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Tsakiroglou M, Evans A, Pirmohamed M. Leveraging transcriptomics for precision diagnosis: Lessons learned from cancer and sepsis. Front Genet 2023; 14:1100352. [PMID: 36968610 PMCID: PMC10036914 DOI: 10.3389/fgene.2023.1100352] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/20/2023] [Indexed: 03/12/2023] Open
Abstract
Diagnostics require precision and predictive ability to be clinically useful. Integration of multi-omic with clinical data is crucial to our understanding of disease pathogenesis and diagnosis. However, interpretation of overwhelming amounts of information at the individual level requires sophisticated computational tools for extraction of clinically meaningful outputs. Moreover, evolution of technical and analytical methods often outpaces standardisation strategies. RNA is the most dynamic component of all -omics technologies carrying an abundance of regulatory information that is least harnessed for use in clinical diagnostics. Gene expression-based tests capture genetic and non-genetic heterogeneity and have been implemented in certain diseases. For example patients with early breast cancer are spared toxic unnecessary treatments with scores based on the expression of a set of genes (e.g., Oncotype DX). The ability of transcriptomics to portray the transcriptional status at a moment in time has also been used in diagnosis of dynamic diseases such as sepsis. Gene expression profiles identify endotypes in sepsis patients with prognostic value and a potential to discriminate between viral and bacterial infection. The application of transcriptomics for patient stratification in clinical environments and clinical trials thus holds promise. In this review, we discuss the current clinical application in the fields of cancer and infection. We use these paradigms to highlight the impediments in identifying useful diagnostic and prognostic biomarkers and propose approaches to overcome them and aid efforts towards clinical implementation.
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Affiliation(s)
- Maria Tsakiroglou
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- *Correspondence: Maria Tsakiroglou,
| | - Anthony Evans
- Computational Biology Facility, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Munir Pirmohamed
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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Chen D, Wang H, Cai X. Curcumin interferes with sepsis-induced cardiomyocyte apoptosis via TLR1 inhibition. Rev Port Cardiol 2023; 42:209-221. [PMID: 36702348 DOI: 10.1016/j.repc.2023.01.013] [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: 07/01/2021] [Accepted: 05/17/2022] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVE Sepsis-induced cardiomyopathy is the leading cause of death in sepsis and is characterized by reversible myocardial depression. However, the specific mechanisms responsible for myocardial injury in sepsis are not known. The present study used bioinformatic analysis to explore the possible mechanisms of sepsis-induced myocardial injury and the therapeutic potential of curcumin. METHODS The GSE125042 microarray gene expression matrix was obtained from the Gene Expression Omnibus database, which includes 10 septic cardiomyocyte samples from cecum ligation perforation constructs and 10 sham-operated groups cardiomyocyte samples. Background correction and matrix data normalization were performed using the robust multiarray average algorithm. Differentially expressed genes (DEGs) screening was performed using the Limma R package expression matrix, and whole gene analysis was performed using the weighted gene co-expression network analysis R package to construct gene networks and identify modules. Enrichment analysis and gene set enrichment analysis was performed on the genes to be selected. Construct cellular and animal models of myocardial injury in sepsis were assessed and the effects of curcumin on a rat or cardiac myocytes were observed. RESULTS A total of 2876 DEGs were screened based on the GSE125042 chip, of which 1424 genes were upregulated and 1452 genes were down regulated. WGCNA analysis of the whole genes was also performed and a total of 20 gene modules were generated. Among them, the selected TLR1 gene was present in the most strongly correlated Brown module. Enrichment analysis of the upregulated DEGs with the Brown module showed that they were significantly enriched in biological processes related to ribosomal protein complex generation, cellular components related to phagocytic vesicles and molecular functions related to Toll-like receptor binding, affecting cardiomyocyte survival as a target for molecular intervention in septic cardiomyopathy. Animal experiments showed that curcumin reduced inflammation levels, improved cardiac function and increased survival in rats with septic myocardial injury. Cellular experiments showed that curcumin increased the survival rate of lipopolysaccharide-treated cardiomyocytes and down regulated TLR1 expression and inhibited NF-κB phosphorylation in cells in a dose-dependent manner. Molecular docking analysis revealed that curcumin interacted with TLR1 by hydrogen bonding and could be stably bound to inhibit the biological function of TLR1. CONCLUSION Our study shows that curcumin attenuates myocardial injury in sepsis by inhibiting TLR1 expression, which provides a molecular theoretical basis for clinical treatment.
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Affiliation(s)
- Dandan Chen
- Department of Critical Care Medicine, Haikou Hospital, Xiangya Medical College, Central South University, China
| | - Hongwu Wang
- Department of Critical Care Medicine, Haikou Hospital, Xiangya Medical College, Central South University, China
| | - Xingjun Cai
- Department of Respiratory and Critical Care Medicine, Hainan General Hospital, China.
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3
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Identification of ceRNA regulatory network in acute pancreatitis and acute recurrent pancreatitis. Eur J Gastroenterol Hepatol 2022; 34:1031-1041. [PMID: 36052691 DOI: 10.1097/meg.0000000000002421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
OBJECTIVE The aim of this study was to find differentially expressed long noncoding RNAs (lncRNAs), microRNAs (miRNAs) and mRNAs and related signaling pathways, contributing to understanding the molecular mechanism of acute recurrent pancreatitis (ARP). METHODS First, peripheral whole blood samples from five acute pancreatitis (AP) patients, five ARP patients and five healthy individuals ( N ) were collected for RNA sequencing. Second, differentially/specifically expressed lncRNAs, miRNAs and mRNAs were identified in AP vs. N , ARP vs. N and ARP. Third, the ceRNA (lncRNA-miRNA-mRNA) networks of common/specifical lncRNAs, miRNAs and mRNAs were constructed in AP vs. N , ARP vs. N and ARP. Finally, functional analysis of common mRNAs in AP vs. N and ARP vs. N was performed. RESULTS A total of 315 common lncRNAs, 12 common miRNAs and 909 common mRNAs were identified between AP and ARP. Ninety-four specifically expressed lncRNAs, one specifically expressed miRNAs and 286 specifically expressed mRNAs were found in ARP. Some interaction pairs were identified in AP and ARP, such as LUCAT1/NEAT1-hsa-miR-16-2-3p-HK2, CHRM3-AS2-hsa-miR-122-5p/hsa-miR-145-3p-DBH/CACNA1C, CHRM3-AS2-hsa-miR-200a-3p-PDGFD, RBM26-AS1-hsa-miR-200b-3p-FHIT and LINC00891/KTN1-AS1-hsa-miR-143-3p-tyrosine kinase (TXK). ASAP1-IT2/DGCR9-hsa-miR-342-5p-ABCC5/MAP2K6 was the only one specific interaction pair identified in ARP. Four significantly enriched signaling pathways were identified in AP vs. N and ARP vs. N , including amino sugar and nucleotide sugar metabolism (involved NPL and HK2), MAPK signaling pathway (involved CACNA1C and PDGFD), metabolic pathways (involved DBH and FHIT) and leukocyte transendothelial migration (involved TXK). CONCLUSION The identified altered lncRNAs, miRNAs, mRNAs and related signaling pathways may be involved in the AP development and recurrence.
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Çakırlar FK. Application of Biomarkers in the Diagnostic Distinction of Bacterial and Viral Infections. Biomark Med 2022. [DOI: 10.2174/9789815040463122010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Infectious diseases, which pose a great threat worldwide, have a significant
impact on public health and the world economy. It contributes to increased healthcare
costs, unnecessary drug-related side effects, and increased antimicrobial resistance. It is
not always easy to distinguish the etiological differentiation of diseases that can
develop with bacteria and viruses. Therefore, one of the biggest challenges in medicine
is how to correctly distinguish between the different causes of these infections and how
to manage the patient. Because bacterial and viral infections often present similar
symptoms. The real decision is whether the infection is caused by bacteria or viruses
and whether to treat the patient with antibiotics. There are many different
methodological approaches to diagnosing infections. Biomarkers have been used in the
diagnosis of diseases and other conditions for many years. Biomarkers are molecules
found in blood and body fluids in measurable amounts, which can evaluate biological
and pathological processes. These key indicators can provide vital information in
determining disease prognosis, predicting response to treatments, adverse events and
drug interactions, and identifying key risks. An effective biomarker is extremely
important for the early diagnosis of various diseases. The explosion of interest in
biomarker research is driving the development of new predictive, diagnostic, and
prognostic products in modern medical practice. The purpose of this review is to
demonstrate the use and diagnostic potential of current and investigational biomarkers
in the distinction between bacterial and viral infections.
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Affiliation(s)
- Fatma Köksal Çakırlar
- Faculty of Cerrahpaşa Medicine, University of İstanbul- Cerrahpaşa,Department of Medical Microbiology,Department of Medical Microbiology, Faculty of Cerrahpaşa Medicine, University of İstanbul- Cerrahpaşa, Istanbul, Turkey,Istanbul,Turkey
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Bandyopadhyay S, Loftus TJ, Peng YC, Lopez MC, Baker HV, Segal MS, Graim K, Ozrazgat-Baslanti T, Rashidi P, Bihorac A. EARLY DIFFERENTIATION BETWEEN SEPSIS AND STERILE INFLAMMATION VIA URINARY GENE SIGNATURES OF METABOLIC DYSREGULATION. Shock 2022; 58:20-27. [PMID: 35904146 PMCID: PMC9391290 DOI: 10.1097/shk.0000000000001952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/20/2022] [Accepted: 05/26/2022] [Indexed: 11/25/2022]
Abstract
ABSTRACT Objective: The aim of this study was to characterize early urinary gene expression differences between patients with sepsis and patients with sterile inflammation and summarize in terms of a reproducible sepsis probability score. Design: This was a prospective observational cohort study. Setting: The study was conducted in a quaternary care academic hospital. Patients: One hundred eighty-six sepsis patients and 78 systemic inflammatory response syndrome (SIRS) patients enrolled between January 2015 and February 2018. Interventions: Whole-genome transcriptomic analysis of RNA was extracted from urine obtained from sepsis patients within 12 hours of sepsis onset and from patients with surgery-acquired SIRS within 4 hours after major inpatient surgery. Measurements and Main Results: We identified 422 of 23,956 genes (1.7%) that were differentially expressed between sepsis and SIRS patients. Differentially expressed probes were provided to a collection of machine learning feature selection models to identify focused probe sets that differentiate between sepsis and SIRS. These probe sets were combined to find an optimal probe set (UrSepsisModel) and calculate a urinary sepsis score (UrSepsisScore), which is the geometric mean of downregulated genes subtracted from the geometric mean of upregulated genes. This approach summarizes the expression values of all decisive genes as a single sepsis score. The UrSepsisModel and UrSepsisScore achieved area under the receiver operating characteristic curves 0.91 (95% confidence interval, 0.86-0.96) and 0.80 (95% confidence interval, 0.70-0.88) on the validation cohort, respectively. Functional analyses of probes associated with sepsis demonstrated metabolic dysregulation manifest as reduced oxidative phosphorylation, decreased amino acid metabolism, and decreased oxidation of lipids and fatty acids. Conclusions: Whole-genome transcriptomic profiling of urinary cells revealed focused probe panels that can function as an early diagnostic tool for differentiating sepsis from sterile SIRS. Functional analysis of differentially expressed genes demonstrated a distinct metabolic dysregulation signature in sepsis.
