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Burnham KL, Milind N, Lee W, Kwok AJ, Cano-Gamez K, Mi Y, Geoghegan CG, Zhang P, McKechnie S, Soranzo N, Hinds CJ, Knight JC, Davenport EE. eQTLs identify regulatory networks and drivers of variation in the individual response to sepsis. CELL GENOMICS 2024:100587. [PMID: 38897207 DOI: 10.1016/j.xgen.2024.100587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/27/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024]
Abstract
Sepsis is a clinical syndrome of life-threatening organ dysfunction caused by a dysregulated response to infection, for which disease heterogeneity is a major obstacle to developing targeted treatments. We have previously identified gene-expression-based patient subgroups (sepsis response signatures [SRS]) informative for outcome and underlying pathophysiology. Here, we aimed to investigate the role of genetic variation in determining the host transcriptomic response and to delineate regulatory networks underlying SRS. Using genotyping and RNA-sequencing data on 638 adult sepsis patients, we report 16,049 independent expression (eQTLs) and 32 co-expression module (modQTLs) quantitative trait loci in this disease context. We identified significant interactions between SRS and genotype for 1,578 SNP-gene pairs and combined transcription factor (TF) binding site information (SNP2TFBS) and predicted regulon activity (DoRothEA) to identify candidate upstream regulators. Overall, these approaches identified putative mechanistic links between host genetic variation, cell subtypes, and the individual transcriptomic response to infection.
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Affiliation(s)
- Katie L Burnham
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Nikhil Milind
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; University of Cambridge, Cambridge, UK
| | - Wanseon Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Andrew J Kwok
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Kiki Cano-Gamez
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yuxin Mi
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Ping Zhang
- Centre for Human Genetics, University of Oxford, Oxford, UK; Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK
| | | | - Nicole Soranzo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Charles J Hinds
- Centre for Translational Medicine & Therapeutics, William Harvey Research Institute, Faculty of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Julian C Knight
- Centre for Human Genetics, University of Oxford, Oxford, UK; Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, UK.
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Mathew AM, Huber A, Sous RD, Weghorn KN, Powers-Fletcher MV, Jose S, Madan R. Effect of Leptin Receptor Q223R Polymorphism on Clostridioides difficile Infection-Induced Macrophage Migration Inhibitory Factor Production. J Infect Dis 2024:jiae141. [PMID: 38687212 DOI: 10.1093/infdis/jiae141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/18/2024] [Indexed: 05/02/2024] Open
Abstract
Proinflammatory cytokine levels and host genetic makeup are key determinants of Clostridioides difficile infection (CDI) outcomes. We previously reported that blocking the inflammatory cytokine macrophage migration inhibitory factor (MIF) ameliorates CDI. Here, we determined kinetics of MIF production and its association with a common genetic variant in leptin receptor (LEPR) using blood from patients with CDI. We found highest plasma MIF early after C difficile exposure and in individuals who express mutant/derived LEPR. Our data suggest that early-phase CDI provides a possible window of opportunity in which MIF targeting, potentially in combination with LEPR genotype, could have therapeutic utility.
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Affiliation(s)
- Ann M Mathew
- Division of Infectious Diseases, University of Cincinnati College of Medicine
- Pathobiology and Molecular Medicine, Department of Internal Medicine, University of Cincinnati College of Medicine
| | - Alexander Huber
- Division of Infectious Diseases, University of Cincinnati College of Medicine
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center
| | - Rowis D Sous
- Division of Infectious Diseases, University of Cincinnati College of Medicine
| | - Kristin N Weghorn
- Division of Infectious Diseases, University of Cincinnati College of Medicine
| | - Margaret V Powers-Fletcher
- Division of Infectious Diseases, University of Cincinnati College of Medicine
- Pathobiology and Molecular Medicine, Department of Internal Medicine, University of Cincinnati College of Medicine
| | - Shinsmon Jose
- Division of Infectious Diseases, University of Cincinnati College of Medicine
| | - Rajat Madan
- Division of Infectious Diseases, University of Cincinnati College of Medicine
- Pathobiology and Molecular Medicine, Department of Internal Medicine, University of Cincinnati College of Medicine
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center
- Veterans Affairs Medical Center Cincinnati, Cincinnati, Ohio
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3
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Cavallazzi R, Ramirez JA. Definition, Epidemiology, and Pathogenesis of Severe Community-Acquired Pneumonia. Semin Respir Crit Care Med 2024; 45:143-157. [PMID: 38330995 DOI: 10.1055/s-0044-1779016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
The clinical presentation of community-acquired pneumonia (CAP) can vary widely among patients. While many individuals with mild symptoms can be managed as outpatients with excellent outcomes, there is a distinct subgroup of patients who present with severe CAP. In these cases, the mortality rate can reach approximately 25% within 30 days and even up to 50% within a year. It is crucial to focus attention on these patients who are at higher risk. Among the various definitions of severe CAP found in the literature, one commonly used criterion is the requirement for admission to intensive care unit. Notable epidemiological characteristics of these patients include the impact of acute cardiovascular diseases on clinical outcomes and the enduring, independent effect of pneumonia on long-term outcomes. Factors such as pathogen virulence, the presence of comorbidities, and the host response are important contributors to the pathogenesis of severe CAP. In these patients, the host response may be dysregulated and compartmentalized. Gaining a better understanding of the epidemiology and pathogenesis of severe CAP will provide a foundation for the development of new therapies for this condition. This manuscript aims to review the definition, epidemiology, and pathogenesis of severe CAP, shedding light on important aspects that can aid in the improvement of patient care and outcomes.
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Affiliation(s)
- Rodrigo Cavallazzi
- Division of Pulmonary, Critical Care Medicine, and Sleep Disorders, University of Louisville, Louisville, Kentucky
| | - Julio A Ramirez
- Norton Infectious Diseases Institute, Norton Healthcare, Louisville, Kentucky
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Jabandziev P, Hubacek JA, Michalek J, Jouza M, Papez J, Pecl J, Slaba K, Slaby O, Urik M, Aulicka S, Kunovsky L, Michalek J, Dominik P, Kratochvil M, Klucka J, Stourac P. A Tagging Polymorphism in Fat Mass and Obesity-Associated ( FTO) Gene Is Associated with Sepsis Status in Children. ROMANIAN JOURNAL OF INTERNAL MEDICINE = REVUE ROUMAINE DE MEDECINE INTERNE 2024; 0:rjim-2024-0008. [PMID: 38470396 DOI: 10.2478/rjim-2024-0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Indexed: 03/13/2024]
Abstract
INTRODUCTION Sepsis is one of the most common causes of death in patients admitted to intensive care units (ICUs). The development of sepsis is significantly influenced by genetic predisposition. In this study, we highlight a potential association between a variant of the fat mass and obesity-associated (FTO) gene and risk of sepsis in children and adolescents. METHODS We investigated a first-intron tagging FTO polymorphism (rs17817449) by comparing a severe condition (SC) group, comprising 598 paediatric patients (ages 0-19 years) admitted to an ICU with fever, systemic inflammatory response syndrome (SIRS), sepsis, severe sepsis, septic shock, or multiple organ dysfunction syndrome (MODS), with a control group consisting of 616 healthy young adults. RESULTS We observed a lower prevalence (p < 0.01; OR = 0.59, 95% CI = 0.39-0.87) of the FTO TT genotype in febrile and SIRS patients compared to patients with severe illness. There was a borderline trend towards a lower prevalence of the FTO TT genotype in the control group compared to the SC group (p < 0.09, OR = 0.81, 95% CI = 0.62-1.06). CONCLUSIONS Our findings suggest that rs17817449, a common FTO polymorphism, may be a predictor of sepsis in paediatric patients, and that higher body weight is protective against this clinical complication.
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Affiliation(s)
- Petr Jabandziev
- 1Department of Pediatrics, University Hospital Brno, Černopolní 212/9, 625 00, Brno, Czech Republic
- 2Faculty of Medicine, Masaryk University, Černopolní 212/9, 625 00, Brno, Czech Republic
- 3Central European Institute of Technology, Žerotínovo nám. 617/9, 601 77, Brno, Czech Republic
| | - Jaroslav Alois Hubacek
- 4Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, Vídeňská 1958/9, 140 21, Prague, Czech Republic
- 5Third Department of Internal Medicine, First Faculty of Medicine, Charles University, U Nemocnice 1, 121 08, Prague, Czech Republic
| | - Jaroslav Michalek
- 6Department of Quantitative Methods, University of Defence, Kounicova 156/65, 662 10, Brno, Czech Republic
| | - Martin Jouza
- 1Department of Pediatrics, University Hospital Brno, Černopolní 212/9, 625 00, Brno, Czech Republic
- 2Faculty of Medicine, Masaryk University, Černopolní 212/9, 625 00, Brno, Czech Republic
| | - Jan Papez
- 1Department of Pediatrics, University Hospital Brno, Černopolní 212/9, 625 00, Brno, Czech Republic
- 2Faculty of Medicine, Masaryk University, Černopolní 212/9, 625 00, Brno, Czech Republic
| | - Jakub Pecl
- 1Department of Pediatrics, University Hospital Brno, Černopolní 212/9, 625 00, Brno, Czech Republic
- 2Faculty of Medicine, Masaryk University, Černopolní 212/9, 625 00, Brno, Czech Republic
| | - Katerina Slaba
- 1Department of Pediatrics, University Hospital Brno, Černopolní 212/9, 625 00, Brno, Czech Republic
- 2Faculty of Medicine, Masaryk University, Černopolní 212/9, 625 00, Brno, Czech Republic
| | - Ondrej Slaby
- 2Faculty of Medicine, Masaryk University, Černopolní 212/9, 625 00, Brno, Czech Republic
- 3Central European Institute of Technology, Žerotínovo nám. 617/9, 601 77, Brno, Czech Republic
| | - Milan Urik
- 2Faculty of Medicine, Masaryk University, Černopolní 212/9, 625 00, Brno, Czech Republic
| | - Stefania Aulicka
- 2Faculty of Medicine, Masaryk University, Černopolní 212/9, 625 00, Brno, Czech Republic
| | - Lumir Kunovsky
- 7Department of Gastroenterology and Internal Medicine, University Hospital Brno, Jihlavská 340, 625 00, Brno, Czech Republic
- 8Department of Surgery, University Hospital Brno, Jihlavská 340, 625 00, Brno, Czech Republic
| | | | - Petr Dominik
- 2Faculty of Medicine, Masaryk University, Černopolní 212/9, 625 00, Brno, Czech Republic
- 10Department of Pediatric Anesthesiology and Intensive Care Medicine, University Hospital Brno, Kamenice 5, 625 00, Brno, Czech Republic
| | - Milan Kratochvil
- 2Faculty of Medicine, Masaryk University, Černopolní 212/9, 625 00, Brno, Czech Republic
- 10Department of Pediatric Anesthesiology and Intensive Care Medicine, University Hospital Brno, Kamenice 5, 625 00, Brno, Czech Republic
| | - Jozef Klucka
- 2Faculty of Medicine, Masaryk University, Černopolní 212/9, 625 00, Brno, Czech Republic
- 10Department of Pediatric Anesthesiology and Intensive Care Medicine, University Hospital Brno, Kamenice 5, 625 00, Brno, Czech Republic
| | - Petr Stourac
- 2Faculty of Medicine, Masaryk University, Černopolní 212/9, 625 00, Brno, Czech Republic
- 10Department of Pediatric Anesthesiology and Intensive Care Medicine, University Hospital Brno, Kamenice 5, 625 00, Brno, Czech Republic
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Santacroce E, D'Angerio M, Ciobanu AL, Masini L, Lo Tartaro D, Coloretti I, Busani S, Rubio I, Meschiari M, Franceschini E, Mussini C, Girardis M, Gibellini L, Cossarizza A, De Biasi S. Advances and Challenges in Sepsis Management: Modern Tools and Future Directions. Cells 2024; 13:439. [PMID: 38474403 DOI: 10.3390/cells13050439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Sepsis, a critical condition marked by systemic inflammation, profoundly impacts both innate and adaptive immunity, often resulting in lymphopenia. This immune alteration can spare regulatory T cells (Tregs) but significantly affects other lymphocyte subsets, leading to diminished effector functions, altered cytokine profiles, and metabolic changes. The complexity of sepsis stems not only from its pathophysiology but also from the heterogeneity of patient responses, posing significant challenges in developing universally effective therapies. This review emphasizes the importance of phenotyping in sepsis to enhance patient-specific diagnostic and therapeutic strategies. Phenotyping immune cells, which categorizes patients based on clinical and immunological characteristics, is pivotal for tailoring treatment approaches. Flow cytometry emerges as a crucial tool in this endeavor, offering rapid, low cost and detailed analysis of immune cell populations and their functional states. Indeed, this technology facilitates the understanding of immune dysfunctions in sepsis and contributes to the identification of novel biomarkers. Our review underscores the potential of integrating flow cytometry with omics data, machine learning and clinical observations to refine sepsis management, highlighting the shift towards personalized medicine in critical care. This approach could lead to more precise interventions, improving outcomes in this heterogeneously affected patient population.
