryan
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - David C. Murray
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Ryan A. Rickels
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Bahar D. Yilmaz
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Emily J. Rendleman
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Jeffrey N. Savas
- Department of Neurology, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Benjamin D. Singer
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
- Division of Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Serdar E. Bulun
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
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