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Affiliation(s)
- Sabyasachi Bandyopadhyay
- Intelligent Critical Care Center, University of Florida, Gainesville, Florida
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida
| | - Tyler J. Loftus
- Intelligent Critical Care Center, University of Florida, Gainesville, Florida
- Department of Surgery, University of Florida, Gainesville, Florida
| | - Ying-Chih Peng
- Division of Nephrology, Hypertension and Renal Transplantation, Department of Medicine, University of Florida, Gainesville, Florida
- Department of Industrial and Systems Engineering, University of Florida, Gainesville, Florida
| | - Maria-Cecilia Lopez
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, Florida
| | - Henry V. Baker
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, Florida
| | - Mark S. Segal
- Division of Nephrology, Hypertension and Renal Transplantation, Department of Medicine, University of Florida, Gainesville, Florida
| | - Kiley Graim
- Intelligent Critical Care Center, University of Florida, Gainesville, Florida
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida
| | - Tezcan Ozrazgat-Baslanti
- Intelligent Critical Care Center, University of Florida, Gainesville, Florida
- Division of Nephrology, Hypertension and Renal Transplantation, Department of Medicine, University of Florida, Gainesville, Florida
| | - Parisa Rashidi
- Intelligent Critical Care Center, University of Florida, Gainesville, Florida
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida
| | - Azra Bihorac
- Intelligent Critical Care Center, University of Florida, Gainesville, Florida
- Division of Nephrology, Hypertension and Renal Transplantation, Department of Medicine, University of Florida, Gainesville, Florida
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Fu M, Zhang K. MAPK interacting serine/threonine kinase 1 ( MKNK1), one target gene of miR-223-3p, correlates with neutrophils in sepsis based on bioinformatic analysis. Bioengineered 2021; 12:2550-2562. [PMID: 34115574 PMCID: PMC8806917 DOI: 10.1080/21655979.2021.1935405] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Sepsis, resulting from a harmful or damaging response to infection, is a complex and severe disease that causes high mortality. Three independent expression profiles of miRNA – GSE94717, GSE149764, and GSE101639 – were collected and integrated to analyze miRNAs associated with sepsis. One miRNA, miR-223-3p, was detected significantly downregulated in patients with sepsis. The upregulated miR-223-3p target genes in patients with sepsis were enriched in central carbon metabolism associated with HIF-1 signaling and galactose metabolism. Specially, three HIF-1 signaling genes – hypoxia-inducible factor 1-alpha (HIF1A), hexokinase 2 (HK2), and MAP kinase-interacting serine/threonine-protein kinase 1 (MKNK1) – were found significantly upregulated in patients with sepsis. Additionally, MKNK1 expression was downregulated in septic responders to early therapeutic treatments. Neutrophils were significantly accumulated in patients with sepsis and decreased in responders after therapy; MKNK1 was significantly positively correlated with neutrophils. Our findings indicate MKNK1, one targets of miR-223-3p, might be involved in sepsis via regulating the neutrophils abundance by mediating the expression inflammation factors.
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Affiliation(s)
- Mingmin Fu
- Department of Intensive Care Unit, Huzhou Cent Hosp, Affiliated Cent Hosp HuZhou University, Huzhou, Zhejiang, Peoples R China
| | - Kai Zhang
- Department of Emergency, Huzhou Cent Hosp, Affiliated Cent Hosp HuZhou University, Huzhou, Zhejiang, Peoples R China
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Traber KE, Dimbo EL, Shenoy AT, Symer EM, Allen E, Mizgerd JP, Quinton LJ. Neutrophil-Derived Oncostatin M Triggers Diverse Signaling Pathways during Pneumonia. Infect Immun 2021; 89:e00655-20. [PMID: 33526570 PMCID: PMC8090961 DOI: 10.1128/iai.00655-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/11/2021] [Indexed: 11/20/2022] Open
Abstract
Pneumonia is a major public health concern, causing significant morbidity and mortality annually despite the broad use of antimicrobial agents. Underlying many of the severe sequelae of acute lung infections is dysfunction of the immune response, which remains incompletely understood yet is an attractive target of adjunct therapy in pneumonia. Here, we investigate the role of oncostatin M (OSM), a pleiotropic cytokine of the interleukin-6 (IL-6) family, and how its signaling modulates multiple innate immune pathways during pneumonia. Previously, we showed that OSM is necessary for neutrophil recruitment to the lungs during pneumonia by stimulating STAT3-driven CXCL5 expression. In this study, transcriptional profiling of whole-lung pneumonia with OSM neutralization revealed 241 differentially expressed genes following only 6 h of infection. Many downregulated genes are associated with STAT1, STAT3, and interferon signaling, suggesting these pathways are induced by OSM early in pneumonia. Interestingly, STAT1 and STAT3 activation was subsequently upregulated with OSM neutralization by 24 h, suggesting that OSM interruption dysregulates these central signaling pathways. When we investigated the source of OSM in pneumonia, neutrophils and, to a lesser extent, macrophages appear to be primary sources, suggesting a positive feedback loop of OSM production by neutrophils. From these studies, we conclude that OSM produced by recruited neutrophils tunes early innate immune signaling pathways, improving pneumonia outcomes.
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Affiliation(s)
- Katrina E Traber
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Ernest L Dimbo
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Anukul T Shenoy
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Elise M Symer
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Eri Allen
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Joseph P Mizgerd
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Lee J Quinton
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
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8
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Young PY, Mueller TF, Sis B, Churchill TA, Khadaroo RG. Oncostatin M Plays a Critical Role in Survival after Acute Intestinal Ischemia: Reperfusion Injury. Surg Infect (Larchmt) 2020; 21:799-806. [PMID: 32379547 DOI: 10.1089/sur.2019.193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background: Acute intestinal ischemia-reperfusion injury (AIIRI) is a devastating clinical condition relevant to multiple diseases processes, including sepsis, trauma, transplantation, and burns. An AIIRI is a contributor to the development of multiple organ dysfunction syndrome (MODS). Oncostatin M (OSM)/oncostatin M receptor (OSMR) signaling is an unrecognized and novel candidate pathway for the mediation of MODS. In this study, we hypothesized that OSM mediates the injury mechanism of AIIRI leading to MODS. Methods: Wild-type (WT) and OSMR-knockout (OSMR-/-) C57BL/6 mice underwent AIIRI using a well-established model of selective occlusion of the superior mesenteric artery (SMA). Serum cytokine concentrations were measured using a multiplex detection system. Further tissue analysis was conducted with polymerase chain reaction, enzyme-linked immunosorbent assay, Western blots, and histologic review. Results: Survival was significantly higher in WT than in OSMR-/- groups at 30 minutes of ischemia with 2 hours of reperfusion (100% versus 42.9%; P = 0.015). No significant differences in the degree of local intestinal injury was seen in the two groups. In contrast, the degree of lung injury, as evidenced by myeloperixodase activity, was lower in OSMR-/- animals in the early AIIRI groups. There was a greater degree of renal dysfunction in OSMR-/- mice. Oncostatin M mediated interleukin (IL)-10 upregulation, with WT animals having significantly lower IL-10 concentrations (52.04 ± 23.06 pg/mL versus 324.37 ± 140.35 pg/mL; P = 0.046). Conclusion: Oncostatin M signalling is essential during acute intestinal ischemia-reperfusion injury. An OSMR deficiency results in decreased early lung injury but increased renal dysfunction. There was a significantly increased mortality rate after AIIRI in mice with OSMR deficiency. Augmentation of OSM may be a novel immunomodulatory strategy for AIIRI.
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Affiliation(s)
- Pang Y Young
- Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Thomas F Mueller
- Department of Medicine, and Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Banu Sis
- Department of Laboratory Medicine and Pathology and Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Thomas A Churchill
- Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Rachel G Khadaroo
- Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.,Department of Division of Critical Care Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
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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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Quantification of Immune Dysregulation by Next-generation Polymerase Chain Reaction to Improve Sepsis Diagnosis in Surgical Patients. Ann Surg 2019; 269:545-553. [PMID: 28692472 DOI: 10.1097/sla.0000000000002406] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVES To quantify immunological dysfunction in surgical patients with presence/absence of sepsis using a droplet digital polymerase chain reaction (ddPCR) transcriptomic analysis. The study also aims to evaluate this approach for improving identification of sepsis in these patients. BACKGROUND Immune dysregulation is a central event in sepsis. Quantification of the expression of immunological genes participating in the pathogenesis of sepsis could represent a new avenue to improve its diagnosis. METHODS Expression of 6 neutrophil protease genes (MMP8, OLFM4, LCN2/NGAL, LTF, PRTN3, MPO) and also of 5 genes involved in the immunological synapse (HLA-DRA, CD40LG, CD3E, CD28, ICOS) was quantified in blood from 101 surgical patients with sepsis, 53 uninfected surgical patients, and 16 blood donors by using ddPCR. Areas under receiver operating characteristic curves (AUROC) and multivariate regression analysis were employed to test individual genes and gene ratios to identify sepsis, in comparison with procalcitonin. RESULTS Sepsis-induced overexpression of neutrophil protease genes and depressed expression of immunological synapse genes. MMP8/HLA-DRA, LCN2/HLA-DRA outperformed procalcitonin in differentiating between patients with sepsis and surgical controls in the AUROC analysis: LCN2/HLA-DRA: 0.90 (0.85-0.96), MMP8/HLA-DRA: 0.89 (0.84-0.95), procalcitonin: 0.80 (0.73-0.88) (AUROC, confidence interval 95%), and also in the multivariate analysis: LCN2/HLA-DRA: 8.57 (2.25-32.62); MMP8/HLA-DRA: 8.03 (2.10-30.76), procalcitonin: 4.20 (1.15-15.43) [odds ratio (confidence interval 95%)]. Gene expression levels of HLA-DRA were an independent marker of hospital mortality. CONCLUSIONS Quantifying the transcriptomic ratios MMP8/HLA-DRA, LCN2/HLA-DRA by ddPCR is a promising approach to improve sepsis diagnosis in surgical patients.
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Skibsted S, Bhasin MK, Henning DJ, Jaminet SC, Lewandowski J, Kirkegaard H, Aird WC, Shapiro NI. Leukocyte Transcriptional Response in Sepsis. Shock 2019; 52:166-173. [PMID: 30211758 PMCID: PMC10608800 DOI: 10.1097/shk.0000000000001258] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The complex host response to sepsis is incompletely understood. The aim of this investigation is to use leukocyte RNA sequencing to characterize biological functions, cellular pathways, and key regulatory molecules driving sepsis pathophysiology. METHODS This was a prospective, observational study of emergency department patients with sepsis, at an urban, academic, tertiary care center. In the derivation cohort, we collected blood at enrollment and 90 days after hospital discharge allowing each patient to serve as an internal control. We performed RNA sequencing to quantify transcriptional expression changes during sepsis and non-sepsis states. We then performed unsupervised and supervised analyses, as well as functional and pathway analyses. We selected the top down and upregulated genes and key regulatory molecules for validation. Validation occurred in a cohort of septic and non-septic using real-time PCR. RESULTS The derivation cohort included 5 patients, and RNA sequencing revealed 916 unique mRNA transcripts differentially expressed during sepsis. Among these, 673 (73%) genes were upregulated, and 243 (27%) were downregulated. Functional enrichment analysis revealed a highly dynamic downstream effect of the transcriptional activity during sepsis. Of the 43 functional cellular pathways activated during sepsis, the top pathways were closely associated with inflammation and response to infection. Validation occurred in 18 septic and 25 non-septic control patients, with 34/45 (76%) of identified genes validated. The regulatory analysis identified several key regulators of sepsis. CONCLUSIONS Highly dynamic transcriptional activity occurs in leukocytes during sepsis, activating key cellular pathways and master regulatory molecules that drive the sepsis process.
