1
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Characteristic Metabolic Changes in Skeletal Muscle Due to Vibrio vulnificus Infection in a Wound Infection Model. mSystems 2023; 8:e0068222. [PMID: 36939368 PMCID: PMC10153474 DOI: 10.1128/msystems.00682-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
Vibrio vulnificus is a bacterium that inhabits warm seawater or brackish water environments and causes foodborne diseases and wound infections. In severe cases, V. vulnificus invades the skeletal muscle tissue, where bacterial proliferation leads to septicemia and necrotizing fasciitis with high mortality. Despite this characteristic, information on metabolic changes in tissue infected with V. vulnificus is not available. Here, we elucidated the metabolic changes in V. vulnificus-infected mouse skeletal muscle using capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS). Metabolome analysis revealed changes in muscle catabolites and energy metabolites during V. vulnificus infection. In particular, succinic acid accumulated but fumaric acid decreased in the infected muscle. However, the virulence factor deletion mutant revealed that changes in metabolites and bacterial proliferation were abolished in skeletal muscle infected with a multifunctional-autoprocessing repeats-in-toxin (MARTX) mutant. On the other hand, mice that were immunosuppressed via cyclophosphamide (CPA) treatment exhibited a similar level of bacterial counts and metabolites between the wild type and MARTX mutant. Therefore, our data indicate that V. vulnificus induces metabolic changes in mouse skeletal muscle and proliferates by using the MARTX toxin to evade the host immune system. This study indicates a new correlation between V. vulnificus infections and metabolic changes that lead to severe reactions or damage to host skeletal muscle. IMPORTANCE V. vulnificus causes necrotizing skin and soft tissue infections (NSSTIs) in severe cases, with high mortality and sign of rapid deterioration. Despite the severity of the infection, the dysfunction of the host metabolism in skeletal muscle triggered by V. vulnificus is poorly understood. In this study, by using a mouse wound infection model, we revealed characteristic changes in muscle catabolism and energy metabolism in skeletal muscle associated with bacterial proliferation in the infected tissues. Understanding such metabolic changes in V. vulnificus-infected tissue may provide crucial information to identify the mechanism via which V. vulnificus induces severe infections. Moreover, our metabolite data may be useful for the recognition, identification, or detection of V. vulnificus infections in clinical studies.
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2
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Fullen AR, Gutierrez-Ferman JL, Rayner RE, Kim SH, Chen P, Dubey P, Wozniak DJ, Peeples ME, Cormet-Boyaka E, Deora R. Architecture and matrix assembly determinants of Bordetella pertussis biofilms on primary human airway epithelium. PLoS Pathog 2023; 19:e1011193. [PMID: 36821596 PMCID: PMC9990917 DOI: 10.1371/journal.ppat.1011193] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 03/07/2023] [Accepted: 02/09/2023] [Indexed: 02/24/2023] Open
Abstract
Traditionally, whooping cough or pertussis caused by the obligate human pathogen Bordetella pertussis (Bp) is described as an acute disease with severe symptoms. However, many individuals who contract pertussis are either asymptomatic or show very mild symptoms and yet can serve as carriers and sources of bacterial transmission. Biofilms are an important survival mechanism for bacteria in human infections and disease. However, bacterial determinants that drive biofilm formation in humans are ill-defined. In the current study, we show that Bp infection of well-differentiated primary human bronchial epithelial cells leads to formation of bacterial aggregates, clusters, and highly structured biofilms which are colocalized with cilia. These findings mimic observations from pathological analyses of tissues from pertussis patients. Distinct arrangements (mono-, bi-, and tri-partite) of the polysaccharide Bps, extracellular DNA, and bacterial cells were visualized, suggesting complex heterogeneity in bacteria-matrix interactions. Analyses of mutant biofilms revealed positive roles in matrix production, cell cluster formation, and biofilm maturity for three critical Bp virulence factors: Bps, filamentous hemagglutinin, and adenylate cyclase toxin. Adherence assays identified Bps as a new Bp adhesin for primary human airway cells. Taken together, our results demonstrate the multi-factorial nature of the biofilm extracellular matrix and biofilm development process under conditions mimicking the human respiratory tract and highlight the importance of model systems resembling the natural host environment to investigate pathogenesis and potential therapeutic strategies.