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Affiliation(s)
- Elena Santacroce
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Miriam D'Angerio
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Alin Liviu Ciobanu
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Linda Masini
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Domenico Lo Tartaro
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Irene Coloretti
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Stefano Busani
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Ignacio Rubio
- Department of Anesthesiology and Intensive Care Medicine, Center for Sepsis Control and Care, Jena University Hospital, 07747 Jena, Germany
| | - Marianna Meschiari
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Erica Franceschini
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Cristina Mussini
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Massimo Girardis
- Department of Surgery, Medicine, Dentistry and Morphological Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Lara Gibellini
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Sara De Biasi
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, 41125 Modena, Italy
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6
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Abstract
Septic shock can be caused by a variety of mechanisms including direct effects of bacterial toxins such as endotoxin. Annually, approximately 5-7 million patients worldwide develop sepsis with very high endotoxin activity in the blood and more than half die. The term endotoxic septic shock has been used for these patients but it is important to emphasize that endotoxin may be a factor in all forms of septic shock including non-bacterial etiologies like COVID-19 since translocation of bacterial products is a common feature of septic shock. A pattern of organ failure including hepatic dysfunction, acute kidney injury and various forms of endothelial dysfunction ranging from disseminated intravascular coagulation to thrombotic microangiopathy characterize endotoxic septic shock. However, while characteristic, the clinical phenotype is not unique to patients with high endotoxin, and the diagnosis relies on the measurement of endotoxin activity in addition to clinical assessment. Therapies for endotoxic septic shock are limited with immune modulating therapies under investigation and extracorporeal blood purification still controversial in many parts of the world.
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Affiliation(s)
- John A Kellum
- Department of Critical Care Medicine, Center for Critical Care Nephrology, University of Pittsburgh, 600 Scaife Hall, 3550 Terrace Street, Pittsburgh, PA, 15261, USA.
- Spectral Medical Inc, Toronto, ON, Canada.
| | - Claudio Ronco
- International Renal Research Institute of Vicenza, IRRIV Foundation, Department of Nephrology, Dialysis and Transplantation, St. Bortolo Hospital, aULSS8 Berica, Via Rodolfi, 37, 36100, Vicenza, Italy
- Department of Medicine (DIMED), University of Padua, Via Giustiniani, 2, 35128, Padua, Italy
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7
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Kamzolas O, Papazoglou AS, Gemousakakis E, Moysidis DV, Kyriakoulis KG, Brilakis ES, Milkas A. Concomitant Coronary Artery Disease in Identical Twins: Case Report and Systematic Literature Review. J Clin Med 2023; 12:5742. [PMID: 37685809 PMCID: PMC10489011 DOI: 10.3390/jcm12175742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Coronary artery disease (CAD) is multifactorial and strongly affected by genetic, epigenetic and environmental factors. Several studies have reported development of concomitant CAD in identical twins. We report a case in which a pair of Caucasian male monozygotic twins presented almost concomitantly with acute coronary syndrome (ACS) and had concordant coronary anatomy and identical site of occlusion. We performed a systematic literature review of PubMed, Web Of Science and Scopus databases from inception until 28 February 2023 of case reports/case series reporting the concomitant development of CAD in monozygotic twins. We found 25 eligible case reports with a total of 31 monozygotic twin pairs (including the case from our center) suffering from CAD and presenting (most of them simultaneously) with ACS (mean age of presentation: 45 ± 12 years, males: 81%). Coronary angiograms demonstrated lesion and anatomy concordance in 77% and 79% of the twin pairs, respectively. Screening for disease-related genetic mutations was performed in six twin pairs leading to the identification of five CAD-related genetic polymorphisms. This is the first systematic literature review of studies reporting identical twin pairs suffering from CAD. In summary, there is high concordance of coronary anatomy and clinical presentation between monozygotic twins. Future monozygotic twin studies-unbiased by age effects-can provide insights into CAD heritability being able to disentangle the traditional dyad of genetic and environmental factors and investigate the within-pair epigenetic drift.
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Affiliation(s)
| | | | | | | | | | - Emmanouil S Brilakis
- Center for Coronary Artery Disease, Minneapolis Heart Institute and Minneapolis Heart Institute Foundation, Abbott Northwestern, Minneapolis, MN 55407, USA
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Jeffrey M, Denny KJ, Lipman J, Conway Morris A. Differentiating infection, colonisation, and sterile inflammation in critical illness: the emerging role of host-response profiling. Intensive Care Med 2023; 49:760-771. [PMID: 37344680 DOI: 10.1007/s00134-023-07108-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/22/2023] [Indexed: 06/23/2023]
Abstract
Infection results when a pathogen produces host tissue damage and elicits an immune response. Critically ill patients experience immune activation secondary to both sterile and infectious insults, with overlapping clinical phenotypes and underlying immunological mechanisms. Patients also undergo a shift in microbiota with the emergence of pathogen-dominant microbiomes. Whilst the combination of inflammation and microbial shift has long challenged intensivists in the identification of true infection, the advent of highly sensitive molecular diagnostics has further confounded the diagnostic dilemma as the number of microbial detections increases. Given the key role of the host immune response in the development and definition of infection, profiling the host response offers the potential to help unravel the conundrum of distinguishing colonisation and sterile inflammation from true infection. This narrative review provides an overview of current approaches to distinguishing colonisation from infection using routinely available techniques and proposes matrices to support decision-making in this setting. In searching for new tools to better discriminate these states, the review turns to the understanding of the underlying pathobiology of the host response to infection. It then reviews the techniques available to assess this response in a clinically applicable context. It will cover techniques including profiling of transcriptome, protein expression, and immune functional assays, detailing the current state of knowledge in diagnostics along with the challenges and opportunities. The ultimate infection diagnostic tool will likely combine an assessment of both host immune response and sensitive pathogen detection to improve patient management and facilitate antimicrobial stewardship.
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Affiliation(s)
- Mark Jeffrey
- John V Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Division of Anaesthesia, Department of Medicine, Level 4, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK
| | - Kerina J Denny
- Department of Intensive Care, Gold Coast University Hospital, Southport, QLD, Australia
- School of Medicine, University of Queensland, Herston, Brisbane, Australia
| | - Jeffrey Lipman
- University of Queensland Centre for Clinical Research, The University of Queensland, Brisbane, Australia
- Jamieson Trauma Institute and Intensive Care Services, Royal Brisbane and Women's Hospital, Brisbane, Australia
- Nimes University Hospital, University of Montpellier, Nimes, France
| | - Andrew Conway Morris
- John V Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Division of Anaesthesia, Department of Medicine, Level 4, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK.
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge, UK.
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9
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Molofsky AB, Locksley RM. The ins and outs of innate and adaptive type 2 immunity. Immunity 2023; 56:704-722. [PMID: 37044061 PMCID: PMC10120575 DOI: 10.1016/j.immuni.2023.03.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 04/14/2023]
Abstract
Type 2 immunity is orchestrated by a canonical group of cytokines primarily produced by innate lymphoid cells, group 2, and their adaptive counterparts, CD4+ helper type 2 cells, and elaborated by myeloid cells and antibodies that accumulate in response. Here, we review the cytokine and cellular circuits that mediate type 2 immunity. Building from insights in cytokine evolution, we propose that innate type 2 immunity evolved to monitor the status of microbe-rich epithelial barriers (outside) and sterile parenchymal borders (inside) to meet the functional demands of local tissue, and, when necessary, to relay information to the adaptive immune system to reinforce demarcating borders to sustain these efforts. Allergic pathology likely results from deviations in local sustaining units caused by alterations imposed by environmental effects during postnatal developmental windows and exacerbated by mutations that increase vulnerabilities. This framework positions T2 immunity as central to sustaining tissue repair and regeneration and provides a context toward understanding allergic disease.
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Affiliation(s)
- Ari B Molofsky
- Department of Lab Medicine, University of California, San Francisco, San Francisco, CA 94143-0451, USA
| | - Richard M Locksley
- Howard Hughes Medical Institute and Department of Medicine, University of California, San Francisco, San Francisco, CA 94143-0795, USA.
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10
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Parsons JB, Westgeest AC, Conlon BP, Fowler VG. Persistent Methicillin-Resistant Staphylococcus aureus Bacteremia: Host, Pathogen, and Treatment. Antibiotics (Basel) 2023; 12:455. [PMID: 36978320 PMCID: PMC10044482 DOI: 10.3390/antibiotics12030455] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 03/02/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a devastating pathogen responsible for a variety of life-threatening infections. A distinctive characteristic of this pathogen is its ability to persist in the bloodstream for several days despite seemingly appropriate antibiotics. Persistent MRSA bacteremia is common and is associated with poor clinical outcomes. The etiology of persistent MRSA bacteremia is a result of the complex interplay between the host, the pathogen, and the antibiotic used to treat the infection. In this review, we explore the factors related to each component of the host-pathogen interaction and discuss the clinical relevance of each element. Next, we discuss the treatment options and diagnostic approaches for the management of persistent MRSA bacteremia.
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Affiliation(s)
- Joshua B. Parsons
- Department of Medicine, Division of Infectious Disease, Duke University Medical Center, Durham, NC 27710, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Annette C. Westgeest
- Department of Medicine, Division of Infectious Disease, Duke University Medical Center, Durham, NC 27710, USA
- Department of Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Brian P. Conlon
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Vance G. Fowler
- Department of Medicine, Division of Infectious Disease, Duke University Medical Center, Durham, NC 27710, USA
- Duke Clinical Research Institute, Durham, NC 27710, USA
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11
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Zhu Z, Chen X, Wang C, Zhang S, Yu R, Xie Y, Yuan S, Cheng L, Shi L, Zhang X. An integrated strategy to identify COVID-19 causal genes and characteristics represented by LRRC37A2. J Med Virol 2023; 95:e28585. [PMID: 36794676 DOI: 10.1002/jmv.28585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/15/2023] [Accepted: 01/29/2023] [Indexed: 02/17/2023]
Abstract
Genome-wide association study (GWAS) could identify host genetic factors associated with coronavirus disease 2019 (COVID-19). The genes or functional DNA elements through which genetic factors affect COVID-19 remain uncharted. The expression quantitative trait locus (eQTL) provides a path to assess the correlation between genetic variations and gene expression. Here, we firstly annotated GWAS data to describe genetic effects, obtaining genome-wide mapped genes. Subsequently, the genetic mechanisms and characteristics of COVID-19 were investigated by an integrated strategy that included three GWAS-eQTL analysis approaches. It was found that 20 genes were significantly associated with immunity and neurological disorders, including prior and novel genes such as OAS3 and LRRC37A2. The findings were then replicated in single-cell datasets to explore the cell-specific expression of causal genes. Furthermore, associations between COVID-19 and neurological disorders were assessed as a causal relationship. Finally, the effects of causal protein-coding genes of COVID-19 were discussed using cell experiments. The results revealed some novel COVID-19-related genes to emphasize disease characteristics, offering a broader insight into the genetic architecture underlying the pathophysiology of COVID-19.
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Affiliation(s)
- Zijun Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xinyu Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Chao Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Sainan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Rui Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yubin Xie
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Shuofeng Yuan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
- NHC Key Laboratory of Molecular Probe and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, Heilongjiang, China
| | - Lei Shi
- NHC Key Laboratory of Molecular Probe and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xue Zhang
- NHC Key Laboratory of Molecular Probe and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, Heilongjiang, China
- 3McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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12
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Shaheen I, Afifi R, Abulata N, Aboukhalil R, Meligy B, Algebaly HF, Abd El Dayem OY. Vitamin D receptor polymorphisms and vitamin D insufficiency are not associated with sepsis in critically ill children: a case-control study. EGYPTIAN PEDIATRIC ASSOCIATION GAZETTE 2022. [DOI: 10.1186/s43054-022-00130-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Abstract
Background
Vitamin D is a fat-soluble vitamin that regulates calcium and phosphorous homeostasis to maintain a healthy mineralized skeleton. It can also influence immune responses and has immunomodulatory properties. Vitamin D receptor (VDR) is a nuclear receptor that mediates the activities of the hormonal form of vitamin D. VDR polymorphisms can alter immunity and susceptibility to infections by modulating VDR expression and vitamin D activity. This study aimed to investigate the levels of serum vitamin D as well as four VDR polymorphisms: FokI, BsmI, ApaI, and TaqI in fifty children admitted to intensive care unit (ICU) with a diagnosis of sepsis and one-hundred age- and sex-matched healthy children.