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Affiliation(s)
- Simon Skibsted
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center & Harvard Medical School, Boston, MA, USA
- Center for Emergency Medicine Research, Aarhus University Hospital & Aarhus University, Aarhus, Denmark
| | - Manoj K. Bhasin
- Center for Genomics, Beth Israel Deaconess Medical Center & Harvard Medical School, Boston, MA, USA
| | - Daniel J. Henning
- Division of Emergency Medicine, University of Washington, Seattle, WA, USA
| | - Shou Ching Jaminet
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center & Harvard Medical School, Boston, MA, USA
- Department of Pathology, Beth Israel Deaconess Medical Center & Harvard Medical School, Boston, MA, USA
| | - Jeffrey Lewandowski
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center & Harvard Medical School, Boston, MA, USA
| | - Hans Kirkegaard
- Center for Emergency Medicine Research, Aarhus University Hospital & Aarhus University, Aarhus, Denmark
| | - William C. Aird
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center & Harvard Medical School, Boston, MA, USA
| | - Nathan I. Shapiro
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center & Harvard Medical School, Boston, MA, USA
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center & Harvard Medical School, Boston, MA, USA
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12
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Khan HN, Perlee D, Schoenmaker L, van der Meer A, Franitza M, Toliat MR, Nürnberg P, Zwinderman AH, van der Poll T, Scicluna BP. Leukocyte transcriptional signatures dependent on LPS dosage in human endotoxemia. J Leukoc Biol 2019; 106:1153-1160. [PMID: 31280495 PMCID: PMC6852106 DOI: 10.1002/jlb.4a0219-050r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/29/2019] [Accepted: 06/15/2019] [Indexed: 12/18/2022] Open
Abstract
The host immune response is characterized by a complex interplay of signal‐specific cellular transcriptional responses. The magnitude of the immune response is dependent on the strength of the external stimulus. Knowledge on leukocyte transcriptional responses altered in response to different stimulus dosages in man is lacking. Here, we sought to identify leukocyte transcriptional signatures dependent on LPS dose in humans. Healthy human volunteers were administered 1 ng/kg (n = 7), 2 ng/kg (n = 6), or 4 ng/kg (n = 7) LPS intravenously. Blood was collected before (pre‐LPS) and 4 h after LPS administration. Total RNA was analyzed by microarrays and generalized linear models. Pathway analysis was performed by using Ingenuity pathway analysis. Leukocyte transcriptomes altered per LPS dosage were predominantly shared, with 47% common signatures relative to pre‐LPS. A univariate linear model identified a set of 3736 genes that exhibited a dependency on differing LPS dosages. Neutrophil, monocyte, and lymphocyte counts explained 38.9% of the variance in the LPS dose‐dependent gene set. A multivariate linear model including leukocyte composition delineated a set of 295 genes with a dependency on LPS dose. Evaluation of the 295 gene signature in patients with sepsis due to abdominal infections showed significant correlations. Promoter regions of the LPS dose gene set were enriched for YY1, EGR1, ELK1, GABPA, KLF4, and REL transcription factor binding sites. Intravenous injection of 1, 2, or 4 ng/kg LPS was accompanied by both shared and distinct leukocyte transcriptional alterations. These data may assist in assessing the severity of the insult in patients with abdominal sepsis.
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Affiliation(s)
- Hina N. Khan
- Center for Experimental Molecular MedicineAmsterdam University Medical CentersAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
- Department of Clinical EpidemiologyBiostatistics and BioinformaticsAmsterdam University Medical Centers, Academic Medical CenterAmsterdamThe Netherlands
| | - Desiree Perlee
- Center for Experimental Molecular MedicineAmsterdam University Medical CentersAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Lieke Schoenmaker
- Center for Experimental Molecular MedicineAmsterdam University Medical CentersAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Anne‐Jan van der Meer
- Center for Experimental Molecular MedicineAmsterdam University Medical CentersAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Marek Franitza
- Cologne Center for Genomics (CCG)University of CologneCologneGermany
| | | | - Peter Nürnberg
- Cologne Center for Genomics (CCG)University of CologneCologneGermany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
- Center for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Aeilko H. Zwinderman
- Department of Clinical EpidemiologyBiostatistics and BioinformaticsAmsterdam University Medical Centers, Academic Medical CenterAmsterdamThe Netherlands
| | - Tom van der Poll
- Center for Experimental Molecular MedicineAmsterdam University Medical CentersAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
- Division of Infectious DiseasesAmsterdam University Medical CentersAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Brendon P. Scicluna
- Center for Experimental Molecular MedicineAmsterdam University Medical CentersAcademic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
- Department of Clinical EpidemiologyBiostatistics and BioinformaticsAmsterdam University Medical Centers, Academic Medical CenterAmsterdamThe Netherlands
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13
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Verboom DM, Koster-Brouwer ME, Varkila MRJ, Bonten MJM, Cremer OL. Profile of the SeptiCyte™ LAB gene expression assay to diagnose infection in critically ill patients. Expert Rev Mol Diagn 2019; 19:95-108. [PMID: 30623693 DOI: 10.1080/14737159.2019.1567333] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Sepsis is a severe and frequently occurring clinical syndrome, caused by the inflammatory response to infections. Recent studies on the human transcriptome during sepsis have yielded several gene-expression assays that might assist physicians during clinical assessment of patients suspected of sepsis. SeptiCyte™ LAB (Immunexpress, Seattle, WA) is the first gene expression assay that was cleared by the FDA in the United States to distinguish infectious from non-infectious causes of systemic inflammation in critically ill patients. The test consists of the simultaneous amplification of four RNA transcripts (CEACAM4, LAMP1, PLAC8, and PLA2G7) in whole blood using a quantitative real-time PCR reaction. This review provides an overview of the challenges in the diagnosis of sepsis, the development of gene expression signatures, and a detailed description of available clinical performance studies evaluating SeptiCyte™ LAB.
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Affiliation(s)
- D M Verboom
- a Julius Center for Health Sciences and Primary Care , University Medical Center Utrecht , Utrecht , The Netherlands.,b Department of Intensive Care , University Medical Center Utrecht , Utrecht , The Netherlands
| | - M E Koster-Brouwer
- a Julius Center for Health Sciences and Primary Care , University Medical Center Utrecht , Utrecht , The Netherlands.,b Department of Intensive Care , University Medical Center Utrecht , Utrecht , The Netherlands
| | - M R J Varkila
- a Julius Center for Health Sciences and Primary Care , University Medical Center Utrecht , Utrecht , The Netherlands.,b Department of Intensive Care , University Medical Center Utrecht , Utrecht , The Netherlands
| | - M J M Bonten
- a Julius Center for Health Sciences and Primary Care , University Medical Center Utrecht , Utrecht , The Netherlands.,c Department of Medical Microbiology , University Medical Center Utrecht , Utrecht , The Netherlands
| | - O L Cremer
- b Department of Intensive Care , University Medical Center Utrecht , Utrecht , The Netherlands
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14
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From traditional biochemical signals to molecular markers for detection of sepsis after burn injuries. Burns 2019; 45:16-31. [DOI: 10.1016/j.burns.2018.04.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 02/28/2018] [Accepted: 04/24/2018] [Indexed: 12/22/2022]
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Průcha M, Zazula R, Russwurm S. Sepsis Diagnostics in the Era of "Omics" Technologies. Prague Med Rep 2018; 119:9-29. [PMID: 29665344 DOI: 10.14712/23362936.2018.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
Sepsis is a multifactorial clinical syndrome with an extremely dynamic clinical course and with high diverse clinical phenotype. Early diagnosis is crucial for the final clinical outcome. Previous studies have not identified a biomarker for the diagnosis of sepsis which would have sufficient sensitivity and specificity. Identification of the infectious agents or the use of molecular biology, next gene sequencing, has not brought significant benefit for the patient in terms of early diagnosis. Therefore, we are currently searching for biomarkers, through "omics" technologies with sufficient diagnostic specificity and sensitivity, able to predict the clinical course of the disease and the patient response to therapy. Current progress in the use of systems biology technologies brings us hope that by using big data from clinical trials such biomarkers will be found.
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Affiliation(s)
- Miroslav Průcha
- Department of Clinical Biochemistry, Haematology and Immunology, Na Homolce Hospital, Prague, Czech Republic.
| | - Roman Zazula
- Department of Anesthesiology and Intensive Care, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czech Republic
| | - Stefan Russwurm
- Department of Anesthesiology and Intensive Care, University Hospital Jena, Jena, Germany
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16
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Research Advances in Biomarker for Sepsis. ADVANCED TRAUMA AND SURGERY 2017. [PMCID: PMC7120075 DOI: 10.1007/978-981-10-2425-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Sepsis is one of the most common causes of death in severely injured patients worldwide. The early detection of sepsis still has to be solved in clinical practice. The delayed diagnosis often contributes to inappropriate antimicrobial treatment and subsequent high mortality. Sepsis biomarkers are produced during the host response to infection. Traditional biomarkers are polypeptides and/or proteins derived from this response. Omics-based biomarkers are screening out from all kinds of molecules of host response while high-throughout omics technologies are emerging. This review describes traditional and potential omics-based sepsis biomarkers from currently available literatures. The combination of these biomarkers would refine the identification of sepsis for further clinical and experimental sepsis studies.
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17
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Reilly JP, Meyer NJ, Christie JD. Genetics in the Prevention and Treatment of Sepsis. SEPSIS 2017. [DOI: 10.1007/978-3-319-48470-9_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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18
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Abstract
BACKGROUND Sepsis is a systemic response to infection that can affect brain function by inducing resident cells (including astrocytes and microglia) to generate brain chemokines and cytokines. However, there are few studies on the human brain. Since this information may shed further light on pathogenesis, our study objective was to measure the expression of 36 chemokines and cytokines in autopsied brain from 3 cases of sepsis and 10 controls, and to relate this to astrocyte and microglial activation. METHODS The right frontal pole was removed at autopsy and chemokine and cytokine expression measured by multiplexed enzyme-linked immunosorbent assay and real-time quantitative polymerase chain reaction (qPCR). Immunohistochemistry and image analysis were carried out to determine the expression of glial fibrillary acidic protein (GFAP), a marker of activated astrocytes, and CD68 and CD45, markers of activated microglial cells. RESULTS Concentrations of the chemokines CXCL8, CXCL10, CXCL12, CCL13 and CCL22 were increased in pooled data from the three cases of sepsis (p<0.05); however, their messenger RNA (mRNA) expression was unaltered. CXCL13, CXCL1, CXCL2, CCL1, CCL2, CCL8, CCL20, (interleukin) IL-16, IL-1β and (tumour necrosis factor) TNF concentrations showed increases in two of three sepsis cases. Additionally, individual sepsis cases showed increases in mRNA expression for HDAC (histone deacetylase) 6 and EIF (eukaryotic translation initiation factor) 4A2. Brain GFAP expression was significantly increased (p<0.05) in pooled data from the three sepsis cases. Individual sepsis cases showed increases in CD68 or CD45 expression. CONCLUSIONS These expression patterns add to our understanding of the pathogenesis of sepsis and its effects on the brain.
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Mackay M, Oswald M, Sanchez-Guerrero J, Lichauco J, Aranow C, Kotkin S, Korsunsky I, Gregersen PK, Diamond B. Molecular signatures in systemic lupus erythematosus: distinction between disease flare and infection. Lupus Sci Med 2016; 3:e000159. [PMID: 27933197 PMCID: PMC5133406 DOI: 10.1136/lupus-2016-000159] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 08/17/2016] [Accepted: 08/19/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Meggan Mackay
- The Feinstein Institute for Medical Research, Manhasset, New York, USA
| | - Michaela Oswald
- The Feinstein Institute for Medical Research, Manhasset, New York, USA
| | | | | | - Cynthia Aranow
- The Feinstein Institute for Medical Research, Manhasset, New York, USA
| | - Sean Kotkin
- The Feinstein Institute for Medical Research, Manhasset, New York, USA
| | - Ilya Korsunsky
- The Feinstein Institute for Medical Research, Manhasset, New York, USA
| | - Peter K Gregersen
- The Feinstein Institute for Medical Research, Manhasset, New York, USA
| | - Betty Diamond
- The Feinstein Institute for Medical Research, Manhasset, New York, USA
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20
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Ahnert P, Creutz P, Scholz M, Schütte H, Engel C, Hossain H, Chakraborty T, Bauer M, Kiehntopf M, Völker U, Hammerschmidt S, Loeffler M, Suttorp N. PROGRESS - prospective observational study on hospitalized community acquired pneumonia. BMC Pulm Med 2016; 16:108. [PMID: 27535544 PMCID: PMC4987996 DOI: 10.1186/s12890-016-0255-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/03/2016] [Indexed: 12/23/2022] Open
Abstract
Background Community acquired pneumonia (CAP) is a high incidence disease resulting in about 260,000 hospital admissions per year in Germany, more than myocardial infarction or stroke. Worldwide, CAP is the most frequent infectious disease with high lethality ranging from 1.2 % in those 20–29 years old to over 10 % in patients older than 70 years, even in industrial nations. CAP poses numerous medical challenges, which the PROGRESS (Pneumonia Research Network on Genetic Resistance and Susceptibility for the Evolution of Severe Sepsis) network aims to tackle: Operationalization of disease severity throughout the course of disease, outcome prediction for hospitalized patients and prediction of transitions from uncomplicated CAP to severe CAP, and finally, to CAP with sepsis and organ failure as a life-threatening condition. It is a major aim of PROGRESS to understand and predict patient heterogeneity regarding outcome in the hospital and to develop novel treatment concepts. Methods PROGRESS was designed as a clinical, observational, multi-center study of patients with CAP requiring hospitalization. More than 1600 patients selected for low burden of co-morbidities have been enrolled, aiming at a total of 3000. Course of disease, along with therapy, was closely monitored by daily assessments and long-term follow-up. Daily blood samples allow in depth molecular-genetic characterization of patients. We established a well-organized workflow for sample logistics and a comprehensive data management system to collect and manage data from more than 50 study centers in Germany and Austria. Samples are stored in a central biobank and clinical data are stored in a central data base which also integrates all data from molecular assessments. Discussion With the PROGRESS study, we established a comprehensive data base of high quality clinical and molecular data allowing investigation of pressing research questions regarding CAP. In-depth molecular characterization will contribute to the discovery of disease mechanisms and establishment of diagnostic and predictive biomarkers. A strength of PROGRESS is the focus on younger patients with low burden of co-morbidities, allowing a more direct look at host biology with less confounding. As a resulting limitation, insights from PROGRESS will require validation in representative patient cohorts to assess clinical utility. Trial registration The PROGRESS study was retrospectively registered on May 24th, 2016 with ClinicalTrials.gov: NCT02782013
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Affiliation(s)
- Peter Ahnert
- Institute for Medical Informatics, Statistics, and Epidemiology (IMISE), Medical Faculty, University of Leipzig, Haertelstr. 16-18, 04107, Leipzig, Germany.