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Affiliation(s)
- Audra R. Fullen
- The Department of Microbial Infection and Immunity, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
| | - Jessica L. Gutierrez-Ferman
- The Department of Microbial Infection and Immunity, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
| | - Rachael E. Rayner
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Sun Hee Kim
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Phylip Chen
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Purnima Dubey
- The Department of Microbial Infection and Immunity, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
| | - Daniel J. Wozniak
- The Department of Microbial Infection and Immunity, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Mark E. Peeples
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
| | - Estelle Cormet-Boyaka
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Rajendar Deora
- The Department of Microbial Infection and Immunity, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
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3
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Kolpen M, Jensen PØ, Faurholt-Jepsen D, Bjarnsholt T. Prevalence of biofilms in acute infections challenges a longstanding paradigm. Biofilm 2022; 4:100080. [PMID: 35721391 PMCID: PMC9198313 DOI: 10.1016/j.bioflm.2022.100080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/16/2022] [Accepted: 06/06/2022] [Indexed: 10/29/2022] Open
Abstract
The significance of bacterial biofilm formation in chronic bacterial lung infections has long been recognized [1]. Likewise, chronic biofilm formation on medical devices is well accepted as a nidus for recurrent bacteremia [2,3]. Even though the prevailing paradigm relies on the dominance of planktonic bacteria in acute endobronchial infections, our understanding of the bacterial organization during acute infection is, so far, limited - virtually absent. However, by comparing similar clinical samples, we have recently demonstrated massive bacterial biofilm formation during acute lung infections resembling the immense bacterial biofilm formation during chronic lung infections. These findings pose major challenges to the basic paradigm of chronic infections being dominated by biofilm forming bacteria while acute infections are dominated by planktonic bacteria. As opposed to the similar high amount of bacterial biofilm found in chronic and acute lung infections, we found that the fast bacterial growth in acute lung infections differed from the slow bacterial growth in chronic lung infections. By highlighting these new findings, we review modes of improved treatment of biofilm infections and the relevance of bacterial growth rates for other bacterial biofilm infections than human lung infections.
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Affiliation(s)
- Mette Kolpen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Peter Østrup Jensen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.,Costerton Biofilm Center, Institute of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Thomas Bjarnsholt
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark.,Costerton Biofilm Center, Institute of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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4
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Lin H, Wang Z, Luo Y, Lin Z, Hong G, Deng K, Huang P, Shen Y. Weighted spectrochemical correlation network analysis-guided GA-PLSR: a potential spectral “fluid biopsy” approach for quantitative assessment of cardiac metabolites in diabetic cardiomyopathy. Microchem J 2022. [DOI: 10.1016/j.microc.2022.108249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5
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Licari C, Tenori L, Giusti B, Sticchi E, Kura A, De Cario R, Inzitari D, Piccardi B, Nesi M, Sarti C, Arba F, Palumbo V, Nencini P, Marcucci R, Gori AM, Luchinat C, Saccenti E. Analysis of Metabolite and Lipid Association Networks Reveals Molecular Mechanisms Associated with 3-Month Mortality and Poor Functional Outcomes in Patients with Acute Ischemic Stroke after Thrombolytic Treatment with Recombinant Tissue Plasminogen Activator. J Proteome Res 2021; 20:4758-4770. [PMID: 34473513 PMCID: PMC8491161 DOI: 10.1021/acs.jproteome.1c00406] [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: 12/29/2022]
Abstract
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Here, we present
an integrated multivariate, univariate, network
reconstruction and differential analysis of metabolite–metabolite
and metabolite–lipid association networks built from an array
of 18 serum metabolites and 110 lipids identified and quantified through
nuclear magnetic resonance spectroscopy in a cohort of 248 patients,
of which 22 died and 82 developed a poor functional outcome within
3 months from acute ischemic stroke (AIS) treated with intravenous
recombinant tissue plasminogen activator. We explored differences
in metabolite and lipid connectivity of patients who did not develop
a poor outcome and who survived the ischemic stroke from the related
opposite conditions. We report statistically significant differences
in the connectivity patterns of both low- and high-molecular-weight
metabolites, implying underlying variations in the metabolic pathway
involving leucine, glycine, glutamine, tyrosine, phenylalanine, citric,
lactic, and acetic acids, ketone bodies, and different lipids, thus
characterizing patients’ outcomes. Our results evidence the
promising and powerful role of the metabolite–metabolite and
metabolite–lipid association networks in investigating molecular
mechanisms underlying AIS patient’s outcome.