Methods
Vitamin D levels were measured in serum, in both patients and controls, using an enzyme-linked immunosorbent assay (ELISA) approach. VDR polymorphisms were also studied in both groups using specific restriction enzymes.
Results
Vitamin D levels were low in both patients and controls. Moreover, serum levels were unaffected by VDR polymorphisms, and their distribution was similar in both groups. Neither the need for mechanical ventilation or inotropic treatment nor the sepsis outcome was impacted by serum vitamin D levels or VDR polymorphisms.
Conclusion
In children admitted to pediatric ICU, neither vitamin D levels nor VDR polymorphisms were associated with sepsis. Further larger studies including different types of sepsis are recommended.
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13
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Hu W, Xu K. Research progress on genetic control of host susceptibility to tuberculosis. Zhejiang Da Xue Xue Bao Yi Xue Ban 2022; 51:679-690. [PMID: 36915969 PMCID: PMC10262011 DOI: 10.3724/zdxbyxb-2022-0484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/11/2022] [Indexed: 02/16/2023]
Abstract
The "Lübeck disaster", twins studies, adoptees studies, and other epidemiological observational studies have shown that host genetic factors play a significant role in determining the host susceptibility to Mycobacterium tuberculosis infection and pathogenesis of tuberculosis. From linkage analyses to genome-wide association studies, it has been discovered that human leucocyte antigen (HLA) genes as well as non-HLA genes (such as SLC11A1, VDR, ASAP1 as well as genes encoding cytokines and pattern recognition receptors) are associated with tuberculosis susceptibility. To provide ideas for subsequent studies about risk prediction of MTB infection and the diagnosis and treatment of tuberculosis, we review the research progress on tuberculosis susceptibility related genes in recent years, focusing on the correlation of HLA genes and non-HLA genes with the pathogenesis of tuberculosis. We also report the results of an enrichment analysis of the genes mentioned in the article. Most of these genes appear to be involved in the regulation of immune system and inflammation, and are also closely related to autoimmune diseases.
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14
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Association Between IL10 Polymorphisms and the Susceptibility to Sepsis: A Meta-Analysis. Biochem Genet 2022; 61:847-860. [DOI: 10.1007/s10528-022-10310-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022]
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15
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Marshall JC, Leligdowicz A. Gaps and opportunities in sepsis translational research. EBioMedicine 2022; 86:104387. [PMID: 36470831 PMCID: PMC9783171 DOI: 10.1016/j.ebiom.2022.104387] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/31/2022] [Accepted: 11/17/2022] [Indexed: 12/04/2022] Open
Abstract
Infection initiates sepsis, but the clinical disease arises through the innate immune response of the host. A rapidly evolving understanding of the biology of that response has not been paralleled by the development of successful new treatment. The COVID-19 pandemic has begun to change this revealing the promise of distinct therapeutic approaches and the feasibility of new approaches to evaluate them. We review the history of mediator-targeted therapy for sepsis and explore the conceptual, biological, technological, and organizational challenges that must be addressed to enable the development of effective treatments for a leading cause of global morbidity and mortality.
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Affiliation(s)
- John C. Marshall
- Departments of Surgery and Critical Care Medicine, Unity Health Toronto, University of Toronto, Canada,Corresponding author. 4th Floor Bond Wing, Rm. 4-007, St. Michael's Hospital, 30 Bond Street, Toronto, Ontario, M5B 1W8, Canada.
| | - Aleksandra Leligdowicz
- Departments of Medicine and Critical Care Medicine, University of Western Ontario, Canada
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16
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Transcriptome profiling of colorectal tumors from patients with sepsis reveals an ethnic basis for viral infection risk and sepsis progression. Sci Rep 2022; 12:20646. [PMID: 36450776 PMCID: PMC9709755 DOI: 10.1038/s41598-022-24489-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 11/16/2022] [Indexed: 12/09/2022] Open
Abstract
Mortality from cancer-associated sepsis varies by cancer site and host responses to sepsis are heterogenous. Native Hawaiians have the highest mortality risk from cancer-associated sepsis and colorectal cancer (CRC), even though they demonstrate lower CRC incidence compared to other ethnicities. We conducted a retrospective transcriptomic analysis of CRC tumors and adjacent non-tumor tissue from adult patients of Native Hawaiian and Japanese ethnicity who died from cancer-associated sepsis. We examined differential gene expression in relation to patient survival and sepsis disease etiology. Native Hawaiian CRC patients diagnosed with sepsis had a median survival of 5 (IQR 4-49) months, compared to 117 (IQR 30-146) months for Japanese patients. Transcriptomic analyses identified two distinct sepsis gene signatures classified as early response and late response sepsis genes that were significantly altered in the Native Hawaiian cohort. Analysis of canonical pathways revealed significant up and downregulation in mechanisms of viral exit from host cells (p = 4.52E-04) and epithelial junction remodeling (p = 4.01E-05). Key genes including elongation initiation factor pathway genes, GSK3B, and regulatory associated protein of mTOR (RPTOR) genes that protect cells from infection were significantly downregulated in Native Hawaiians. Genes promoting sepsis progression including CLOCK, PPBP and Rho family GTPASE 2 (RND2) were upregulated in Native Hawaiian patients. Our transcriptomic approach advances understanding of sepsis heterogeneity by revealing a role of genetic background and defining patient subgroups with altered early and late biological responses to sepsis. This study is the first to investigate differential gene expression in CRC-associated sepsis patients in relation to ethnicity. Our findings may lead to personalized approaches in stratifying patient mortality risk for sepsis and in the development of effective targeted therapies for sepsis.
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17
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Abstract
Since the identification of sickle cell trait as a heritable form of resistance to malaria, candidate gene studies, linkage analysis paired with sequencing, and genome-wide association (GWA) studies have revealed many examples of genetic resistance and susceptibility to infectious diseases. GWA studies enabled the identification of many common variants associated with small shifts in susceptibility to infectious diseases. This is exemplified by multiple loci associated with leprosy, malaria, HIV, tuberculosis, and coronavirus disease 2019 (COVID-19), which illuminate genetic architecture and implicate pathways underlying pathophysiology. Despite these successes, most of the heritability of infectious diseases remains to be explained. As the field advances, current limitations may be overcome by applying methodological innovations such as cellular GWA studies and phenome-wide association (PheWA) studies as well as by improving methodological rigor with more precise case definitions, deeper phenotyping, increased cohort diversity, and functional validation of candidate loci in the laboratory or human challenge studies.
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Affiliation(s)
- Kyle D Gibbs
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, USA;
| | - Benjamin H Schott
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, USA; .,Duke University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, USA; .,Duke University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA.,Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, North Carolina, USA
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18
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Jiang L, Kerchberger VE, Shaffer C, Dickson AL, Ormseth MJ, Daniel LL, Leon BGC, Cox NJ, Chung CP, Wei WQ, Stein CM, Feng Q. Genome-wide association analyses of common infections in a large practice-based biobank. BMC Genomics 2022; 23:672. [PMID: 36167494 PMCID: PMC9512962 DOI: 10.1186/s12864-022-08888-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/26/2022] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION Infectious diseases are common causes of morbidity and mortality worldwide. Susceptibility to infection is highly heritable; however, little has been done to identify the genetic determinants underlying common infectious diseases. One GWAS was performed using 23andMe information about self-reported infections; we set out to confirm previous loci and identify new ones using medically diagnosed infections. METHODS We used the electronic health record (EHR)-based biobank at Vanderbilt and diagnosis codes to identify cases of 12 infectious diseases in white patients: urinary tract infection, pneumonia, chronic sinus infections, otitis media, candidiasis, streptococcal pharyngitis, herpes zoster, herpes labialis, hepatitis B, infectious mononucleosis, tuberculosis (TB) or a positive TB test, and hepatitis C. We selected controls from patients with no diagnosis code for the candidate disease and matched by year of birth, sex, and calendar year at first and last EHR visits. We conducted GWAS using SAIGE and transcriptome-wide analysis (TWAS) using S-PrediXcan. We also conducted phenome-wide association study to understand associations between identified genetic variants and clinical phenotypes. RESULTS We replicated three 23andMe loci (p ≤ 0.05): herpes zoster and rs7047299-A (p = 2.6 × 10-3) and rs2808290-C (p = 9.6 × 10-3;); otitis media and rs114947103-C (p = 0.04). We also identified 2 novel regions (p ≤ 5 × 10-8): rs113235453-G for otitis media (p = 3.04 × 10-8), and rs10422015-T for candidiasis (p = 3.11 × 10-8). In TWAS, four gene-disease associations were significant: SLC30A9 for otitis media (p = 8.06 × 10-7); LRP3 and WDR88 for candidiasis (p = 3.91 × 10-7 and p = 1.95 × 10-6); and AAMDC for hepatitis B (p = 1.51 × 10-6). CONCLUSION We conducted GWAS and TWAS for 12 infectious diseases and identified novel genetic contributors to the susceptibility of infectious diseases.
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Affiliation(s)
- Lan Jiang
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - V Eric Kerchberger
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christian Shaffer
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alyson L Dickson
- Division of Rheumatology and Immunology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michelle J Ormseth
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Division of Rheumatology and Immunology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Division of Research and Development, Tennessee Valley Healthcare System, U.S. Department of Veterans Affairs, Nashville, TN, USA
| | - Laura L Daniel
- Division of Rheumatology and Immunology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Barbara G Carranza Leon
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nancy J Cox
- Department of Medicine, Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cecilia P Chung
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Division of Rheumatology and Immunology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Medicine, Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - C Michael Stein
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - QiPing Feng
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA. .,Department of Medicine, Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA.
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19
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Casanova JL, Abel L. From rare disorders of immunity to common determinants of infection: Following the mechanistic thread. Cell 2022; 185:3086-3103. [PMID: 35985287 PMCID: PMC9386946 DOI: 10.1016/j.cell.2022.07.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/11/2022] [Accepted: 07/07/2022] [Indexed: 12/12/2022]
Abstract
The immense interindividual clinical variability during any infection is a long-standing enigma. Inborn errors of IFN-γ and IFN-α/β immunity underlying rare infections with weakly virulent mycobacteria and seasonal influenza virus have inspired studies of two common infections: tuberculosis and COVID-19. A TYK2 genotype impairing IFN-γ production accounts for about 1% of tuberculosis cases, and autoantibodies neutralizing IFN-α/β account for about 15% of critical COVID-19 cases. The discovery of inborn errors and mechanisms underlying rare infections drove the identification of common monogenic or autoimmune determinants of related common infections. This "rare-to-common" genetic and mechanistic approach to infectious diseases may be of heuristic value.