| | - Petra Creutz
- Department of Infectious Disease and Respiratory Medicine, Charité - University Medicine Berlin, Campus Virchowklinikum, Augustenburgerplatz 1, 13353, Berlin, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics, and Epidemiology (IMISE), Medical Faculty, University of Leipzig, Haertelstr. 16-18, 04107, Leipzig, Germany
| | - Hartwig Schütte
- Department of Pulmonary Medicine, Ernst von Bergmann Hospital, Charlottenstr. 72, 14467, Potsdam, Germany
| | - Christoph Engel
- Institute for Medical Informatics, Statistics, and Epidemiology (IMISE), Medical Faculty, University of Leipzig, Haertelstr. 16-18, 04107, Leipzig, Germany
| | - Hamid Hossain
- Institute of Medical Microbiology, Justus-Liebig University Giessen, Schubertstr. 81, 35392, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus-Liebig University Giessen, Schubertstr. 81, 35392, Giessen, Germany
| | - Michael Bauer
- Department of Anesthesiology and Intensive Medicine, Jena University Hospital, Erlanger Allee 101, 07747, Jena, Germany
| | - Michael Kiehntopf
- Integrated Biobank Jena (IBBJ) and Institute of Clinical Chemistry and Laboratory Diagnostics, Jena University Hospital, Erlanger Allee 101, 07747, Jena, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, Ernst-Moritz-Arndt University Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17487, Greifswald, Germany
| | - Sven Hammerschmidt
- Interfaculty Institute for Genetics and Functional Genomics, Department Genetics of Microorganisms, Ernst-Moritz-Arndt University Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17487, Greifswald, Germany
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics, and Epidemiology (IMISE), Medical Faculty, University of Leipzig, Haertelstr. 16-18, 04107, Leipzig, Germany
| | - Norbert Suttorp
- Department of Infectious Disease and Respiratory Medicine, Charité - University Medicine Berlin, Campus Virchowklinikum, Augustenburgerplatz 1, 13353, Berlin, Germany
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21
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Friggeri A, Cazalis MA, Pachot A, Cour M, Argaud L, Allaouchiche B, Floccard B, Schmitt Z, Martin O, Rimmelé T, Fontaine-Kesteloot O, Page M, Piriou V, Bohé J, Monneret G, Morisset S, Textoris J, Vallin H, Blein S, Maucort-Boulch D, Lepape A, Venet F. Decreased CX3CR1 messenger RNA expression is an independent molecular biomarker of early and late mortality in critically ill patients. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2016; 20:204. [PMID: 27364780 PMCID: PMC4929760 DOI: 10.1186/s13054-016-1362-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/27/2016] [Indexed: 01/31/2023]
Abstract
Background Chemokine (C-X3-C motif) receptor 1 (CX3CR1) was identified as the most differentially expressed gene between survivors and non-survivors in two independent cohorts of septic shock patients and was proposed as a marker of sepsis-induced immunosuppression. Whether such a biomarker is associated with mortality in the heterogeneous group of critically ill patients is unknown. The primary objective of this study was to evaluate the association between CX3CR1 messenger RNA (mRNA) expression and mortality in intensive care unit (ICU) patients. The secondary objective was to evaluate similar endpoints in the subgroup of septic shock patients. Methods We performed a prospective, multicentre, non-interventional study in six ICUs of university hospitals in Lyon, France. Every consecutive adult patient with systemic inflammatory response syndrome and an expected length of stay in the ICU over 2 days was included. Whole-blood CX3CR1 mRNA expression was measured by quantitative real-time polymerase chain reaction at day 1 (D1) and D3 after inclusion. Results In ICU patients (n = 725), decreased CX3CR1 mRNA expression at D1 was associated with high D7 mortality (AUC 0.70, adjusted OR [aOR] 2.03, 95 % CI 1.19–3.46), while decreased expression at D3 was associated with increased D28 mortality (AUC 0.64, aOR 2.34, 95 % CI 1.45–3.77). In septic shock patients (n = 279), similar associations were observed between decreased D1 CX3CR1 mRNA expression and D7 mortality (AUC 0.69, aOR 2.76, 95 % CI 1.32–5.75) as well as decreased D3 expression and D28 mortality (AUC 0.72, aOR 3.98, 95 % CI 1.72–9.23). These associations were independent of lactacidaemia, Simplified Acute Physiology Score II, Sepsis-related Organ Failure Assessment score and Charlson comorbidity index. Conclusions This study represents the largest evaluation of such an mRNA marker in a heterogeneous cohort of severely injured patients. Our results show that decreased CX3CR1 mRNA expression is associated with increased mortality in ICU patients. This suggests a link between injury-induced immunosuppression and mortality in critically ill patients. In this context, the monitoring of such a host response molecular biomarker could prove very helpful for the identification of patients at high risk of death in the ICU. Electronic supplementary material The online version of this article (doi:10.1186/s13054-016-1362-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Arnaud Friggeri
- Hospices Civils de Lyon, Intensive Care Unit, Centre Hospitalier Lyon Sud, Pierre Bénite, France.,Hospices Civils de Lyon-bioMérieux Joint Research Unit, Groupement Hospitalier Edouard Herriot, Lyon, France
| | - Marie-Angélique Cazalis
- Hospices Civils de Lyon-bioMérieux Joint Research Unit, Groupement Hospitalier Edouard Herriot, Lyon, France
| | - Alexandre Pachot
- Hospices Civils de Lyon-bioMérieux Joint Research Unit, Groupement Hospitalier Edouard Herriot, Lyon, France
| | - Martin Cour
- Hospices Civils de Lyon, Medical Intensive Care Unit, Groupement Hospitalier Edouard Herriot, Lyon, France
| | - Laurent Argaud
- Hospices Civils de Lyon, Medical Intensive Care Unit, Groupement Hospitalier Edouard Herriot, Lyon, France
| | - Bernard Allaouchiche
- Hospices Civils de Lyon, Intensive Care Unit, Centre Hospitalier Lyon Sud, Pierre Bénite, France
| | - Bernard Floccard
- Hospices Civils de Lyon, Department of Anaesthesiology and Critical Care Medicine, Groupement Hospitalier Edouard Herriot, University Claude Bernard Lyon 1, Lyon, France
| | - Zoé Schmitt
- Hospices Civils de Lyon, Intensive Care Unit, Hôpital de la Croix Rousse, Lyon, France
| | - Olivier Martin
- Hospices Civils de Lyon, Department of Anaesthesiology and Critical Care Medicine, Groupement Hospitalier Edouard Herriot, University Claude Bernard Lyon 1, Lyon, France
| | - Thomas Rimmelé
- Hospices Civils de Lyon-bioMérieux Joint Research Unit, Groupement Hospitalier Edouard Herriot, Lyon, France.,Hospices Civils de Lyon, Department of Anaesthesiology and Critical Care Medicine, Groupement Hospitalier Edouard Herriot, University Claude Bernard Lyon 1, Lyon, France
| | | | - Mathieu Page
- Hospices Civils de Lyon, Department of Anaesthesiology and Critical Care Medicine, Groupement Hospitalier Edouard Herriot, University Claude Bernard Lyon 1, Lyon, France
| | - Vincent Piriou
- Hospices Civils de Lyon, Intensive Care Unit, Centre Hospitalier Lyon Sud, Pierre Bénite, France
| | - Julien Bohé
- Hospices Civils de Lyon, Intensive Care Unit, Centre Hospitalier Lyon Sud, Pierre Bénite, France
| | - Guillaume Monneret
- Hospices Civils de Lyon-bioMérieux Joint Research Unit, Groupement Hospitalier Edouard Herriot, Lyon, France.,Hospices Civils de Lyon, Immunology Laboratory, Groupement Hospitalier Edouard Herriot, Lyon, France
| | - Stéphane Morisset
- Hospices Civils de Lyon-bioMérieux Joint Research Unit, Groupement Hospitalier Edouard Herriot, Lyon, France
| | - Julien Textoris
- Hospices Civils de Lyon-bioMérieux Joint Research Unit, Groupement Hospitalier Edouard Herriot, Lyon, France.,Hospices Civils de Lyon, Department of Anaesthesiology and Critical Care Medicine, Groupement Hospitalier Edouard Herriot, University Claude Bernard Lyon 1, Lyon, France
| | - Hélène Vallin
- Hospices Civils de Lyon, Intensive Care Unit, Centre Hospitalier Lyon Sud, Pierre Bénite, France.,Hospices Civils de Lyon-bioMérieux Joint Research Unit, Groupement Hospitalier Edouard Herriot, Lyon, France
| | - Sophie Blein
- Hospices Civils de Lyon-bioMérieux Joint Research Unit, Groupement Hospitalier Edouard Herriot, Lyon, France
| | - Delphine Maucort-Boulch
- Hospices Civils de Lyon, Université Lyon 1, CNRS, UMR5558, Service de Biostatistique et Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique-Santé, Lyon, France
| | - Alain Lepape
- Hospices Civils de Lyon, Intensive Care Unit, Centre Hospitalier Lyon Sud, Pierre Bénite, France.,Hospices Civils de Lyon-bioMérieux Joint Research Unit, Groupement Hospitalier Edouard Herriot, Lyon, France
| | - Fabienne Venet
- Hospices Civils de Lyon-bioMérieux Joint Research Unit, Groupement Hospitalier Edouard Herriot, Lyon, France. .,Hospices Civils de Lyon, Immunology Laboratory, Groupement Hospitalier Edouard Herriot, Lyon, France. .,Immunology Laboratory, Hôpital E. Herriot - Hospices Civils de Lyon, 5 place d'Arsonval, 69437, Lyon Cedex 03, France.
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22
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Sterile post-traumatic immunosuppression. Clin Transl Immunology 2016; 5:e77. [PMID: 27195120 PMCID: PMC4855263 DOI: 10.1038/cti.2016.13] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 03/09/2016] [Accepted: 03/09/2016] [Indexed: 02/07/2023] Open
Abstract
After major trauma, the human immune system initiates a series of inflammatory events at the injury site that is later followed by suppression of local inflammation favoring the repair and remodeling of the damaged tissues. This local immune response involves complex interactions between resident cells such as macrophages and dendritic cells, soluble mediators such as cytokines and chemokines, and recruited cells such as neutrophils, monocytes and mesenchymal stromal cells. If of sufficient magnitude, these initial immune responses nevertheless have systemic consequences resulting in a state called post-traumatic immunosuppression (PTI). However, controversy exists regarding the exact immunological changes occurring in systemic compartments triggered by these local immune responses. PTI is one of the leading causes of post-surgical mortality and makes patients vulnerable to hospital-acquired infections, multiple organ failure and many other complications. In addition, hemorrhage, blood transfusion, immunesenescence and immunosuppressant drugs aggravate PTI. PTI has been intensively studied, but published results are frequently cloudy. The purpose of this review is to focus on the contributions made by different responsive modalities to immunosuppression following sterile trauma and to try to integrate these into an overall scheme of PTI.
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23
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Similarly Lethal Strains of Extraintestinal Pathogenic Escherichia coli Trigger Markedly Diverse Host Responses in a Zebrafish Model of Sepsis. mSphere 2016; 1:mSphere00062-16. [PMID: 27303721 PMCID: PMC4894679 DOI: 10.1128/msphere.00062-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 03/29/2016] [Indexed: 02/06/2023] Open
Abstract
In individuals with sepsis, the infecting microbes are commonly viewed as generic inducers of inflammation while the host background is considered the primary variable affecting disease progression and outcome. To study the effects of bacterial strain differences on the maladaptive immune responses that are induced during sepsis, we employed a novel zebrafish embryo infection model using extraintestinal pathogenic Escherichia coli (ExPEC) isolates. These genetically diverse pathogens are a leading cause of sepsis and are becoming increasingly dangerous because of the rise of multidrug-resistant strains. Zebrafish infected with ExPEC isolates exhibit many of the pathophysiological features seen in septic human patients, including dysregulated inflammatory responses (cytokine storms), tachycardia, endothelial leakage, and progressive edema. However, only a limited subset of ExPEC isolates can trigger a sepsis-like state and death of the host when introduced into the bloodstream. Mirroring the situation in human patients, antibiotic therapy reduced ExPEC titers and improved host survival rates but was only effective within limited time frames that varied, depending on the infecting pathogen. Intriguingly, we find that phylogenetically distant but similarly lethal ExPEC isolates can stimulate markedly different host transcriptional responses, including disparate levels of inflammatory mediators. These differences correlate with the amounts of bacterial flagellin expression during infection, as well as differential activation of Toll-like receptor 5 by discrete flagellar serotypes. Altogether, this work establishes zebrafish as a relevant model of key aspects of human sepsis and highlights the ability of genetically distinct ExPEC isolates to induce divergent host responses independently of baseline host attributes. IMPORTANCE Sepsis is a life-threatening systemic inflammatory condition that is initiated by the presence of microorganisms in the bloodstream. In the United States, sepsis due to ExPEC and other pathogens kills well over a quarter of a million people each year and is associated with tremendous health care costs. A high degree of heterogeneity in the signs and symptomology of sepsis makes this disease notoriously difficult to effectively diagnose and manage. Here, using a zebrafish model of sepsis, we find that similarly lethal but genetically distinct ExPEC isolates can elicit notably disparate host responses. These variances are in part due to differences in the levels and types of flagellin that are expressed by the infecting ExPEC strains. A better understanding of the variable impact that bacterial factors like flagellin have on host responses during sepsis could lead to improved diagnostic and therapeutic approaches to these often deadly infections. Podcast: A podcast concerning this article is available.
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Abstract
Sepsis mortality rates have decreased in recent years but remain unacceptably high. Risk stratification and prognostication is of particular importance because high-risk patients may benefit from earlier clinical interventions, whereas low-risk patients may benefit from not undergoing unnecessary procedures. Prognostication is currently done mostly via clinical criteria and blood lactate levels. This article summarizes the literature on the complexity of changes at the molecular level for the casual reader.
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Affiliation(s)
- Timothy E Sweeney
- Department of Surgery, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Hector R Wong
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati Children's Research Foundation, 3333 Burnet Avenue, MLC2005, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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A Transcriptomic Biomarker to Quantify Systemic Inflammation in Sepsis - A Prospective Multicenter Phase II Diagnostic Study. EBioMedicine 2016; 6:114-125. [PMID: 27211554 PMCID: PMC4856796 DOI: 10.1016/j.ebiom.2016.03.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 03/05/2016] [Indexed: 12/29/2022] Open
Abstract
Development of a dysregulated immune response discriminates sepsis from uncomplicated infection. Currently used biomarkers fail to describe simultaneously occurring pro- and anti-inflammatory responses potentially amenable to therapy. Marker candidates were screened by microarray and, after transfer to a platform allowing point-of-care testing, validated in a confirmation set of 246 medical and surgical patients. We identified up-regulated pathways reflecting innate effector mechanisms, while down-regulated pathways related to adaptive lymphocyte functions. A panel of markers composed of three up- (Toll-like receptor 5; Protectin; Clusterin) and 4 down-regulated transcripts (Fibrinogen-like 2; Interleukin-7 receptor; Major histocompatibility complex class II, DP alpha1; Carboxypeptidase, vitellogenic-like) described the magnitude of immune alterations. The created gene expression score was significantly greater in patients with definite as well as with possible/probable infection than with no infection (median (Q25/Q75): 80 (60/101)) and 81 (58/97 vs. 49 (27/66), AUC-ROC = 0.812 (95%-CI 0.755–0.869), p < 0.0001). Down-regulated lymphocyte markers were associated with prognosis with good sensitivity but limited specificity. Quantifying systemic inflammation by assessment of both pro- and anti-inflammatory innate and adaptive immune responses provides a novel option to identify patients-at-risk and may facilitate immune interventions in sepsis. Pro- and anti-inflammatory signaling occurs simultaneously in the host response to infection. This response is currently monitored using biomarkers restricted to the pro-inflammatory component of innate immunity. We developed a biomarker panel consisting of 7 transcripts that can assess both facets at the point of care.
The concept that a selective, overwhelming systemic inflammation, the “Systemic Inflammatory Response Syndrome (SIRS)”, triggers organ failure subsequent to infection has lately been abandoned as it neglects parallel occurring anti-inflammatory responses or defects in the adaptive immune system. The present findings suggest that a compound panel of nucleic acid biomarkers that was developed in independent training and verification cohorts and transferred to a point-of-care platform can more comprehensively describe the host response. Quantification of an enhanced innate immunity might inform studies of anti-inflammatory therapies, while measurement of derangements in specific immunity might guide strategies to restore immune effector functions.
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Tsalik EL, Li Y, Hudson LL, Chu VH, Himmel T, Limkakeng AT, Katz JN, Glickman SW, McClain MT, Welty-Wolf KE, Fowler VG, Ginsburg GS, Woods CW, Reed SD. Potential Cost-effectiveness of Early Identification of Hospital-acquired Infection in Critically Ill Patients. Ann Am Thorac Soc 2016; 13:401-13. [PMID: 26700878 DOI: 10.1513/annalsats.201504-205oc] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
RATIONALE Limitations in methods for the rapid diagnosis of hospital-acquired infections often delay initiation of effective antimicrobial therapy. New diagnostic approaches offer potential clinical and cost-related improvements in the management of these infections. OBJECTIVES We developed a decision modeling framework to assess the potential cost-effectiveness of a rapid biomarker assay to identify hospital-acquired infection in high-risk patients earlier than standard diagnostic testing. METHODS The framework includes parameters representing rates of infection, rates of delayed appropriate therapy, and impact of delayed therapy on mortality, along with assumptions about diagnostic test characteristics and their impact on delayed therapy and length of stay. Parameter estimates were based on contemporary, published studies and supplemented with data from a four-site, observational, clinical study. Extensive sensitivity analyses were performed. The base-case analysis assumed 17.6% of ventilated patients and 11.2% of nonventilated patients develop hospital-acquired infection and that 28.7% of patients with hospital-acquired infection experience delays in appropriate antibiotic therapy with standard care. We assumed this percentage decreased by 50% (to 14.4%) among patients with true-positive results and increased by 50% (to 43.1%) among patients with false-negative results using a hypothetical biomarker assay. Cost of testing was set at $110/d. MEASUREMENTS AND MAIN RESULTS In the base-case analysis, among ventilated patients, daily diagnostic testing starting on admission reduced inpatient mortality from 12.3 to 11.9% and increased mean costs by $1,640 per patient, resulting in an incremental cost-effectiveness ratio of $21,389 per life-year saved. Among nonventilated patients, inpatient mortality decreased from 7.3 to 7.1% and costs increased by $1,381 with diagnostic testing. The resulting incremental cost-effectiveness ratio was $42,325 per life-year saved. Threshold analyses revealed the probabilities of developing hospital-acquired infection in ventilated and nonventilated patients could be as low as 8.4 and 9.8%, respectively, to maintain incremental cost-effectiveness ratios less than $50,000 per life-year saved. CONCLUSIONS Development and use of serial diagnostic testing that reduces the proportion of patients with delays in appropriate antibiotic therapy for hospital-acquired infections could reduce inpatient mortality. The model presented here offers a cost-effectiveness framework for future test development.
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Affiliation(s)
- Ephraim L Tsalik
- 1 Emergency Medicine Service, and
- 2 Department of Medicine
- 3 Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina
| | | | - Lori L Hudson
- 2 Department of Medicine
- 3 Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina
| | - Vivian H Chu
- 2 Department of Medicine
- 4 Duke Clinical Research Institute, and
| | | | - Alex T Limkakeng
- 5 Department of Surgery, Duke University School of Medicine, Durham, North Carolina
| | - Jason N Katz
- 6 Department of Medicine, University of North Carolina Health Care, Chapel Hill, North Carolina; and
| | - Seth W Glickman
- 7 Department of Emergency Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Micah T McClain
- 8 Medicine Service, Durham Veterans Affairs Medical Center, Durham, North Carolina
- 2 Department of Medicine
- 3 Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina
| | - Karen E Welty-Wolf
- 8 Medicine Service, Durham Veterans Affairs Medical Center, Durham, North Carolina
- 2 Department of Medicine
| | | | - Geoffrey S Ginsburg
- 2 Department of Medicine
- 3 Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina
| | - Christopher W Woods
- 8 Medicine Service, Durham Veterans Affairs Medical Center, Durham, North Carolina
- 2 Department of Medicine
- 3 Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina
| | - Shelby D Reed
- 2 Department of Medicine
- 4 Duke Clinical Research Institute, and
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Sweeney TE, Shidham A, Wong HR, Khatri P. A comprehensive time-course-based multicohort analysis of sepsis and sterile inflammation reveals a robust diagnostic gene set. Sci Transl Med 2016; 7:287ra71. [PMID: 25972003 DOI: 10.1126/scitranslmed.aaa5993] [Citation(s) in RCA: 216] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although several dozen studies of gene expression in sepsis have been published, distinguishing sepsis from a sterile systemic inflammatory response syndrome (SIRS) is still largely up to clinical suspicion. We hypothesized that a multicohort analysis of the publicly available sepsis gene expression data sets would yield a robust set of genes for distinguishing patients with sepsis from patients with sterile inflammation. A comprehensive search for gene expression data sets in sepsis identified 27 data sets matching our inclusion criteria. Five data sets (n = 663 samples) compared patients with sterile inflammation (SIRS/trauma) to time-matched patients with infections. We applied our multicohort analysis framework that uses both effect sizes and P values in a leave-one-data set-out fashion to these data sets. We identified 11 genes that were differentially expressed (false discovery rate ≤1%, inter-data set heterogeneity P > 0.01, summary effect size >1.5-fold) across all discovery cohorts with excellent diagnostic power [mean area under the receiver operating characteristic curve (AUC), 0.87; range, 0.7 to 0.98]. We then validated these 11 genes in 15 independent cohorts comparing (i) time-matched infected versus noninfected trauma patients (4 cohorts), (ii) ICU/trauma patients with infections over the clinical time course (3 cohorts), and (iii) healthy subjects versus sepsis patients (8 cohorts). In the discovery Glue Grant cohort, SIRS plus the 11-gene set improved prediction of infection (compared to SIRS alone) with a continuous net reclassification index of 0.90. Overall, multicohort analysis of time-matched cohorts yielded 11 genes that robustly distinguish sterile inflammation from infectious inflammation.
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Affiliation(s)
- Timothy E Sweeney
- Department of Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA. Stanford Center for Biomedical Informatics Research, Stanford University, Palo Alto, CA 94305, USA.
| | - Aaditya Shidham
- Stanford Center for Biomedical Informatics Research, Stanford University, Palo Alto, CA 94305, USA
| | - Hector R Wong
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45223, USA. Department of Pediatrics, University of Cincinnati College of Medicine, 231 Albert Sabin Way, Cincinnati, OH 45267, USA
| | - Purvesh Khatri
- Stanford Center for Biomedical Informatics Research, Stanford University, Palo Alto, CA 94305, USA. Stanford Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Palo Alto, CA 94305, USA.