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Affiliation(s)
- Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France; Paris Cité University, Imagine Institute, Paris, France; Department of Pediatrics, Necker Hospital for Sick Children, Paris, France; Howard Hughes Medical Institute, New York, NY, USA.
| | - Laurent Abel
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France; Paris Cité University, Imagine Institute, Paris, France
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20
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Kellum JA, Formeck CL, Kernan KF, Gómez H, Carcillo JA. Subtypes and Mimics of Sepsis. Crit Care Clin 2022; 38:195-211. [DOI: 10.1016/j.ccc.2021.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Li P, Zhang Y, Shen W, Shi S, Zhao Z. dbGSRV: A manually curated database of genetic susceptibility to respiratory virus. PLoS One 2022; 17:e0262373. [PMID: 35298480 PMCID: PMC8929643 DOI: 10.1371/journal.pone.0262373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/23/2022] [Indexed: 11/18/2022] Open
Abstract
Human genetics has been proposed to play an essential role in inter-individual differences in respiratory virus infection occurrence and outcomes. To systematically understand human genetic contributions to respiratory virus infection, we developed the database dbGSRV, a manually curated database that integrated the host genetic susceptibility and severity studies of respiratory viruses scattered over literatures in PubMed. At present, dbGSRV contains 1932 records of genetic association studies relating 1010 unique variants and seven respiratory viruses, manually curated from 168 published articles. Users can access the records by quick searching, batch searching, advanced searching and browsing. Reference information, infection status, population information, mutation information and disease relationship are provided for each record, as well as hyperlinks to public databases in convenient of users accessing more information. In addition, a visual overview of the topological network relationship between respiratory viruses and associated genes is provided. Therefore, dbGSRV offers a convenient resource for researchers to browse and retrieve genetic associations with respiratory viruses, which may inspire future studies and provide new insights in our understanding and treatment of respiratory virus infection. Database URL: http://www.ehbio.com/dbGSRV/front/
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Affiliation(s)
- Ping Li
- Beijing Institute of Biotechnology, Beijing, China
| | - Yan Zhang
- Beijing Institute of Biotechnology, Beijing, China
| | - Wenlong Shen
- Beijing Institute of Biotechnology, Beijing, China
| | - Shu Shi
- Beijing Institute of Biotechnology, Beijing, China
| | - Zhihu Zhao
- Beijing Institute of Biotechnology, Beijing, China
- * E-mail:
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22
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Genetic variants associated with sepsis. PLoS One 2022; 17:e0265052. [PMID: 35275946 PMCID: PMC8916629 DOI: 10.1371/journal.pone.0265052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/22/2022] [Indexed: 11/19/2022] Open
Abstract
Background The variable presentations and different phenotypes of sepsis suggest that risk of sepsis comes from many genes each having a small effect. The cumulative effect can be used to create individual risk profile. The purpose of this study was to create a polygenic risk score and determine the genetic variants associated with sepsis. Methods We sequenced ~14 million single nucleotide polymorphisms with a minimac imputation quality R2>0.3 and minor allele frequency >10−6 in patients with Sepsis-2 or Sepsis-3. Genome-wide association was performed using Firth bias-corrected logistic regression. Semi-parsimonious logistic regression was used to create polygenic risk scores and reduced regression to determine the genetic variants independently associated with sepsis. Findings 2261 patients had sepsis and 13,068 control patients did not. The polygenic risk scores had good discrimination: c-statistic = 0.752 ± 0.005 for Sepsis-2 and 0.752 ± 0.007 for Sepsis-3. We found 772 genetic variants associated with Sepsis-2 and 442 with Sepsis-3, p<0.01. After multivariate adjustment, 100 variants on 85 genes were associated with Sepsis-2 and 69 variants in 54 genes with Sepsis-3. Twenty-five variants were present in both the Sepsis-2 and Sepsis-3 groups out of 32 genes that were present in both groups. The other 7 genes had different variants present. Most variants had small effect sizes. Conclusions Sepsis-2 and Sepsis-3 have both separate and shared genetic variants. Most genetic variants have small effects sizes, but cumulatively, the polygenic risk scores have good discrimination.
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23
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Schmidt A, M. Groh A, S. Frick J, Vehreschild MJGT, U. Ludwig K. Genetic Predisposition and the Variable Course of Infectious Diseases. DEUTSCHES ARZTEBLATT INTERNATIONAL 2022; 119:117-123. [PMID: 35101171 PMCID: PMC9160423 DOI: 10.3238/arztebl.m2022.0105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 08/31/2021] [Accepted: 01/11/2022] [Indexed: 05/07/2023]
Abstract
BACKGROUND Contact with a pathogen is followed by variable courses of infectious disease, which are only partly explicable by classical risk factors. The susceptibility to infection is variable, as is the course of disease after infection. In this review, we discuss the extent to which this variation is due to genetic factors of the affected individual (the host). METHODS Selective review of the literature on host genetics in infectious disease, with special attention to the pathogens SARSCoV- 2, influenza viruses, Mycobacterium tuberculosis, and human immunodeficiency virus (HIV). RESULTS Genetic variants of the host contribute to the pathogenesis of infectious diseases. For example, in HIV infection, a relatively common variant leading to a loss of function of the HIV co-receptor CCR5 affects the course of the disease, as do variants in genes of the major histocompatibility complex (MHC) region. Rare monogenic variants of the interferon immune response system contribute to severe disease courses in COVID-19 and influenza (type I interferon in these two cases) and in tuberculosis (type II interferon). An estimated 1.8% of life-threatening courses of COVID-19 in men under age 60 are caused by a deficiency of toll-like receptor 7. The scientific understanding of host genetic factors has already been beneficial to the development of effective drugs. In a small number of cases, genetic information has also been used for individual therapeutic decision-making and for the identification of persons at elevated risk. CONCLUSION A comprehensive understanding of host genetics can improve the care of patients with infectious diseases. Until the present, the clinical utility of host genetics has been limited to rare cases; in the future, polygenic risk scores summarizing the relevant genetic variants in each patient will enable a wider benefit. To make this possible, multicenter studies are needed that will systematically integrate clinical and genetic data.
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Affiliation(s)
- Axel Schmidt
- Institute of Human Genetics, Medical Faculty of the University of Bonn & Bonn University Hospital
| | - Ana M. Groh
- Medical Department II, Infectiology, University HospitalFrankfurt, Goethe University Frankfurt
| | - Julia S. Frick
- Interfaculty Institute for Microbiology and Infection Medicine, University Hospital and Faculty of Medicine Tübingen
- MVZ Laboratory Ludwigsburg GbR
| | | | - Kerstin U. Ludwig
- Institute of Human Genetics, Medical Faculty of the University of Bonn & Bonn University Hospital
- * Institut für Humangenetik, Department of Genomics Universitätsklinikum Bonn Venusberg-Campus 1, Gebäude 76 53127 Bonn, Germany
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24
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The Role of Genetic Factors in the Development of Acute Respiratory Viral Infection COVID-19: Predicting Severe Course and Outcomes. Biomedicines 2022; 10:biomedicines10030549. [PMID: 35327350 PMCID: PMC8945420 DOI: 10.3390/biomedicines10030549] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 12/14/2022] Open
Abstract
The aim of this study was to identify single nucleotide variants in genes associated with susceptibility to or severe outcomes of COVID-19. A total of 319 genomic DNA samples from patients with varying degrees of disease severity and 78 control DNA samples from people who had regular or prolonged contact with patients with COVID-19 but did not have clinical manifestations and/or antibodies to SARS-CoV-2. Seven SNPs were identified that were statistically associated with disease risk or severe course, rs1799864 in the CCR2 gene (OR = 2.21), rs1990760 in the IFIH1 gene (OR = 2.41), rs1800629 in the TNF gene (OR = 1.98), rs75603675 in the TMPRSS2 gene (OR = 1.86), rs7842 in the C3AR1 gene (OR = 2.08), rs179008 in the gene TLR7 (OR = 1.85), rs324011 in the C3AR1 gene (OR = 2.08), rs179008 in the TLR7 gene (OR = 1.85), and rs324011 in the STAT6 gene (OR = 1.84), as well as two variants associated with protection from COVID-19, rs744166 in the STAT3 gene (OR = 0.36) and rs1898830 in the TLR2 gene (OR = 0.47). The genotype in the region of these markers can be the criterion of the therapeutic approach for patients with COVID-19.
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25
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Evidence for an Inherited Contribution to Sepsis Susceptibility Among a Cohort of U.S. Veterans. Crit Care Explor 2022; 4:e0603. [PMID: 35036923 PMCID: PMC8754185 DOI: 10.1097/cce.0000000000000603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Analyze a unique clinical and genealogical resource for evidence of familial clustering of sepsis to test for an inherited contribution to sepsis predisposition.
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26
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Fernández-Sarmiento J, Schlapbach LJ, Acevedo L, Santana CR, Acosta Y, Diana A, Monsalve M, Carcillo JA. Endothelial Damage in Sepsis: The Importance of Systems Biology. Front Pediatr 2022; 10:828968. [PMID: 35356443 PMCID: PMC8959536 DOI: 10.3389/fped.2022.828968] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/19/2022] [Indexed: 12/29/2022] Open
Abstract
The early diagnosis and appropriate stratification of sepsis continues to be one of the most important challenges in modern medicine. Single isolated biomarkers have not been enough to improve diagnostic and prognostic strategies and to progress toward therapeutic goals. The information generated by the human genome project has allowed a more holistic approach to the problem. The integration of genomics, transcriptomics, proteomics and metabolomics in sepsis has allowed us to progress in the knowledge of new pathways which are pathophysiologically involved in this disease. Thus, we have understood the importance of and complex interaction between the inflammatory response and the endothelium. Understanding the role of important parts of the microcirculation, such as the endothelial glycocalyx and its interaction with the inflammatory response, has provided early recognition elements for clinical practice that allow the rational use of traditional medical interventions in sepsis. This comprehensive approach, which differs from the classical mechanistic approach, uses systems biology to increase the diagnostic and prognostic spectrum of endothelial damage biomarkers in sepsis, and to provide information on new pathways involved in the pathophysiology of the disease. This, in turn, provides tools for perfecting traditional medical interventions, using them at the appropriate times according to the disease's pathophysiological context, while at the same time discovering new and improved therapeutic alternatives. We have the challenge of transferring this ideal scenario to our daily clinical practice to improve our patients' care. The purpose of this article is to provide a general description of the importance of systems biology in integrating the complex interaction between the endothelium and the inflammatory response in sepsis.
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Affiliation(s)
- Jaime Fernández-Sarmiento
- Department of Pediatrics and Intensive Care, Fundación Cardioinfantil-Instituto de Cardiología, Universidad de La Sabana, Escuela de Graduados CES, Bogotá, Colombia
| | - Luregn J Schlapbach
- Department of Paediatric Critical Care Research Group, The University of Queensland and Queensland Children's Hospital, Brisbane, QLD, Australia.,Department of Paediatric Critical Care, Queensland Children's Hospital, Brisbane, QLD, Australia.,Department of Paediatric Critical Care, University Children's Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Lorena Acevedo
- Department of Pediatrics and Intensive Care, Fundación Cardioinfantil-Instituto de Cardiología, Universidad de La Sabana, Escuela de Graduados CES, Bogotá, Colombia
| | - Carolina Ramírez Santana
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Yeny Acosta
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Ampudia Diana
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - M Monsalve
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Joseph A Carcillo
- Department of Critical Care Medicine and Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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27
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Onyishi CU, May RC. Human immune polymorphisms associated with the risk of cryptococcal disease. Immunology 2021; 165:143-157. [PMID: 34716931 PMCID: PMC9426616 DOI: 10.1111/imm.13425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 10/07/2021] [Accepted: 10/16/2021] [Indexed: 11/29/2022] Open
Abstract
Cryptococcus neoformans is an opportunistic fungal pathogen that can cause lethal cryptococcal meningitis in immunocompromised individuals such as those with HIV/AIDS. In addition, cryptococcal infections occasionally arise in immunocompetent individuals or those with previously undiagnosed immunodeficiencies. The course of cryptococcosis is highly variable in both patient groups, and there is rapidly growing evidence that genetic polymorphisms may have a significant impact on the trajectory of disease. Here, we review what is currently known about the nature of these polymorphisms and their impact on host response to C. neoformans infection. Thus far, polymorphisms in Fc gamma receptors, mannose‐binding lectin, Dectin‐2, Toll‐like receptors and macrophage colony‐stimulating factor have been associated with susceptibility to cryptococcal disease. Notably, however, in some cases the impact of these polymorphisms depends on the genetic background of the population; for example, the FCGR3A 158 F/V polymorphism was associated with an increased risk of cryptococcal disease in both HIV‐positive and HIV‐negative white populations, but not in Han Chinese patients. In most cases, the precise mechanism by which the identified polymorphisms influence disease progression remains unclear, although impaired fungal recognition and phagocytosis by innate immune cells appears to play a major role. Finally, we highlight outstanding questions in the field and emphasize the need for future research to include more diverse populations in their genetic association studies.