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28
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Scicluna BP, Klein Klouwenberg PMC, van Vught LA, Wiewel MA, Ong DSY, Zwinderman AH, Franitza M, Toliat MR, Nürnberg P, Hoogendijk AJ, Horn J, Cremer OL, Schultz MJ, Bonten MJ, van der Poll T. A molecular biomarker to diagnose community-acquired pneumonia on intensive care unit admission. Am J Respir Crit Care Med 2016; 192:826-35. [PMID: 26121490 DOI: 10.1164/rccm.201502-0355oc] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
RATIONALE Community-acquired pneumonia (CAP) accounts for a major proportion of intensive care unit (ICU) admissions for respiratory failure and sepsis. Diagnostic uncertainty complicates case management, which may delay appropriate cause-specific treatment. OBJECTIVES To characterize the blood genomic response in patients with suspected CAP and identify a candidate biomarker for the rapid diagnosis of CAP on ICU admission. METHODS The study comprised two cohorts of consecutively enrolled patients treated for suspected CAP on ICU admission. Patients were designated CAP (cases) and no-CAP patients (control subjects) by post hoc assessment. The first (discovery) cohort (101 CAP and 33 no-CAP patients) was enrolled between January 2011 and July 2012; the second (validation) cohort (70 CAP and 30 no-CAP patients) between July 2012 and June 2013. Blood was collected within 24 hours of ICU admission. MEASUREMENTS AND MAIN RESULTS Blood microarray analysis of CAP and no-CAP patients revealed shared and distinct gene expression patterns. A 78-gene signature was defined for CAP, from which a FAIM3:PLAC8 gene expression ratio was derived with area under curve of 0.845 (95% confidence interval, 0.764-0.917) and positive and negative predictive values of 83% and 81%, respectively. Robustness of the FAIM3:PLAC8 ratio was ascertained by quantitative polymerase chain reaction in the validation cohort. The FAIM3:PLAC8 ratio outperformed plasma procalcitonin and IL-8 and IL-6 in discriminating between CAP and no-CAP patients. CONCLUSIONS CAP and no-CAP patients presented shared and distinct blood genomic responses. We propose the FAIM3:PLAC8 ratio as a candidate biomarker to assist in the rapid diagnosis of CAP on ICU admission. Clinical trial registered with www.clinicaltrials.gov (NCT 01905033).
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Affiliation(s)
- Brendon P Scicluna
- 1 Center for Experimental Molecular Medicine and Center for Infection and Immunity Amsterdam
| | - Peter M C Klein Klouwenberg
- 2 Department of Intensive Care Medicine.,3 Department of Medical Microbiology, and.,4 Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands; and
| | - Lonneke A van Vught
- 1 Center for Experimental Molecular Medicine and Center for Infection and Immunity Amsterdam
| | - Maryse A Wiewel
- 1 Center for Experimental Molecular Medicine and Center for Infection and Immunity Amsterdam
| | - David S Y Ong
- 2 Department of Intensive Care Medicine.,3 Department of Medical Microbiology, and.,4 Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands; and
| | | | - Marek Franitza
- 6 Cologne Center for Genomics.,7 Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, and
| | | | - Peter Nürnberg
- 6 Cologne Center for Genomics.,7 Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, and.,8 Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Arie J Hoogendijk
- 1 Center for Experimental Molecular Medicine and Center for Infection and Immunity Amsterdam
| | | | | | | | - Marc J Bonten
- 3 Department of Medical Microbiology, and.,4 Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands; and
| | - Tom van der Poll
- 1 Center for Experimental Molecular Medicine and Center for Infection and Immunity Amsterdam.,10 Division of Infectious Diseases, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
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Rasid O, Cavaillon JM. Recent developments in severe sepsis research: from bench to bedside and back. Future Microbiol 2016; 11:293-314. [PMID: 26849633 DOI: 10.2217/fmb.15.133] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Severe sepsis remains a worldwide threat, not only in industrialized countries, due to their aging population, but also in developing countries where there still are numerous cases of neonatal and puerperal sepsis. Tools for early diagnosis, a prerequisite for rapid and appropriate antibiotic therapy, are still required. In this review, we highlight some recent developments in our understanding of the associated systemic inflammatory response that help deciphering pathophysiology (e.g., epigenetic, miRNA, regulatory loops, compartmentalization, apoptosis and synergy) and discuss some of the consequences of sepsis (e.g., immune status, neurological and muscular alterations). We also emphasize the challenge to better define animal models and discuss past failures in clinical investigations in order to define new efficient therapies.
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Affiliation(s)
- Orhan Rasid
- Unit Cytokines & Inflammation, Institut Pasteur, 28 rue Dr. Roux, Paris, France
| | - Jean-Marc Cavaillon
- Unit Cytokines & Inflammation, Institut Pasteur, 28 rue Dr. Roux, Paris, France
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30
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Mechanistic similarities between trauma, atherosclerosis, and other inflammatory processes. J Crit Care 2015; 30:1344-8. [DOI: 10.1016/j.jcrc.2015.07.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 07/21/2015] [Accepted: 07/23/2015] [Indexed: 12/31/2022]
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Abstract
BACKGROUND The traditional hypothesis-driven scientific approach cannot so far sufficiently elucidate complex pathophysiologies, such as posttraumatic systemic inflammation and subsequent multiple organ failure. This complex system includes different biological and functional levels, the genome, the transcriptome, the proteome, the biome (cells), the organs and finally the whole organism. METHODS Microarray techniques enable a simultaneous search for these different biological levels and their functional relationships on a large scale and to discover new functional pathways and networks and potentially new biomarkers for different pathologies. Microarray technologies lead to a new paradigm in science, the hypothesis-generating approach. AIM This article reviews important microarray findings in trauma and systemic inflammation research and discusses potentials and limitations of these biotechnological screening methods.
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Affiliation(s)
- V Bogner
- Klinik für Allgemeine, Unfall-, Hand- und Plastische Chirurgie, Ludwig Maximilians Universität München, Campus Innenstadt, Nussbaumstraße 20, 80336, München, Deutschland,
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32
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Innate immunity gene expression changes in critically ill patients with sepsis and disease-related malnutrition. Cent Eur J Immunol 2015; 40:311-24. [PMID: 26648775 PMCID: PMC4655381 DOI: 10.5114/ceji.2015.54593] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 07/14/2015] [Indexed: 12/26/2022] Open
Abstract
The aim of this study was an attempt to determine whether the expression of genes involved in innate antibacterial response (TL R2, NOD 1, TRAF6, HMGB 1 and Hsp70) in peripheral blood leukocytes in critically ill patients, may undergo significant changes depending on the severity of the infection and the degree of malnutrition. The study was performed in a group of 128 patients with infections treated in the intensive care and surgical ward. In 103/80.5% of patients, infections had a severe course (sepsis, severe sepsis, septic shock, mechanical ventilation of the lungs). Clinical monitoring included diagnosis of severe infection (according to the criteria of the ACC P/SCC M), assessment of severity of the patient condition and risk of death (APACHE II and SAPS II), nutritional assessment (NRS 2002 and SGA scales) and the observation of the early results of treatment. Gene expression at the mRNA level was analyzed by real-time PCR. The results of the present study indicate that in critically ill patients treated in the IC U there are significant disturbances in the expression of genes associated with innate antimicrobial immunity, which may have a significant impact on the clinical outcome. The expression of these genes varies depending on the severity of the patient condition, severity of infection and nutritional status. Expression disorders of genes belonging to innate antimicrobial immunity should be diagnosed as early as possible, monitored during the treatment and taken into account during early therapeutic treatment (including early nutrition to support the functions of immune cells).
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33
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Opal S. Is Genomic Medicine Finally Coming of Age for the Diagnosis of Pneumonia? Am J Respir Crit Care Med 2015; 192:773-4. [DOI: 10.1164/rccm.201507-1340ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Parlato M, Cavaillon JM. Host response biomarkers in the diagnosis of sepsis: a general overview. Methods Mol Biol 2015; 1237:149-211. [PMID: 25319788 DOI: 10.1007/978-1-4939-1776-1_15] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Critically ill patients who display a systemic inflammatory response syndrome (SIRS) are prone to develop nosocomial infections. The challenge remains to distinguish as early as possible among SIRS patients those who are developing sepsis. Following a sterile insult, damage-associated molecular patterns (DAMPs) released by damaged tissues and necrotic cells initiate an inflammatory response close to that observed during sepsis. During sepsis, pathogen-associated molecular patterns (PAMPs) trigger the release of host mediators involved in innate immunity and inflammation through identical receptors as DAMPs. In both clinical settings, a compensatory anti-inflammatory response syndrome (CARS) is concomitantly initiated. The exacerbated production of pro- or anti-inflammatory mediators allows their detection in biological fluids and particularly within the bloodstream. Some of these mediators can be used as biomarkers to decipher among the patients those who developed sepsis, and eventually they can be used as prognosis markers. In addition to plasma biomarkers, the analysis of some surface markers on circulating leukocytes or the study of mRNA and miRNA can be helpful. While there is no magic marker, a combination of few biomarkers might offer a high accuracy for diagnosis.
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Affiliation(s)
- Marianna Parlato
- Unit of Cytokines and Inflammation, Institut Pasteur, 28 rue du Dr Roux, 75724, Paris Cedex 15, France
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35
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Dix A, Hünniger K, Weber M, Guthke R, Kurzai O, Linde J. Biomarker-based classification of bacterial and fungal whole-blood infections in a genome-wide expression study. Front Microbiol 2015; 6:171. [PMID: 25814982 PMCID: PMC4356159 DOI: 10.3389/fmicb.2015.00171] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/15/2015] [Indexed: 01/11/2023] Open
Abstract
Sepsis is a clinical syndrome that can be caused by bacteria or fungi. Early knowledge on the nature of the causative agent is a prerequisite for targeted anti-microbial therapy. Besides currently used detection methods like blood culture and PCR-based assays, the analysis of the transcriptional response of the host to infecting organisms holds great promise. In this study, we aim to examine the transcriptional footprint of infections caused by the bacterial pathogens Staphylococcus aureus and Escherichia coli and the fungal pathogens Candida albicans and Aspergillus fumigatus in a human whole-blood model. Moreover, we use the expression information to build a random forest classifier to classify if a sample contains a bacterial, fungal, or mock-infection. After normalizing the transcription intensities using stably expressed reference genes, we filtered the gene set for biomarkers of bacterial or fungal blood infections. This selection is based on differential expression and an additional gene relevance measure. In this way, we identified 38 biomarker genes, including IL6, SOCS3, and IRG1 which were already associated to sepsis by other studies. Using these genes, we trained the classifier and assessed its performance. It yielded a 96% accuracy (sensitivities >93%, specificities >97%) for a 10-fold stratified cross-validation and a 92% accuracy (sensitivities and specificities >83%) for an additional test dataset comprising Cryptococcus neoformans infections. Furthermore, the classifier is robust to Gaussian noise, indicating correct class predictions on datasets of new species. In conclusion, this genome-wide approach demonstrates an effective feature selection process in combination with the construction of a well-performing classification model. Further analyses of genes with pathogen-dependent expression patterns can provide insights into the systemic host responses, which may lead to new anti-microbial therapeutic advances.
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Affiliation(s)
- Andreas Dix
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute Jena, Germany
| | - Kerstin Hünniger
- Septomics Research Centre, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute Jena, Germany
| | - Michael Weber
- Septomics Research Centre, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute Jena, Germany
| | - Reinhard Guthke
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute Jena, Germany
| | - Oliver Kurzai
- Septomics Research Centre, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute Jena, Germany
| | - Jörg Linde
- Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute Jena, Germany
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36
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Almansa R, Heredia-Rodríguez M, Gomez-Sanchez E, Andaluz-Ojeda D, Iglesias V, Rico L, Ortega A, Gomez-Pesquera E, Liu P, Aragón M, Eiros JM, Jiménez-Sousa MÁ, Resino S, Gómez-Herreras I, Bermejo-Martín JF, Tamayo E. Transcriptomic correlates of organ failure extent in sepsis. J Infect 2014; 70:445-56. [PMID: 25557485 DOI: 10.1016/j.jinf.2014.12.010] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 12/22/2014] [Accepted: 12/23/2014] [Indexed: 10/24/2022]
Abstract
OBJECTIVES Sepsis is characterised by the frequent presence of organ failure and marked immunologic alterations. We studied the association between the extent of organ failure and the transcriptomic response of septic patients. METHODS Gene expression profiles in the blood of 74 surgical patients with sepsis were compared with those of 30 surgical patients with no sepsis. Differentially expressed genes were assessed for their correlation with the sequential organ failure (SOFA) score. RESULTS The expression levels of a group of genes participating in the cell cycle (HIST1H1C, CKS2, CCNA2, CDK1, CCNB2, CIT, CCNB1, AURKA, RAD51), neutrophil protease activity (ELANE, ADORA3, MPO, MMP8, CTSG), IL-1R and IL-18R response correlated directly with SOFA and mortality. Genes involved in T cell (LCK, CD3G, CD3D, ZAP70, ICOS, CD3E, CD28, IL2RB, CD8B, CD8A, CD40LG, IL23A, CCL5, SH2D1A, ITK, CD247, TBX21, GATA3, CCR7, LEF1, STAT4) and NK cell immunity (CD244, KLRK1, KLRD1) were inversely associated with SOFA and mortality. CONCLUSIONS The extent of organ failure in sepsis correlates directly with the existence of imbalanced innate and adaptive responses at the transcriptomic level. Quantification of the expression levels of the genes identified here could contribute to the simultaneous assessment of disease severity and immunological alterations in sepsis.
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Affiliation(s)
- Raquel Almansa
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, SACYL/IECSYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Unidad Apoyo a la Investigación, Hospital Clínico Universitario de Valladolid, SACYL/IECSYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
| | - María Heredia-Rodríguez
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, SACYL/IECSYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Servicio de Anestesiología, Hospital Clínico Universitario de Valladolid, SACYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
| | - Esther Gomez-Sanchez
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, SACYL/IECSYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Servicio de Anestesiología, Hospital Clínico Universitario de Valladolid, SACYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
| | - David Andaluz-Ojeda
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, SACYL/IECSYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Servicio de Medicina Intensiva, Hospital Clínico Universitario de Valladolid, SACYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
| | - Verónica Iglesias
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, SACYL/IECSYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Unidad Apoyo a la Investigación, Hospital Clínico Universitario de Valladolid, SACYL/IECSYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
| | - Lucia Rico
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, SACYL/IECSYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Unidad Apoyo a la Investigación, Hospital Clínico Universitario de Valladolid, SACYL/IECSYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
| | - Alicia Ortega
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, SACYL/IECSYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Unidad Apoyo a la Investigación, Hospital Clínico Universitario de Valladolid, SACYL/IECSYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
| | - Estefanía Gomez-Pesquera
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, SACYL/IECSYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Servicio de Anestesiología, Hospital Clínico Universitario de Valladolid, SACYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
| | - Pilar Liu
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, SACYL/IECSYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Servicio de Anestesiología, Hospital Clínico Universitario de Valladolid, SACYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
| | - Marta Aragón
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, SACYL/IECSYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Servicio de Anestesiología, Hospital Clínico Universitario de Valladolid, SACYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
| | - Jose Maria Eiros
- Dpto de Microbiología, Universidad de Valladolid, Avenida Ramón y Cajal, 7, 47005 Valladolid, Spain.
| | - Maria Ángeles Jiménez-Sousa
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, SACYL/IECSYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología - Instituto de Salud Carlos III, Carretera Majadahonda- Pozuelo km. 2, Majadahonda, 28220 Madrid, Spain.
| | - Salvador Resino
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, SACYL/IECSYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología - Instituto de Salud Carlos III, Carretera Majadahonda- Pozuelo km. 2, Majadahonda, 28220 Madrid, Spain.
| | - Ignacio Gómez-Herreras
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, SACYL/IECSYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Servicio de Anestesiología, Hospital Clínico Universitario de Valladolid, SACYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
| | - Jesús F Bermejo-Martín
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, SACYL/IECSYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Unidad Apoyo a la Investigación, Hospital Clínico Universitario de Valladolid, SACYL/IECSYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
| | - Eduardo Tamayo
- Grupo de Investigación Biomédica en Cuidados Críticos (BioCritic), Hospital Clínico Universitario de Valladolid, SACYL/IECSYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain; Servicio de Anestesiología, Hospital Clínico Universitario de Valladolid, SACYL, Avenida Ramón y Cajal, 3, 47005 Valladolid, Spain.
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Islam N, Whitehouse M, Mehendale S, Hall M, Tierney J, O'Connell E, Blom A, Bannister G, Hinde J, Ceredig R, Bradley BA. Post-traumatic immunosuppression is reversed by anti-coagulated salvaged blood transfusion: deductions from studying immune status after knee arthroplasty. Clin Exp Immunol 2014; 177:509-20. [PMID: 24749651 DOI: 10.1111/cei.12351] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2014] [Indexed: 12/28/2022] Open
Abstract
Major trauma increases vulnerability to systemic infections due to poorly defined immunosuppressive mechanisms. It confers no evolutionary advantage. Our objective was to develop better biomarkers of post-traumatic immunosuppression (PTI) and to extend our observation that PTI was reversed by anti-coagulated salvaged blood transfusion, in the knowledge that others have shown that non-anti-coagulated (fibrinolysed) salvaged blood was immunosuppressive. A prospective non-randomized cohort study of patients undergoing primary total knee arthroplasty included 25 who received salvaged blood transfusions collected post-operatively into acid-citrate-dextrose anti-coagulant (ASBT cohort), and 18 non-transfused patients (NSBT cohort). Biomarkers of sterile trauma included haematological values, damage-associated molecular patterns (DAMPs), cytokines and chemokines. Salvaged blood was analysed within 1 and 6 h after commencing collection. Biomarkers were expressed as fold-changes over preoperative values. Certain biomarkers of sterile trauma were common to all 43 patients, including supranormal levels of: interleukin (IL)-6, IL-1-receptor-antagonist, IL-8, heat shock protein-70 and calgranulin-S100-A8/9. Other proinflammatory biomarkers which were subnormal in NSBT became supranormal in ASBT patients, including IL-1β, IL-2, IL-17A, interferon (IFN)-γ, tumour necrosis factor (TNF)-α and annexin-A2. Furthermore, ASBT exhibited subnormal levels of anti-inflammatory biomarkers: IL-4, IL-5, IL-10 and IL-13. Salvaged blood analyses revealed sustained high levels of IL-9, IL-10 and certain DAMPs, including calgranulin-S100-A8/9, alpha-defensin and heat shock proteins 27, 60 and 70. Active synthesis during salvaged blood collection yielded increasingly elevated levels of annexin-A2, IL-1β, Il-1-receptor-antagonist, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12p70, IL-17A, IFN-γ, TNF-α, transforming growth factor (TGF)-β1, monocyte chemotactic protein-1 and macrophage inflammatory protein-1α. Elevated levels of high-mobility group-box protein-1 decreased. In conclusion, we demonstrated that anti-coagulated salvaged blood reversed PTI, and was attributed to immune stimulants generated during salvaged blood collection.
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Affiliation(s)
- N Islam
- Musculoskeletal Research Unit, 1st Floor Learning & Research Building, Southmead Hospital, University of Bristol, Bristol, United Kingdom; National Centre for Biomedical Engineering Science, National University of Ireland, Galway; Shannon Applied Biotechnology Centre, Institute of Technology Tralee, Tralee, County Kerry, Ireland
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Dios S, Balseiro P, Costa MM, Romero A, Boltaña S, Roher N, Mackenzie S, Figueras A, Novoa B. The involvement of cholesterol in sepsis and tolerance to lipopolysaccharide highlighted by the transcriptome analysis of zebrafish (Danio rerio). Zebrafish 2014; 11:421-33. [PMID: 25181277 DOI: 10.1089/zeb.2014.0995] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Septic shock is the most common cause of death in intensive care units due to an aggressive inflammatory response that leads to multiple organ failure. However, a lipopolysaccharide (LPS) tolerance phenomenon (a nonreaction to LPS), is also often described. Neither the inflammatory response nor the tolerance is completely understood. In this work, both of these responses were analyzed using microarrays in zebrafish. Fish that were 4 or 6 days postfertilization (dpf) and received a lethal dose (LD) of LPS exhibited 100% mortality in a few days. Their transcriptome profile, even at 4 dpf, resembled the profile in humans with severe sepsis. Moreover, we selected 4-dpf fish to set up a tolerance protocol: fish treated with a nonlethal concentration of Escherichia coli LPS exhibited complete protection against the LD of LPS. Most of the main inflammatory molecules described in mammals were represented in the zebrafish microarray experiments. Additionally and focusing on this tolerance response, the use of cyclodextrins may mobilize cholesterol reservoirs to decrease mortality after a LD dose of LPS. Therefore, it is possible that the use of the whole animal could provide some clues to enhance the understanding of the inflammatory/tolerance response and to guide drug discovery.
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Affiliation(s)
- Sonia Dios
- 1 Instituto de Investigaciones Marinas (IIM)-Consejo Superior de Investigaciones Científicas (CSIC) , Vigo, Spain
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39
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Rello J, Lisboa T, Koulenti D. Respiratory infections in patients undergoing mechanical ventilation. THE LANCET RESPIRATORY MEDICINE 2014; 2:764-74. [PMID: 25151022 DOI: 10.1016/s2213-2600(14)70171-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Lower respiratory tract infections in mechanically ventilated patients are a frequent cause of antibiotic treatment in intensive-care units. These infections present as severe sepsis or septic shock with respiratory dysfunction in intubated patients. Purulent respiratory secretions are needed for diagnosis, but distinguishing between pneumonia and tracheobronchitis is not easy. Both presentations are associated with longlasting mechanical ventilation and extended intensive-care unit stay, providing a rationale for antibiotic treatment initiation. Differentiation of colonisers from true pathogens is difficult, and microbiological data show Staphylococcus aureus and Pseudomonas aeruginosa to be of great concern because of clinical outcomes and therapeutic challenges. Key management issues include identification of the pathogen, choice of initial empirical antibiotic, and decisions with regard to the resolution pattern.
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Affiliation(s)
- Jordi Rello
- Critical Care Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain; Centro de Investigación Biomédica en Red Enfermedades Respiratorias, Barcelona, Spain; Universitat Autonoma de Barcelona, Barcelona, Spain.
| | - Thiago Lisboa
- Critical Care Department and Infection Control Committee, Programa de Pós-Graduação Pneumologia, Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Rede Institucional de Pesquisa e Inovação em Medicina Intensiva, Complexo Hospitalar Santa Casa, Porto Alegre, Brazil
| | - Despoina Koulenti
- 2nd Critical Care Department, Attikon University Hospital, Athens, Greece; Burns Trauma and Critical Care Research Centre, The University of Queensland, Brisbane, QLD, Australia
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Smith CL, Dickinson P, Forster T, Craigon M, Ross A, Khondoker MR, France R, Ivens A, Lynn DJ, Orme J, Jackson A, Lacaze P, Flanagan KL, Stenson BJ, Ghazal P. Identification of a human neonatal immune-metabolic network associated with bacterial infection. Nat Commun 2014; 5:4649. [PMID: 25120092 PMCID: PMC4143936 DOI: 10.1038/ncomms5649] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 07/09/2014] [Indexed: 12/26/2022] Open
Abstract
Understanding how human neonates respond to infection remains incomplete. Here, a system-level investigation of neonatal systemic responses to infection shows a surprisingly strong but unbalanced homeostatic immune response; developing an elevated set-point of myeloid regulatory signalling and sugar-lipid metabolism with concomitant inhibition of lymphoid responses. Innate immune-negative feedback opposes innate immune activation while suppression of T-cell co-stimulation is coincident with selective upregulation of CD85 co-inhibitory pathways. By deriving modules of co-expressed RNAs, we identify a limited set of networks associated with bacterial infection that exhibit high levels of inter-patient variability. Whereas, by integrating immune and metabolic pathways, we infer a patient-invariant 52-gene-classifier that predicts bacterial infection with high accuracy using a new independent patient population. This is further shown to have predictive value in identifying infection in suspected cases with blood culture-negative tests. Our results lay the foundation for future translation of host pathways in advancing diagnostic, prognostic and therapeutic strategies for neonatal sepsis. Infection remains a leading cause of morbidity and mortality in neonates worldwide. Here the authors report disproportionate immune stimulatory, co-inhibitory and metabolic pathway responses that specifically mark bacterial infection and can be used to predict sepsis in neonatal patients at the first clinical signs of infection.