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Affiliation(s)
- Chinaemerem U Onyishi
- Institute of Microbiology & Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Robin C May
- Institute of Microbiology & Infection, School of Biosciences, University of Birmingham, Birmingham, UK
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Sun J, Zhang H, Liu D, Cui L, Wang Q, Gan L, Wen D, Wang J, Du J, Huang H, Zhang A, Deng J, Jiang J, Zeng L. A Functional Variant of CXCL16 Is Associated With Predisposition to Sepsis and MODS in Trauma Patients: Genetic Association Studies. Front Genet 2021; 12:720313. [PMID: 34539750 PMCID: PMC8446271 DOI: 10.3389/fgene.2021.720313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/12/2021] [Indexed: 12/20/2022] Open
Abstract
PURPOSE CXC chemokines are mediators which mediate immune cells migration to sites of inflammation and injury. Chemokine C-X-C motif ligand 16 (CXCL16) plays an important role in the occurrence and development of sepsis through leukocyte chemotaxis, leukocyte adhesion and endotoxin clearance. In this study, we selected a set of tagging single nucleotide polymorphisms (tag SNPs) in the CXCL16 gene and investigated their clinical relevance to the development of sepsis and multiple organ dysfunction syndrome (MODS) in patients with major trauma in three independent Chinese Han populations. METHODS A total of 1,620 major trauma patients were enrolled in this study. Among these patients, 920 came from Chongqing in western China, 350 came from Zhejiang Province in eastern China, and 350 came from Guizhou Province in southwestern China. The improved multiplex ligation detection reaction (iMLDR) method was employed in the genotyping and genetic association analyses to determine the associations between CXCL16 haplotypes and sepsis morbidity rate and higher MOD scores in three cohorts. RESULTS Only CXCL16 T123V181 haplotype was associated with an increased risk for sepsis morbidity and higher MOD scores in the three cohorts (OR = 1.89, P = 0.001 for the Chongqing cohort; OR = 1.76, P = 0.004 for the Zhejiang cohort; OR = 1.55, P = 0.012 for the Guizhou cohort). The effect of T123V181 haplotype on the chemotaxis, migration and endotoxin clearance of immune cells were further observed. Protein modeling analysis showed that T123 and V181 might alter the structure of the CXCL16 active center. Thus it enhanced the chemotaxis and adhesion ability of immunocytes. CONCLUSION We demonstrate the mechanism of CXCL16 T123V181 haplotype which regulates the sepsis morbidity rate and thus provide a new biomarker for early diagnosis of sepsis and MODS. CLINICAL TRIAL REGISTRATION www.ClinicalTrials.gov, identifier NCT01713205 (https://www.clinicaltrials.gov/ct2/results?cond=&term=+NCT01713205&cntry=&state=&city=&dist=).
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Affiliation(s)
- Jianhui Sun
- Department of Trauma Medical Center, Daping Hospital, Army Medical University, Chongqing, China
| | - Huacai Zhang
- Department of Trauma Medical Center, Daping Hospital, Army Medical University, Chongqing, China
| | - Di Liu
- Department of Trauma Medical Center, Daping Hospital, Army Medical University, Chongqing, China
| | - Li Cui
- Department of Trauma Medical Center, Daping Hospital, Army Medical University, Chongqing, China
| | - Qiang Wang
- Department of Emergency, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Lebin Gan
- Department of Trauma Medical Center, Daping Hospital, Army Medical University, Chongqing, China
- Department of Emergency, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Dalin Wen
- Department of Trauma Medical Center, Daping Hospital, Army Medical University, Chongqing, China
| | - Jun Wang
- Department of Emergency, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Juan Du
- Department of Trauma Medical Center, Daping Hospital, Army Medical University, Chongqing, China
| | - Hong Huang
- Department of Trauma Medical Center, Daping Hospital, Army Medical University, Chongqing, China
| | - Anqiang Zhang
- Department of Trauma Medical Center, Daping Hospital, Army Medical University, Chongqing, China
| | - Jin Deng
- Department of Emergency, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Jianxin Jiang
- Department of Trauma Medical Center, Daping Hospital, Army Medical University, Chongqing, China
| | - Ling Zeng
- Department of Trauma Medical Center, Daping Hospital, Army Medical University, Chongqing, China
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Challenges and Opportunities in Understanding Genetics of Fungal Diseases: Towards a Functional Genomics Approach. Infect Immun 2021; 89:e0000521. [PMID: 34031131 DOI: 10.1128/iai.00005-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Infectious diseases are a leading cause of morbidity and mortality worldwide, and human pathogens have long been recognized as one of the main sources of evolutionary pressure, resulting in a high variable genetic background in immune-related genes. The study of the genetic contribution to infectious diseases has undergone tremendous advances over the last decades. Here, focusing on genetic predisposition to fungal diseases, we provide an overview of the available approaches for studying human genetic susceptibility to infections, reviewing current methodological and practical limitations. We describe how the classical methods available, such as family-based studies and candidate gene studies, have contributed to the discovery of crucial susceptibility factors for fungal infections. We will also discuss the contribution of novel unbiased approaches to the field, highlighting their success but also their limitations for the fungal immunology field. Finally, we show how a systems genomics approach can overcome those limitations and can lead to efficient prioritization and identification of genes and pathways with a critical role in susceptibility to fungal diseases. This knowledge will help to stratify at-risk patient groups and, subsequently, develop early appropriate prophylactic and treatment strategies.
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30
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Meng L, Song Z, Liu A, Dahmen U, Yang X, Fang H. Effects of Lipopolysaccharide-Binding Protein (LBP) Single Nucleotide Polymorphism (SNP) in Infections, Inflammatory Diseases, Metabolic Disorders and Cancers. Front Immunol 2021; 12:681810. [PMID: 34295331 PMCID: PMC8290185 DOI: 10.3389/fimmu.2021.681810] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/08/2021] [Indexed: 01/11/2023] Open
Abstract
Inflammation, which is induced by the immune response, is recognized as the driving factor in many diseases, including infections and inflammatory diseases, metabolic disorders and cancers. Genetic variations in pivotal genes associated with the immune response, particularly single nucleotide polymorphisms (SNPs), may account for predisposition and clinical outcome of diseases. Lipopolysaccharide (LPS)-binding protein (LBP) functions as an enhancer of the host response to LPS, the main component of the outer membrane of gram-native bacteria. Given the crucial role of LBP in inflammation, we will review the impact of SNPs in the LBP gene on infections and inflammatory diseases, metabolic disorders and cancers.
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Affiliation(s)
- Leilei Meng
- Department of Pathophysiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Zichen Song
- Department of Pathophysiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Anding Liu
- Experimental Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Uta Dahmen
- Experimental Transplantation Surgery, Department of General, Visceral and Vascular Surgery, Friedrich-Schiller-University Jena, Jena, Germany
| | - Xiao Yang
- Experimental Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haoshu Fang
- Department of Pathophysiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
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31
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Friedrich VK, Rubel MA, Schurr TG. Mitochondrial genetic variation in human bioenergetics, adaptation, and adult disease. Am J Hum Biol 2021; 34:e23629. [PMID: 34146380 DOI: 10.1002/ajhb.23629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES Mitochondria are critical for the survival of eukaryotic organisms due to their ability to produce cellular energy, which drives virtually all aspects of host biology. However, the effects of mitochondrial DNA (mtDNA) variation in relation to disease etiology and adaptation within contemporary global human populations remains incompletely understood. METHODS To develop a more holistic understanding of the role of mtDNA diversity in human adaptation, health, and disease, we investigated mitochondrial biology and bioenergetics. More specifically, we synthesized details from studies of mitochondrial function and variation in the context of haplogroup background, climatic adaptation, and oxidative disease. RESULTS The majority of studies show that mtDNA variation arose during modern human dispersal around the world. Some of these variants appear to have been positively selected for their adaptiveness in colder climates, with these sequence changes having implications for tissue-specific function and thermogenic capacity. In addition, many variants modulating energy production are also associated with damaging metabolic byproducts and mitochondrial dysfunction, which, in turn, are implicated in the onset and severity of several different adult mitochondrial diseases. Thus, mtDNA variation that governs bioenergetics, metabolism, and thermoregulation may potentially have adverse consequences for human health, depending on the genetic background and context in which it occurs. CONCLUSIONS Our review suggests that the mitochondrial research field would benefit from independently replicating mtDNA haplogroup-phenotype associations across global populations, incorporating potentially confounding environmental, demographic, and disease covariates into studies of mtDNA variation, and extending association-based studies to include analyses of complete mitogenomes and assays of mitochondrial function.
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Affiliation(s)
- Volney K Friedrich
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Meagan A Rubel
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Center for Translational Imaging and Precision Medicine, University of California - San Diego, La Jolla, California, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Genome-Wide Linkage Analysis of the Risk of Contracting a Bloodstream Infection in 47 Pedigrees Followed for 23 Years Assembled From a Population-Based Cohort (the HUNT Study). Crit Care Med 2021; 48:1580-1586. [PMID: 32885941 DOI: 10.1097/ccm.0000000000004520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Bloodstream infection is an important cause of death worldwide. The main objective of this study was to identify genetic loci linked to risk of contracting a bloodstream infection. DESIGN Genome-wide linkage analysis. SETTING Population-based, Norwegian cohort, followed between 1995 and 2017. SUBJECTS Among 69,423 genotyped subjects, there were 47 families with two or more second-degree relatives with bloodstream infection in the follow-up period. There were 365 subjects in these families, of which 110 were affected. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS The cohort was genotyped using Illumina HumanCoreExome (Illumina, San Diego, CA) arrays. Before linkage analysis, single-nucleotide polymorphisms were pruned and clumped. In nonparametric linkage analysis using an exponential model, we found three loci with a suggestive linkage to bloodstream infection, all on chromosome 4, at 46.6 centimorgan (logarithm of odds, 2.3), 57.7 centimorgan (logarithm of odds, 3.2), and 70.0 centimorgan (logarithm of odds, 2.1). At the peak of the lead region are three genes: TLR10, TLR1, and TLR6. CONCLUSIONS Variations in the TLR10/1/6 locus appear to be linked with the risk of contracting a bloodstream infection.
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Abstract
OBJECTIVES Recent evidence from the fields of microbiology and immunology, as well as a small number of human sepsis studies, suggest that epigenetic regulation may play a central role in the pathogenesis of sepsis. The term "epigenetics" refers to regulatory mechanisms that control gene expression but are not related to changes in DNA sequence. These include DNA methylation, histone modifications, and regulation of transcription via non-coding RNAs. Epigenetic modifications, occurring in response to external stressors, lead to changes in gene expression, and thus lie at the intersection between genetics and the environment. In this review, we examine data from in vitro studies, animal studies, and the existing human sepsis studies in epigenetics to demonstrate that epigenetic mechanisms are likely central to the pathogenesis of sepsis and that epigenetic therapies may have potential in the treatment of sepsis and its associated organ failures. DATA SOURCES Online search of published scientific literature via Pubmed using the term "epigenetics" in combination with the terms "sepsis", "infection", "bacterial infection", "viral infection", "critical illness", "acute respiratory distress syndrome", and "acute lung injury". STUDY SELECTION Articles were chosen for inclusion based on their relevance to sepsis, acute inflammation, sepsis-related immune suppression, and sepsis-related organ failure. Reference lists were reviewed to identify additional relevant articles. DATA EXTRACTION Relevant data was extracted and synthesized for narrative review. DATA SYNTHESIS Epigenetic regulation is a key determinant of gene expression in sepsis. At the onset of infection, host-pathogen interactions often result in epigenetic alterations to host cells that favor pathogen survival. In parallel, the host inflammatory response is characterized by epigenetic modifications in key regulatory genes, including tumor necrosis factor and interleukin-1β. In human sepsis patients, multiple epigenetic modifying enzymes show differential expression in early sepsis, suggesting a role for epigenetics in coordinating the response to infection. In the later stages of sepsis, epigenetic modifications accompany endotoxin tolerance and the immune-suppressed state. In animal models, treatment with epigenetic modifiers can mitigate the effects of sepsis and improve survival as well as reverse sepsis-associated organ injury. CONCLUSIONS Epigenetic modifications are associated with key phases of sepsis, from the host-pathogen interaction, to acute inflammation, to immune suppression. Epigenetic markers show promise in the diagnosis and prognosis of sepsis and epigenetic modifying agents show promise as therapeutic tools in animal models of sepsis. Human studies in the area of epigenetics are sorely lacking and should be a priority for sepsis researchers.
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Lawler PR, Bhatt DL, Godoy LC, Lüscher TF, Bonow RO, Verma S, Ridker PM. Targeting cardiovascular inflammation: next steps in clinical translation. Eur Heart J 2021; 42:113-131. [PMID: 32176778 DOI: 10.1093/eurheartj/ehaa099] [Citation(s) in RCA: 133] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/30/2019] [Accepted: 02/03/2020] [Indexed: 12/31/2022] Open
Abstract
Systemic vascular inflammation plays multiple maladaptive roles which contribute to the progression and destabilization of atherosclerotic cardiovascular disease (ASCVD). These roles include: (i) driving atheroprogression in the clinically stable phase of disease; (ii) inciting atheroma destabilization and precipitating acute coronary syndromes (ACS); and (iii) responding to cardiomyocyte necrosis in myocardial infarction (MI). Despite an evolving understanding of these biologic processes, successful clinical translation into effective therapies has proven challenging. Realizing the promise of targeting inflammation in the prevention and treatment of ASCVD will likely require more individualized approaches, as the degree of inflammation differs among cardiovascular patients. A large body of evidence has accumulated supporting the use of high-sensitivity C-reactive protein (hsCRP) as a clinical measure of inflammation. Appreciating the mechanistic diversity of ACS triggers and the kinetics of hsCRP in MI may resolve purported inconsistencies from prior observational studies. Future clinical trial designs incorporating hsCRP may hold promise to enable individualized approaches. The aim of this Clinical Review is to summarize the current understanding of how inflammation contributes to ASCVD progression, destabilization, and adverse clinical outcomes. We offer forward-looking perspective on what next steps may enable successful clinical translation into effective therapeutic approaches-enabling targeting the right patients with the right therapy at the right time-on the road to more individualized ASCVD care.
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Affiliation(s)
- Patrick R Lawler
- Peter Munk Cardiac Centre, University Health Network, 190 Elizabeth Street, Toronto, ON M5G 2C4, Canada.,Ted Rogers Centre for Heart Research, 661 University Avenue, Toronto, ON M5G 1X8, Canada.,University of Toronto, 27 King's College Cir, Toronto, ON M5S 1K1, Canada
| | - Deepak L Bhatt
- Brigham and Women's Hospital, Division of Cardiovascular Medicine, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Lucas C Godoy
- Peter Munk Cardiac Centre, University Health Network, 190 Elizabeth Street, Toronto, ON M5G 2C4, Canada.,Instituto do Coracao (InCor), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, 44, Doutor Enéas Carvalho de Aguiar Avenue, São Paulo, SP 05403-900, Brazil
| | - Thomas F Lüscher
- Royal Brompton & Harefield Hospital, Imperial College, 77 Wimpole Street, London W1G 9RU, UK
| | - Robert O Bonow
- Northwestern Memorial Hospital, Northwestern University Feinberg School of Medicine, 251 E Huron, Chicago, IL 60611, USA
| | - Subodh Verma
- University of Toronto, 27 King's College Cir, Toronto, ON M5S 1K1, Canada.,Division of Cardiac Surgery, St Michael's Hospital, University of Toronto, 30 Bond St, Toronto, ON M5B 1W8, Canada
| | - Paul M Ridker
- Brigham and Women's Hospital, Division of Cardiovascular Medicine, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA.,Brigham and Women's Hospital, Center for Cardiovascular Disease Prevention, Harvard Medical School, 900 Commonwealth Avenue, Boston, MA 02215, USA
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35
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Schuurman AR, Reijnders TDY, Kullberg RFJ, Butler JM, van der Poll T, Wiersinga WJ. Sepsis: deriving biological meaning and clinical applications from high-dimensional data. Intensive Care Med Exp 2021; 9:27. [PMID: 33961170 PMCID: PMC8105470 DOI: 10.1186/s40635-021-00383-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023] Open
Abstract
The pathophysiology of sepsis is multi-facetted and highly complex. As sepsis is a leading cause of global mortality that still lacks targeted therapies, increased understanding of its pathogenesis is vital for improving clinical care and outcomes. An increasing number of investigations seeks to unravel the complexity of sepsis through high-dimensional data analysis, enabled by advances in -omics technologies. Here, we summarize progress in the following major -omics fields: genomics, epigenomics, transcriptomics, proteomics, lipidomics, and microbiomics. We describe what these fields can teach us about sepsis, and highlight current trends and future challenges. Finally, we focus on multi-omics integration, and discuss the challenges in deriving biological meaning and clinical applications from these types of data.
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Affiliation(s)
- Alex R Schuurman
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands
| | - Tom D Y Reijnders
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands
| | - Robert F J Kullberg
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands
| | - Joe M Butler
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands.,Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands
| | - W Joost Wiersinga
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands. .,Amsterdam Institute for Infection and Immunity, Amsterdam UMC, Noord-Holland, Amsterdam, 1105 AZ, The Netherlands.
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Association of TLR4 gene polymorphisms with sepsis after a burn injury: findings of the functional role of rs2737190 SNP. Genes Immun 2021; 22:24-34. [PMID: 33531683 DOI: 10.1038/s41435-021-00121-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 11/11/2020] [Accepted: 01/13/2021] [Indexed: 02/01/2023]
Abstract
Sepsis is a life-threatening organ dysfunction condition caused by a dysregulated response to an infection that is common among patients with moderate to severe burn injury. Previously, genomic variants in Toll-like receptor 4 (TLR4), a key innate immunity receptor, have been associated with sepsis and infection susceptibility. In this study, the association of six TLR4 SNPs with sepsis after burn injury was tested in the Mexican mestizo population. We found that the rs2737190 polymorphism is associated with sepsis after burn trauma. Interestingly, the G allele and GG genotype were associated with a lower risk of developing sepsis. Since the rs2737190 SNP is in the promoter region of the TLR4 gene, we analyzed the possibility that this polymorphism regulates the TLR4 pathway. We cultured peripheral blood mononuclear cells from different genotype carriers and found, after stimulation with LPS, that carriers of the GG genotype showed a higher expression of TLR4, IL6, and TNFα than AA genotype carriers. The results suggest that the GG genotype produces an increase in the TLR4 expression, and therefore an improvement in the immune response. We conclude that the rs2737190 polymorphism may become a useful marker for genetic studies of sepsis in patients after a burn injury.
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Bertrams W, Jung AL, Maxheim M, Schmeck B. [Role of genetic factors in pneumonia and COVID-19]. PNEUMOLOGE 2021; 18:212-217. [PMID: 33716601 PMCID: PMC7934978 DOI: 10.1007/s10405-021-00385-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 11/25/2022]
Abstract
Die Pneumonie ist die Infektionskrankheit mit der weltweit höchsten Mortalität. Die häufigsten Erreger sind Bakterien, es gibt jedoch auch epidemisch oder pandemisch auftretende virale Lungenentzündungen durch Influenza- oder Coronaviren, wie die aktuelle Pandemie durch das SARS Coronavirus 3766 Fälle (SARS-CoV-2). Wichtige Herausforderungen liegen neben dem Auftreten von Antibiotikaresistenzen und Immunpathologien etwa in der Sepsis in der Betrachtung der Suszeptibilität individueller Patienten: Hier werden vor allen Dingen das Lebensalter, Medikamente und Komorbiditäten betrachtet. Es gibt jedoch auch klare Hinweise für genetische Einflüsse auf das individuelle Risiko, an einer Pneumonie zu erkranken oder einen schweren Verlauf der Erkrankung zu entwickeln. In diesem Beitrag wollen wir die genetischen Einflüsse auf die Pneumonie und ihre klinische Bedeutung darstellen.
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Affiliation(s)
- Wilhelm Bertrams
- Institut für Lungenforschung, Universities of Gießen and Marburg Lung Center (UGMLC), Philipps-Universität Marburg, Hans-Meerwein-Str. 2, 35043 Marburg, Deutschland
| | - Anna Lena Jung
- Institut für Lungenforschung, Universities of Gießen and Marburg Lung Center (UGMLC), Philipps-Universität Marburg, Hans-Meerwein-Str. 2, 35043 Marburg, Deutschland
| | - Michael Maxheim
- Klinik für Innere Medizin mit Schwerpunkt Pneumologie, Universitätsklinikum Marburg, Philipps-Universität Marburg, Marburg, Deutschland
| | - Bernd Schmeck
- Institut für Lungenforschung, Universities of Gießen and Marburg Lung Center (UGMLC), Philipps-Universität Marburg, Hans-Meerwein-Str. 2, 35043 Marburg, Deutschland
- Klinik für Innere Medizin mit Schwerpunkt Pneumologie, Universitätsklinikum Marburg, Philipps-Universität Marburg, Marburg, Deutschland
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Pairo-Castineira E, Clohisey S, Klaric L, Bretherick AD, Rawlik K, Pasko D, Walker S, Parkinson N, Fourman MH, Russell CD, Furniss J, Richmond A, Gountouna E, Wrobel N, Harrison D, Wang B, Wu Y, Meynert A, Griffiths F, Oosthuyzen W, Kousathanas A, Moutsianas L, Yang Z, Zhai R, Zheng C, Grimes G, Beale R, Millar J, Shih B, Keating S, Zechner M, Haley C, Porteous DJ, Hayward C, Yang J, Knight J, Summers C, Shankar-Hari M, Klenerman P, Turtle L, Ho A, Moore SC, Hinds C, Horby P, Nichol A, Maslove D, Ling L, McAuley D, Montgomery H, Walsh T, Pereira AC, Renieri A, Shen X, Ponting CP, Fawkes A, Tenesa A, Caulfield M, Scott R, Rowan K, Murphy L, Openshaw PJM, Semple MG, Law A, Vitart V, Wilson JF, Baillie JK. Genetic mechanisms of critical illness in COVID-19. Nature 2021; 591:92-98. [PMID: 33307546 DOI: 10.1038/s41586-020-03065-y] [Citation(s) in RCA: 813] [Impact Index Per Article: 271.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023]
Abstract
Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 × 10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice.
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Affiliation(s)
- Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Sara Clohisey
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Andrew D Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Konrad Rawlik
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | - Nick Parkinson
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Clark D Russell
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - James Furniss
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Elvina Gountouna
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Nicola Wrobel
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - David Harrison
- Intensive Care National Audit & Research Centre, London, UK
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Alison Meynert
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | | | | | | | | | - Zhijian Yang
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ranran Zhai
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chenqing Zheng
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Graeme Grimes
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | | | | | - Barbara Shih
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Marie Zechner
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Chris Haley
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Manu Shankar-Hari
- Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, UK
- School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Paul Klenerman
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lance Turtle
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Shona C Moore
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Charles Hinds
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
- Australian and New Zealand Intensive Care Research Centre, Monash University, Melbourne, Victoria, Australia
- Intensive Care Unit, Alfred Hospital, Melbourne, Victoria, Australia
| | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | - Hugh Montgomery
- UCL Centre for Human Health and Performance, University College London, London, UK
| | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Alexandre C Pereira
- Faculty of Medicine, University of São Paulo, São Paulo, Brazil
- Heart Institute, University of São Paulo, São Paulo, Brazil
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Xia Shen
- Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Mark Caulfield
- Genomics England, London, UK
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Richard Scott
- Genomics England, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Kathy Rowan
- Intensive Care National Audit & Research Centre, London, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust London, London, UK
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital, Institute in The Park, University of Liverpool, Liverpool, UK
| | - Andrew Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
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39
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Yin A, Chen W, Cao L, Li Q, Zhu X, Wang L. FAM96A knock-out promotes alternative macrophage polarization and protects mice against sepsis. Clin Exp Immunol 2021; 203:433-447. [PMID: 33232517 PMCID: PMC7874832 DOI: 10.1111/cei.13555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 12/21/2022] Open
Abstract
Sepsis is an intractable clinical syndrome characterized by organ dysfunction when the body over-responds to an infection. Sepsis has a high fatality rate and lacks effective treatment. Family with sequence similarity 96 member A (FAM96A) is an evolutionarily conserved protein with high expression in the immune system and is related to cytosolic iron assembly and tumour suppression; however, research has been rarely conducted on its immune functions. Our study found that Fam96a-/- mice significantly resisted lesions during sepsis simulated by caecal ligation and puncture (CLP) or endotoxicosis models. After a challenge with lipopolysaccharide (LPS) or infection, Fam96a-/- mice exhibited less organ damage, longer survival and better bacterial clearance with decreased levels of proinflammatory cytokines. While screening several subsets of immune cells, FAM96A-expressing macrophages as the key cell type inhibited sepsis development. In-vivo macrophage depletion or adoptive transfer experiments abrogated significant differences in the survival of sepsis between Fam96a-/- and wild-type mice. Results of the bone marrow-derived macrophage (BMDM) polarization experiment indicated that FAM96A deficiency promotes the transformation of uncommitted monocytes/macrophages (M0) into M2 macrophages, secreting fewer proinflammatory cytokines. FAM96A may mediate an immunometabolism shift - from oxidative phosphorylation (OXPHOS) to glycolysis - in macrophages during sepsis, mirrored by reactive oxygen species (ROS) and glucose uptake. These data demonstrate that FAM96A regulates inflammatory response and provide a novel genomic insight for sepsis treatment.