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Affiliation(s)
- Claire L Smith
- 1] Neonatal Unit, Simpson Centre for Reproductive Health, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK [2] Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK [3]
| | - Paul Dickinson
- 1] Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK [2] SynthSys-Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3JD, UK [3]
| | - Thorsten Forster
- 1] Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK [2] SynthSys-Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3JD, UK
| | - Marie Craigon
- Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Alan Ross
- Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Mizanur R Khondoker
- 1] Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK [2]
| | - Rebecca France
- Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Alasdair Ivens
- 1] Fios Genomics Ltd., ETTC, King's Buildings, Edinburgh EH9 3JL, UK [2]
| | - David J Lynn
- 1] Animal Bioscience Research Department, AGRIC, Teagasc, Grange, Dunsany, Co. Meath, Ireland [2]
| | - Judith Orme
- Neonatal Unit, Simpson Centre for Reproductive Health, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Allan Jackson
- Neonatal Unit, Simpson Centre for Reproductive Health, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Paul Lacaze
- Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Katie L Flanagan
- 1] MRC Research Laboratories, Atlantic Boulevard, PO Box 273, Fajara, Gambia [2]
| | - Benjamin J Stenson
- Neonatal Unit, Simpson Centre for Reproductive Health, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Peter Ghazal
- 1] Division of Pathway Medicine, Edinburgh Infectious Diseases, University of Edinburgh, Edinburgh EH16 4SB, UK [2] SynthSys-Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3JD, UK
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41
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Tasker A, Hughes A, Kelly M. (i) Managing polytrauma: picking a way through the inflammatory cascade. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.mporth.2014.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Cernada M, Serna E, Bauerl C, Collado MC, Pérez-Martínez G, Vento M. Genome-wide expression profiles in very low birth weight infants with neonatal sepsis. Pediatrics 2014; 133:e1203-11. [PMID: 24709930 DOI: 10.1542/peds.2013-2552] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Bacterial sepsis is associated with high morbidity and mortality in preterm infants. However, diagnosis of sepsis and identification of the causative agent remains challenging. Our aim was to determine genome-wide expression profiles of very low birth weight (VLBW) infants with and without bacterial sepsis and assess differences. METHODS This was a prospective observational double-cohort study conducted in VLBW (<1500 g) infants with culture-positive bacterial sepsis and non-septic matched controls. Blood samples were collected as soon as clinical signs of sepsis were identified and before antibiotics were initiated. Total RNA was processed for genome-wide expression analysis using Affymetrix gene arrays. RESULTS During a 19-month period, 17 septic VLBW infants and 19 matched controls were enrolled. First, a three-dimensional unsupervised principal component analysis based on the entire genome (28 000 transcripts) identified 3 clusters of patients based on gene expression patterns: Gram-positive sepsis, Gram-negative sepsis, and noninfected control infants. Furthermore, these groups were confirmed by using analysis of variance, which identified a transcriptional signature of 554 of genes. These genes had a significantly different expression among the groups. Of the 554 identified genes, 66 belonged to the tumor necrosis factor and 56 to cytokine signaling. The most significantly overexpressed pathways in septic neonates related with innate immune and inflammatory responses and were validated by real-time reverse transcription polymerase chain reaction. CONCLUSIONS Our preliminary results suggest that genome-wide expression profiles discriminate septic from nonseptic VLBW infants early in the neonatal period. Further studies are needed to confirm these findings.
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Affiliation(s)
- María Cernada
- Health Research Institute (Instituto de Investigación Sanitaria) La Fe, Valencia, Spain; Division of Neonatology, University and Polytechnic Hospital, Valencia, Spain
| | - Eva Serna
- Central Research Unit-INCLIVA, Faculty of Medicine, University of Valencia, Spain; and
| | - Christine Bauerl
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas, Valencia; Spain
| | - María Carmen Collado
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas, Valencia; Spain
| | - Gaspar Pérez-Martínez
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas, Valencia; Spain
| | - Máximo Vento
- Health Research Institute (Instituto de Investigación Sanitaria) La Fe, Valencia, Spain; Division of Neonatology, University and Polytechnic Hospital, Valencia, Spain;
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Christaki E, Giamarellos-Bourboulis EJ. The beginning of personalized medicine in sepsis: small steps to a bright future. Clin Genet 2014; 86:56-61. [PMID: 24579691 DOI: 10.1111/cge.12368] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 02/24/2014] [Accepted: 02/24/2014] [Indexed: 02/04/2023]
Abstract
There is a growing recognition that there is a need for a more personalized approach towards sepsis care. In most clinical trials investigating novel therapeutic interventions against sepsis, patients have been considered a rather homogeneous population. However, there is probably more individual variability between septic patients than previously considered. The pathophysiology of sepsis is a complex and dynamic process that originates from the host immune response to infection and varies according to the genetic predisposition, immune status and co-morbid conditions of the host, the type of pathogen and the site and extent of infection. Until now, efforts to stratify septic patients according to their immune profile were hampered by the lack of specific biomarkers. Recent advances in molecular medicine have made it possible to develop tools that will facilitate a faster and more precise diagnosis of infection. Individual variability between each patient's responses to infection can assist in tailoring therapeutic interventions to the individual's disease profile and monitoring treatment response. In this review, we describe those recent advances in genomics and theragnostics, which are slowly entering clinical practice and which will make possible a more personalized approach to each septic patient in the next decade.
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Affiliation(s)
- E Christaki
- First Department of Internal Medicine, AHEPA University Hospital, Thessaloniki, Greece; Infectious Diseases Division, Alpert School of Medicine of Brown University, Providence, RI, USA
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Abstract
Sepsis is a common cause of death in hospitalized patients worldwide. The early detection of sepsis remains a great challenge for clinicians, and delayed diagnosis frequently undermines treatment efforts, thereby contributing to high mortality. Omics technologies allow high-throughput screening of sepsis biomarkers. This review describes currently available and novel sepsis biomarkers in the context of genomics, transcriptomics, proteomics, and metabolomics. The combination of these technologies can help refine the diagnosis of sepsis. This review paper serves as a reference for future studies that employ an integrated, multi-omics approach to disease identification.
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Skibsted S, Bhasin MK, Aird WC, Shapiro NI. Bench-to-bedside review: future novel diagnostics for sepsis - a systems biology approach. Crit Care 2013; 17:231. [PMID: 24093155 PMCID: PMC4057467 DOI: 10.1186/cc12693] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The early, accurate diagnosis and risk stratification of sepsis remains an important challenge in the critically ill. Since traditional biomarker strategies have not yielded a gold standard marker for sepsis, focus is shifting towards novel strategies that improve assessment capabilities. The combination of technological advancements and information generated through the human genome project positions systems biology at the forefront of biomarker discovery. While previously available, developments in the technologies focusing on DNA, gene expression, gene regulatory mechanisms, protein and metabolite discovery have made these tools more feasible to implement and less costly, and they have taken on an enhanced capacity such that they are ripe for utilization as tools to advance our knowledge and clinical research. Medicine is in a genome-level era that can leverage the assessment of thousands of molecular signals beyond simply measuring selected circulating proteins. Genomics is the study of the entire complement of genetic material of an individual. Epigenetics is the regulation of gene activity by reversible modifications of the DNA. Transcriptomics is the quantification of the relative levels of messenger RNA for a large number of genes in specific cells or tissues to measure differences in the expression levels of different genes, and the utilization of patterns of differential gene expression to characterize different biological states of a tissue. Proteomics is the large-scale study of proteins. Metabolomics is the study of the small molecule profiles that are the terminal downstream products of the genome and consists of the total complement of all low-molecular-weight molecules that cellular processes leave behind. Taken together, these individual fields of study may be linked during a systems biology approach. There remains a valuable opportunity to deploy these technologies further in human research. The techniques described in this paper not only have the potential to increase the spectrum of diagnostic and prognostic biomarkers in sepsis, but they may also enable the discovery of new disease pathways. This may in turn lead us to improved therapeutic targets. The objective of this paper is to provide an overview and basic framework for clinicians and clinical researchers to better understand the 'omics technologies' to enhance further use of these valuable tools.
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Affiliation(s)
- Simon Skibsted
- Department of Emergency Medicine and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, 99 Brookline Street, Boston, MA 02215, USA
| | - Manoj K Bhasin
- Beth Israel Deaconess Medical Center Genomics and Core, 99 Brookline Avenue, Boston, MA 02115, USA
| | - William C Aird
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, 99 Brookline Street, Boston, MA 02215, USA
| | - Nathan I Shapiro
- Department of Emergency Medicine and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, 99 Brookline Street, Boston, MA 02215, USA
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46
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Rello J, Lipman J. Antibiotic prescription for respiratory tract infections in ventilated patients: where are we heading? Intensive Care Med 2013; 39:1644-6. [PMID: 23812337 DOI: 10.1007/s00134-013-2983-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 05/25/2013] [Indexed: 11/29/2022]
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47
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Potential of surface acoustic wave biosensors for early sepsis diagnosis. J Clin Monit Comput 2013; 27:427-31. [PMID: 23471596 DOI: 10.1007/s10877-013-9446-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Accepted: 02/28/2013] [Indexed: 01/07/2023]
Abstract
Early diagnosis of sepsis is a difficult problem for intensivists and new biomarkers for early diagnosis have been difficult to come by. Here we discuss the potential of adapting a technology from the electronics industry, surface acoustic wave (SAW) sensors, for diagnosis of multiple markers of sepsis in real time, using non-invasive assays of exhaled breath condensate. The principles and advantages of the SAW technology are reviewed as well as a proposed plan for adapting this flexible technology to early sepsis detection.
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48
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Abstract
Sepsis is among the most common causes of death in hospitals. It arises from the host response to infection. Currently, diagnosis relies on nonspecific physiological criteria and culture-based pathogen detection. This results in diagnostic uncertainty, therapeutic delays, the mis- and overuse of antibiotics, and the failure to identify patients who might benefit from immunomodulatory therapies. There is a need for new sepsis biomarkers that can aid in therapeutic decision making and add information about screening, diagnosis, risk stratification, and monitoring of the response to therapy. The host response involves hundreds of mediators and single molecules, many of which have been proposed as biomarkers. It is, however, unlikely that one single biomarker is able to satisfy all the needs and expectations for sepsis research and management. Among biomarkers that are measurable by assays approved for clinical use, procalcitonin (PCT) has shown some usefulness as an infection marker and for antibiotic stewardship. Other possible new approaches consist of molecular strategies to improve pathogen detection and molecular diagnostics and prognostics based on transcriptomic, proteomic, or metabolic profiling. Novel approaches to sepsis promise to transform sepsis from a physiologic syndrome into a group of distinct biochemical disorders and help in the development of better diagnostic tools and effective adjunctive sepsis therapies.
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49
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Clinical application of sepsis biomarkers. J Anesth 2012; 27:269-83. [DOI: 10.1007/s00540-012-1502-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 10/03/2012] [Indexed: 10/27/2022]
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Abstract
OBJECTIVES Pediatric septic shock continues to be an important public health problem. Several investigative groups have applied genetic and genomic approaches as a means of identifying novel pathways and therapeutic targets, discovery of sepsis-related biomarkers, and identification of septic shock subclasses. This review will highlight studies in pediatric sepsis with a focus on gene association studies and genome-wide expression profiling. DATA SOURCES A summary of published literature involving gene association and expression profiling studies specifically involving pediatric sepsis and septic shock. SUMMARY Several polymorphisms of genes broadly involved in inflammation, immunity, and coagulation have been linked with susceptibility to sepsis, or outcome of sepsis in children. Many of these studies involve meningococcemia, and the strongest association involves a functional polymorphism of the plasminogen activator inhibitor-1 promoter region and meningococcal sepsis. Expression profiling studies in pediatric septic shock have identified zinc supplementation and inhibition of matrix metalloproteinase-8 activity as potential, novel therapeutic approaches in sepsis. Studies focused on discovery of sepsis-related biomarkers have identified interleukin-8 as a robust outcome biomarker in pediatric septic shock. Additional studies have demonstrated the feasibility and clinical relevance of gene expression-based subclassification of pediatric septic shock. CONCLUSIONS Pediatric sepsis and septic shock are increasingly being studied by genetic and genomic approaches and the accumulating data hold the promise of enhancing our future approach to this ongoing clinical problem.
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