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Affiliation(s)
- A. Yin
- Center for Human Disease GenomicsDepartment of ImmunologyHealth Science CenterSchool of Basic Medical SciencesPeking UniversityBeijingChina
- Key Laboratory of Medical ImmunologySchool of Basic Medical SciencePeking UniversityMinistry of HealthBeijingPR China
| | - W. Chen
- Center for Human Disease GenomicsDepartment of ImmunologyHealth Science CenterSchool of Basic Medical SciencesPeking UniversityBeijingChina
- Key Laboratory of Medical ImmunologySchool of Basic Medical SciencePeking UniversityMinistry of HealthBeijingPR China
| | - L. Cao
- Center for Human Disease GenomicsDepartment of ImmunologyHealth Science CenterSchool of Basic Medical SciencesPeking UniversityBeijingChina
- Key Laboratory of Medical ImmunologySchool of Basic Medical SciencePeking UniversityMinistry of HealthBeijingPR China
| | - Q. Li
- Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - X. Zhu
- Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
| | - L. Wang
- Center for Human Disease GenomicsDepartment of ImmunologyHealth Science CenterSchool of Basic Medical SciencesPeking UniversityBeijingChina
- Key Laboratory of Medical ImmunologySchool of Basic Medical SciencePeking UniversityMinistry of HealthBeijingPR China
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40
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Solé-Violán J, Hernández-Brito E, Valencia-Gallardo JM, Herrera-Ramos E, Borderías L, Briones ML, Rajas O, Freixinet J, Lorente L, Payeras A, Ferreres J, Carbonell N, González-Quevedo N, González-Martín JM, Rodríguez de Castro F, Rodríguez-Gallego C. Challenges in understanding host genetics and severity of community-acquired pneumonia. ERJ Open Res 2021; 7:00745-2020. [PMID: 33532473 PMCID: PMC7836604 DOI: 10.1183/23120541.00745-2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 11/07/2022] Open
Abstract
A heritable predisposition to early death due to infection was observed three decades ago [1]. Apart from exciting discoveries in the field of primary immunodeficiencies, genetic variants predisposing to severe infection and outcome at a population level remain largely elusive [2, 3]. Genetic association studies on sepsis were largely based on a candidate gene approach. In 2015, Rautanenet al. [4] reported the first genome-wide association study (GWAS) in sepsis. A meta-analysis of three independent cohorts of critically ill patients with sepsis recruited in numerous centres from Europe, Canada, United States, Australia, New Zealand and South Africa was performed. They reported that the C allele of the single-nucleotide variant (SNV) rs4957796 at the FER gene was associated with a protective additive effect in 28-day survival only in patients with pneumonia, but not in those with other causes of sepsis. Schönewecket al. [5] did not replicate the findings Rautanenet al. [4] in a mixed cohort of patients of European ancestry with severe sepsis admitted at German intensive care units (ICUs). However, their study was underpowered for mortality. Hinzet al.[6], in a cohort of white patients with acute respiratory distress syndrome (ARDS) due to pneumonia from a single Centre in Germany, found that the rs4957796 TT genotype was associated with a higher 90-day mortality exclusively in the small subgroup of patients with severe ARDS. This study found no association of the top two associated FER variants with severity of community-acquired pneumonia. Precise characterisation of phenotypes may be required in order to unravel the genetic mechanisms predisposing to poor outcome in sepsis.https://bit.ly/3jc9SmR
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Affiliation(s)
- Jordi Solé-Violán
- Intensive Care Unit, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,These authors contributed equally to this work
| | - Elisa Hernández-Brito
- Dept of Immunology, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain.,Dept of Medical and Surgical Sciences, School of Medicine, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain.,These authors contributed equally to this work
| | | | - Estefanía Herrera-Ramos
- Dept of Medical and Surgical Sciences, School of Medicine, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Luis Borderías
- Dept of Respiratory Diseases, Hospital San Jorge, Huesca, Spain
| | - M Luisa Briones
- Dept of Respiratory Diseases, Hospital Clínico y Universitario de Valencia, Valencia, Spain
| | - Olga Rajas
- Dept of Respiratory Diseases, Hospital Universitario de la Princesa, Madrid, Spain
| | - Jorge Freixinet
- Dept of Thoracic Surgery, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - Leonardo Lorente
- Intensive Care Unit, Hospital Universitario de Canarias, La Laguna, Spain
| | - Antoni Payeras
- Dept of Internal Medicine, Hospital Son Llatzer, Palma de Mallorca, Spain
| | - José Ferreres
- Intensive Care Unit, Hospital Clínico y Universitario de Valencia, Valencia, Spain
| | - Nieves Carbonell
- Intensive Care Unit, Hospital Clínico y Universitario de Valencia, Valencia, Spain
| | - Nereida González-Quevedo
- Dept of Immunology, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - Jesús M González-Martín
- Biostatistics Division, Research Unit, Hospital Universitario Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - Felipe Rodríguez de Castro
- Dept of Medical and Surgical Sciences, School of Medicine, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain.,Dept of Respiratory Diseases, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - Carlos Rodríguez-Gallego
- Dept of Immunology, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de Gran Canaria, Spain.,University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
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41
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Forbester JL, Humphreys IR. Genetic influences on viral-induced cytokine responses in the lung. Mucosal Immunol 2021; 14:14-25. [PMID: 33184476 PMCID: PMC7658619 DOI: 10.1038/s41385-020-00355-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/14/2020] [Accepted: 10/20/2020] [Indexed: 02/06/2023]
Abstract
Infection with respiratory viruses such as influenza, respiratory syncytial virus and coronavirus provides a difficult immunological challenge for the host, where a balance must be established between controlling viral replication and limiting damage to the delicate lung structure. Although the genetic architecture of host responses to respiratory viral infections is not yet understood, it is clear there is underlying heritability that influences pathogenesis. Immune control of virus replication is essential in respiratory infections, but overt activation can enhance inflammation and disease severity. Cytokines initiate antiviral immune responses but are implicated in viral pathogenesis. Here, we discuss how host genetic variation may influence cytokine responses to respiratory viral infections and, based on our current understanding of the role that cytokines play in viral pathogenesis, how this may influence disease severity. We also discuss how induced pluripotent stem cells may be utilised to probe the mechanistic implications of allelic variation in genes in virus-induced inflammatory responses. Ultimately, this could help to design better immune modulators, stratify high risk patients and tailor anti-inflammatory treatments, potentially expanding the ability to treat respiratory virus outbreaks in the future.
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Affiliation(s)
- Jessica L Forbester
- Division of Infection and Immunity/Systems Immunity University Research Institute, Cardiff University, Henry Wellcome Building, Heath Park, Cardiff, CF14 4XN, UK.
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DS, UK.
| | - Ian R Humphreys
- Division of Infection and Immunity/Systems Immunity University Research Institute, Cardiff University, Henry Wellcome Building, Heath Park, Cardiff, CF14 4XN, UK
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42
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Host genetics and infectious disease: new tools, insights and translational opportunities. Nat Rev Genet 2020; 22:137-153. [PMID: 33277640 PMCID: PMC7716795 DOI: 10.1038/s41576-020-00297-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2020] [Indexed: 12/22/2022]
Abstract
Understanding how human genetics influence infectious disease susceptibility offers the opportunity for new insights into pathogenesis, potential drug targets, risk stratification, response to therapy and vaccination. As new infectious diseases continue to emerge, together with growing levels of antimicrobial resistance and an increasing awareness of substantial differences between populations in genetic associations, the need for such work is expanding. In this Review, we illustrate how our understanding of the host–pathogen relationship is advancing through holistic approaches, describing current strategies to investigate the role of host genetic variation in established and emerging infections, including COVID-19, the need for wider application to diverse global populations mirroring the burden of disease, the impact of pathogen and vector genetic diversity and a broad array of immune and inflammation phenotypes that can be mapped as traits in health and disease. Insights from study of inborn errors of immunity and multi-omics profiling together with developments in analytical methods are further advancing our knowledge of this important area. Infectious diseases are an ever-present global threat. In this Review, Kwok, Mentzer and Knight discuss our latest understanding of how human genetics influence susceptibility to disease. Furthermore, they discuss emerging progress in the interplay between host and pathogen genetics, molecular responses to infection and vaccination, and opportunities to bring these aspects together for rapid responses to emerging diseases such as COVID-19.
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43
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Di Maria E, Latini A, Borgiani P, Novelli G. Genetic variants of the human host influencing the coronavirus-associated phenotypes (SARS, MERS and COVID-19): rapid systematic review and field synopsis. Hum Genomics 2020; 14:30. [PMID: 32917282 PMCID: PMC7484929 DOI: 10.1186/s40246-020-00280-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 08/31/2020] [Indexed: 12/15/2022] Open
Abstract
The COVID-19 pandemic has strengthened the interest in the biological mechanisms underlying the complex interplay between infectious agents and the human host. The spectrum of phenotypes associated with the SARS-CoV-2 infection, ranging from the absence of symptoms to severe systemic complications, raised the question as to what extent the variable response to coronaviruses (CoVs) is influenced by the variability of the hosts' genetic background.To explore the current knowledge about this question, we designed a systematic review encompassing the scientific literature published from Jan. 2003 to June 2020, to include studies on the contemporary outbreaks caused by SARS-CoV-1, MERS-CoV and SARS-CoV-2 (namely SARS, MERS and COVID-19 diseases). Studies were eligible if human genetic variants were tested as predictors of clinical phenotypes.An ad hoc protocol for the rapid review process was designed according to the PRISMA paradigm and registered at the PROSPERO database (ID: CRD42020180860). The systematic workflow provided 32 articles eligible for data abstraction (28 on SARS, 1 on MERS, 3 on COVID-19) reporting data on 26 discovery cohorts. Most studies considered the definite clinical diagnosis as the primary outcome, variably coupled with other outcomes (severity was the most frequently analysed). Ten studies analysed HLA haplotypes (1 in patients with COVID-19) and did not provide consistent signals of association with disease-associated phenotypes. Out of 22 eligible articles that investigated candidate genes (2 as associated with COVID-19), the top-ranked genes in the number of studies were ACE2, CLEC4M (L-SIGN), MBL, MxA (n = 3), ACE, CD209, FCER2, OAS-1, TLR4, TNF-α (n = 2). Only variants in MBL and MxA were found as possibly implicated in CoV-associated phenotypes in at least two studies. The number of studies for each predictor was insufficient to conduct meta-analyses.Studies collecting large cohorts from different ancestries are needed to further elucidate the role of host genetic variants in determining the response to CoVs infection. Rigorous design and robust statistical methods are warranted.
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Affiliation(s)
- Emilio Di Maria
- Department of Health Sciences, University of Genova, Genova, Italy.
- Unit of Medical Genetics, Galliera Hospital, Genova, Italy.
| | - Andrea Latini
- Department of Biomedicine and Prevention, Genetics Unit, University of Roma "Tor Vergata", Roma, Italy
| | - Paola Borgiani
- Department of Biomedicine and Prevention, Genetics Unit, University of Roma "Tor Vergata", Roma, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Genetics Unit, University of Roma "Tor Vergata", Roma, Italy
- IRCCS Neuromed, Pozzilli (IS), Italy
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
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44
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Abstract
Previous genetic association studies have failed to identify loci robustly associated with sepsis, and there have been no published genetic association studies or polygenic risk score analyses of patients with septic shock, despite evidence suggesting genetic factors may be involved. We systematically collected genotype and clinical outcome data in the context of a randomized controlled trial from patients with septic shock to enrich the presence of disease-associated genetic variants. We performed genomewide association studies of susceptibility and mortality in septic shock using 493 patients with septic shock and 2442 population controls, and polygenic risk score analysis to assess genetic overlap between septic shock risk/mortality with clinically relevant traits. One variant, rs9489328, located in AL589740.1 noncoding RNA, was significantly associated with septic shock (p = 1.05 × 10-10); however, it is likely a false-positive. We were unable to replicate variants previously reported to be associated (p < 1.00 × 10-6 in previous scans) with susceptibility to and mortality from sepsis. Polygenic risk scores for hematocrit and granulocyte count were negatively associated with 28-day mortality (p = 3.04 × 10-3; p = 2.29 × 10-3), and scores for C-reactive protein levels were positively associated with susceptibility to septic shock (p = 1.44 × 10-3). Results suggest that common variants of large effect do not influence septic shock susceptibility, mortality and resolution; however, genetic predispositions to clinically relevant traits are significantly associated with increased susceptibility and mortality in septic individuals.
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45
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Liu AC, Patel K, Vunikili RD, Johnson KW, Abdu F, Belman SK, Glicksberg BS, Tandale P, Fontanez R, Mathew OK, Kasarskis A, Mukherjee P, Subramanian L, Dudley JT, Shameer K. Sepsis in the era of data-driven medicine: personalizing risks, diagnoses, treatments and prognoses. Brief Bioinform 2020; 21:1182-1195. [PMID: 31190075 PMCID: PMC8179509 DOI: 10.1093/bib/bbz059] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 04/04/2019] [Accepted: 04/18/2019] [Indexed: 12/26/2022] Open
Abstract
Sepsis is a series of clinical syndromes caused by the immunological response to infection. The clinical evidence for sepsis could typically attribute to bacterial infection or bacterial endotoxins, but infections due to viruses, fungi or parasites could also lead to sepsis. Regardless of the etiology, rapid clinical deterioration, prolonged stay in intensive care units and high risk for mortality correlate with the incidence of sepsis. Despite its prevalence and morbidity, improvement in sepsis outcomes has remained limited. In this comprehensive review, we summarize the current landscape of risk estimation, diagnosis, treatment and prognosis strategies in the setting of sepsis and discuss future challenges. We argue that the advent of modern technologies such as in-depth molecular profiling, biomedical big data and machine intelligence methods will augment the treatment and prevention of sepsis. The volume, variety, veracity and velocity of heterogeneous data generated as part of healthcare delivery and recent advances in biotechnology-driven therapeutics and companion diagnostics may provide a new wave of approaches to identify the most at-risk sepsis patients and reduce the symptom burden in patients within shorter turnaround times. Developing novel therapies by leveraging modern drug discovery strategies including computational drug repositioning, cell and gene-therapy, clustered regularly interspaced short palindromic repeats -based genetic editing systems, immunotherapy, microbiome restoration, nanomaterial-based therapy and phage therapy may help to develop treatments to target sepsis. We also provide empirical evidence for potential new sepsis targets including FER and STARD3NL. Implementing data-driven methods that use real-time collection and analysis of clinical variables to trace, track and treat sepsis-related adverse outcomes will be key. Understanding the root and route of sepsis and its comorbid conditions that complicate treatment outcomes and lead to organ dysfunction may help to facilitate identification of most at-risk patients and prevent further deterioration. To conclude, leveraging the advances in precision medicine, biomedical data science and translational bioinformatics approaches may help to develop better strategies to diagnose and treat sepsis in the next decade.
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Affiliation(s)
- Andrew C Liu
- Department of Information Services, Northwell Health, New Hyde Park, NY, USA
- Donald and Barbara School of Medicine at Hofstra/Northwell, Northwell Health, Hempstead, NY, USA
| | - Krishna Patel
- Department of Information Services, Northwell Health, New Hyde Park, NY, USA
- Donald and Barbara School of Medicine at Hofstra/Northwell, Northwell Health, Hempstead, NY, USA
| | - Ramya Dhatri Vunikili
- Center for Research Informatics and Innovation, Northwell Health, New Hyde Park, NY, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Kipp W Johnson
- Department of Genetics and Genomic Sciences, Mount Sinai Health System, New York, NY, USA
- Institute for Next Generation Healthcare, Mount Sinai Health System, New York, NY, USA
| | - Fahad Abdu
- Center for Research Informatics and Innovation, Northwell Health, New Hyde Park, NY, USA
- Stonybrook University, 100 Nicolls Rd, Stony Brook, NY, USA
| | - Shivani Kamath Belman
- Center for Research Informatics and Innovation, Northwell Health, New Hyde Park, NY, USA
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Benjamin S Glicksberg
- Department of Genetics and Genomic Sciences, Mount Sinai Health System, New York, NY, USA
- Institute for Next Generation Healthcare, Mount Sinai Health System, New York, NY, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Pratyush Tandale
- Center for Research Informatics and Innovation, Northwell Health, New Hyde Park, NY, USA
- School of Biotechnology and Bioinformatics, D Y Patil University, Navi Mumbai, India
| | - Roberto Fontanez
- Department of Information Services, Northwell Health, New Hyde Park, NY, USA
- Center for Research Informatics and Innovation, Northwell Health, New Hyde Park, NY, USA
| | | | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Mount Sinai Health System, New York, NY, USA
| | | | | | - Joel T Dudley
- Department of Genetics and Genomic Sciences, Mount Sinai Health System, New York, NY, USA
- Institute for Next Generation Healthcare, Mount Sinai Health System, New York, NY, USA
| | - Khader Shameer
- Department of Information Services, Northwell Health, New Hyde Park, NY, USA
- Center for Research Informatics and Innovation, Northwell Health, New Hyde Park, NY, USA
- Institute for Next Generation Healthcare, Mount Sinai Health System, New York, NY, USA
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46
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Cao L, Zhu T, Lang X, Jia S, Yang Y, Zhu C, Wang Y, Feng S, Wang C, Zhang P, Chen J, Jiang H. Inhibiting DNA Methylation Improves Survival in Severe Sepsis by Regulating NF-κB Pathway. Front Immunol 2020; 11:1360. [PMID: 32714333 PMCID: PMC7343767 DOI: 10.3389/fimmu.2020.01360] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/28/2020] [Indexed: 12/17/2022] Open
Abstract
Organ dysfunction caused by sepsis is life-threatening and results in high mortality. Therapeutic options for sepsis are limited. Pathogenic factors are considered as components of environmental pressure that modify DNA methylation patterns thereby enhancing disease progression. Here, we found that sepsis patients exhibited higher levels of genomic DNA methylation patterns and hypermethylated genes associated with the NF-kB signaling pathway. Therefore, we hypothesized that a DNA methyl transferase inhibitor, Decitabine, may mitigate inflammation and improve survival by inhibiting the NF-κB signaling pathway. To test the hypothesis, mice challenged with caecal ligation and puncture (CLP) were subcutaneously injected with Decitabine solution (0.5, 1, and 1.5 mg/kg) 2 h following operation. Our results indicated that Decitabine reduces DNA methyltransferases (DNMTs), attenuates NF-κB activation, downregulates inflammatory cytokine levels, and inhibits the progression of sepsis. Thus, DNA methylation may be indispensable for sepsis and serve as a predicting factor. The use of Decitabine could represent a novel strategy in the treatment of sepsis.
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Affiliation(s)
- Luxi Cao
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Tingting Zhu
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Xiabing Lang
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Sha Jia
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Yi Yang
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Chaohong Zhu
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Yucheng Wang
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Shi Feng
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Cuili Wang
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Ping Zhang
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Jianghua Chen
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
| | - Hong Jiang
- Kidney Disease Center, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Key Laboratory of Nephropathy, Hangzhou, China.,Kidney Disease Immunology Laboratory, The Third-Grade Laboratory, State Administration of Traditional Chinese Medicine of China, Beijing, China.,Key Laboratory of Multiple Organ Transplantation, Ministry of Health of China, Hangzhou, China.,Institute of Nephropathy, Zhejiang University, Hangzhou, China
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47
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The human genetic determinism of life-threatening infectious diseases: genetic heterogeneity and physiological homogeneity? Hum Genet 2020; 139:681-694. [PMID: 32462426 PMCID: PMC7251220 DOI: 10.1007/s00439-020-02184-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Multicellular eukaryotes emerged late in evolution from an ocean of viruses, bacteria, archaea, and unicellular eukaryotes. These macroorganisms are exposed to and infected by a tremendous diversity of microorganisms. Those that are large enough can even be infected by multicellular fungi and parasites. Each interaction is unique, if only because it operates between two unique living organisms, in an infinite diversity of circumstances. This is neatly illustrated by the extraordinarily high level of interindividual clinical variability in human infections, even for a given pathogen, ranging from a total absence of clinical manifestations to death. We discuss here the idea that the determinism of human life-threatening infectious diseases can be governed by single-gene inborn errors of immunity, which are rarely Mendelian and frequently display incomplete penetrance. We briefly review the evidence in support of this notion obtained over the last two decades, referring to a number of focused and thorough reviews published by eminent colleagues in this issue of Human Genetics. It seems that almost any life-threatening infectious disease can be driven by at least one, and, perhaps, a great many diverse monogenic inborn errors, which may nonetheless be immunologically related. While the proportions of monogenic cases remain unknown, a picture in which genetic heterogeneity is combined with physiological homogeneity is emerging from these studies. A preliminary sketch of the human genetic architecture of severe infectious diseases is perhaps in sight.
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48
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Abstract
Abstract
To date it is unknown if there is a predisposition to sepsis. In this respect, genetic studies have been conducted with the aim to find gene variants which can point out a higher predisposition to developing sepsis. The primary objective of this study is to highlight whether the genetic polymorphism of Angiopoietin-2 gene (ANG2-35G>C) is present mainly in septic patients. As secondary objectives we aimed to evaluate if there are any associations between ANG2-35G>C polymorphism and the severity scores Acute Physiology and Chronic Health Evaluation II (APACHE II) and Simplified Acute Physiology Score (SAPS) as well as routine tests in septic patients such as C reactive protein (CRP), procalcitonin (PCT). We enrolled adult patients admitted to the Intensive Care Unit (ICU). After admission to the ICU and the diagnosis of sepsis, blood samples were collected and the severity scores: APACHE II, SAPS were calculated on the first day of ICU admission. We recorded the following from the blood samples: CRP, PCT, angiopoietine2 (Ang-2). We performed several one-way ANOVA tests to determine any significant mean difference of the analyzed variables. We observed that variant genotypes of ANG2-35G>C gene polymorphism are significantly related to CRP, aspect which increases this biomarker credibility compared with others (i.e., PCT), in septic patients. ANG2-35G>C gene polymorphism is associated with severity scores, APACHE II, and SAPS in sepsis.
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49
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Abstract
Biomarker panels have the potential to advance the field of critical care medicine by stratifying patients according to prognosis and/or underlying pathophysiology. This article discusses the discovery and validation of biomarker panels, along with their translation to the clinical setting. The current literature on the use of biomarker panels in sepsis, acute respiratory distress syndrome, and acute kidney injury is reviewed.
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Affiliation(s)
- Susan R Conway
- Division of Critical Care Medicine, Children's National Medical Center, 111 Michigan Avenue Northwest, Washington, DC 20010, USA; Department of Pediatrics, George Washington University School of Medicine, Washington, DC, USA.
| | - Hector R Wong
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati Children's Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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50
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Thompson K, Venkatesh B, Finfer S. Sepsis and septic shock: current approaches to management. Intern Med J 2019; 49:160-170. [PMID: 30754087 DOI: 10.1111/imj.14199] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/28/2018] [Accepted: 09/28/2018] [Indexed: 12/15/2022]
Abstract
Sepsis, defined as life-threatening organ dysfunction due to a dysregulated host response to infection, is recognised by the World Health Organization as a global health priority. Each year, 5000 of the 18 000 adults with sepsis treated in Australian intensive care units die, with survivors suffering long-term physical, cognitive and psychological dysfunction, which is poorly recognised and frequently untreated. There are currently no effective pharmacological treatments for sepsis, making early recognition, resuscitation and immediate treatment with appropriate antibiotics the key to reducing the burden of resulting disease. The majority of sepsis, around 70-80%, is community acquired making emergency departments and primary care key targets to improve recognition and early management. Case fatality rates for sepsis are decreasing in many countries with the reduction attributed to national or regional screening and quality improvement programmes focused on early identification and immediate treatment. The optimum approach to treating established sepsis has been informed by high-quality, multicentre investigator initiated randomised trials with much of the valuable data coming from National Health and Medical Research Council-funded trials run from Australia. While early recognition and improved management of the acute episode are important steps in reducing death and disability from sepsis, a substantial reduction in the burden of sepsis-related disease requires action across the entire healthcare system. In this narrative review, we provide a summary of current knowledge on epidemiology of sepsis and septic shock and recommendations on the optimum approach to the management of these conditions in adults.
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Affiliation(s)
- Kelly Thompson
- The George Institute for Global Health, Sydney, New South Wales, Australia.,University of New South Wales, Sydney, New South Wales, Australia
| | - Balasubramanian Venkatesh
- The George Institute for Global Health, Sydney, New South Wales, Australia.,University of New South Wales, Sydney, New South Wales, Australia.,The Princess Alexandra Hospital, University of Queensland, Brisbane, Queensland, Australia.,The Wesley Hospital, Brisbane, Queensland, Australia
| | - Simon Finfer
- The George Institute for Global Health, Sydney, New South Wales, Australia.,University of New South Wales, Sydney, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia.,Malcolm Fisher Department of Intensive Care Medicine, Royal North Shore Hospital, Sydney, New South Wales, Australia
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