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Affiliation(s)
- Cristina Licari
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, Florence 50019, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, Florence 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (C.I.R.M.M.P.), Via Luigi Sacconi 6, Sesto Fiorentino, Florence 50019, Italy.,Department of Chemistry, University of Florence, Via della Lastruccia, 3, Sesto Fiorentino, Florence 50019, Italy
| | - Betti Giusti
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, Florence 50134, Italy.,Atherothrombotic Diseases Center, Careggi Hospital, Florence, Largo Brambilla 3, Florence 50134, Italy.,Excellence Centre for Research, Transfer and High Education for the Development of DE NOVO Therapies (DENOTHE), University of Florence, Viale Pieraccini 6, Firenze 50139, Italy
| | - Elena Sticchi
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, Florence 50134, Italy
| | - Ada Kura
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, Florence 50134, Italy.,Atherothrombotic Diseases Center, Careggi Hospital, Florence, Largo Brambilla 3, Florence 50134, Italy
| | - Rosina De Cario
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, Florence 50134, Italy
| | - Domenico Inzitari
- Stroke Unit, Careggi University Hospital, Florence 50134, Italy.,Institute of Neuroscience, Italian National Research Council (CNR), Via Madonna del Piano, 10, Sesto Fiorentino, Florence 50019, Italy
| | | | - Mascia Nesi
- Stroke Unit, Careggi University Hospital, Florence 50134, Italy
| | - Cristina Sarti
- NEUROFARBA Department, Neuroscience Section, University of Florence, Largo Brambilla 3, Florence 50134, Italy
| | - Francesco Arba
- Department of Neurology, Careggi University Hospital, Largo Brambilla 3, Florence 50134, Italy
| | - Vanessa Palumbo
- Stroke Unit, Careggi University Hospital, Florence 50134, Italy
| | | | - Rossella Marcucci
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, Florence 50134, Italy.,Atherothrombotic Diseases Center, Careggi Hospital, Florence, Largo Brambilla 3, Florence 50134, Italy.,Excellence Centre for Research, Transfer and High Education for the Development of DE NOVO Therapies (DENOTHE), University of Florence, Viale Pieraccini 6, Firenze 50139, Italy
| | - Anna Maria Gori
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, Florence 50134, Italy.,Atherothrombotic Diseases Center, Careggi Hospital, Florence, Largo Brambilla 3, Florence 50134, Italy.,Excellence Centre for Research, Transfer and High Education for the Development of DE NOVO Therapies (DENOTHE), University of Florence, Viale Pieraccini 6, Firenze 50139, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, Florence 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (C.I.R.M.M.P.), Via Luigi Sacconi 6, Sesto Fiorentino, Florence 50019, Italy.,Department of Chemistry, University of Florence, Via della Lastruccia, 3, Sesto Fiorentino, Florence 50019, Italy
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, Wageningen 6708 WE, the Netherlands
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6
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Palma Medina LM, Rath E, Jahagirdar S, Bruun T, Madsen MB, Strålin K, Unge C, Hansen MB, Arnell P, Nekludov M, Hyldegaard O, Lourda M, dos Santos VAM, Saccenti E, Skrede S, Svensson M, Norrby-Teglund A. Discriminatory plasma biomarkers predict specific clinical phenotypes of necrotizing soft-tissue infections. J Clin Invest 2021; 131:149523. [PMID: 34263738 PMCID: PMC8279592 DOI: 10.1172/jci149523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/25/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUNDNecrotizing soft-tissue infections (NSTIs) are rapidly progressing infections frequently complicated by septic shock and associated with high mortality. Early diagnosis is critical for patient outcome, but challenging due to vague initial symptoms. Here, we identified predictive biomarkers for NSTI clinical phenotypes and outcomes using a prospective multicenter NSTI patient cohort.METHODSLuminex multiplex assays were used to assess 36 soluble factors in plasma from NSTI patients with positive microbiological cultures (n = 251 and n = 60 in the discovery and validation cohorts, respectively). Control groups for comparative analyses included surgical controls (n = 20), non-NSTI controls (i.e., suspected NSTI with no necrosis detected upon exploratory surgery, n = 20), and sepsis patients (n = 24).RESULTSThrombomodulin was identified as a unique biomarker for detection of NSTI (AUC, 0.95). A distinct profile discriminating mono- (type II) versus polymicrobial (type I) NSTI types was identified based on differential expression of IL-2, IL-10, IL-22, CXCL10, Fas-ligand, and MMP9 (AUC >0.7). While each NSTI type displayed a distinct array of biomarkers predicting septic shock, granulocyte CSF (G-CSF), S100A8, and IL-6 were shared by both types (AUC >0.78). Finally, differential connectivity analysis revealed distinctive networks associated with specific clinical phenotypes.CONCLUSIONSThis study identifies predictive biomarkers for NSTI clinical phenotypes of potential value for diagnostic, prognostic, and therapeutic approaches in NSTIs.TRIAL REGISTRATIONClinicalTrials.gov NCT01790698.FUNDINGCenter for Innovative Medicine (CIMED); Region Stockholm; Swedish Research Council; European Union; Vinnova; Innovation Fund Denmark; Research Council of Norway; Netherlands Organisation for Health Research and Development; DLR Federal Ministry of Education and Research; and Swedish Children's Cancer Foundation.
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Affiliation(s)
- Laura M. Palma Medina
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Eivind Rath
- Department of Medicine, Division for Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Sanjeevan Jahagirdar
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Trond Bruun
- Department of Medicine, Division for Infectious Diseases, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Martin B. Madsen
- Department of Intensive Care, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Kristoffer Strålin
- Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
- Department of Infectious Diseases and
| | - Christian Unge
- Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
- Functional Area of Emergency Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Marco Bo Hansen
- Department of Anaesthesia, Centre of Head and Orthopaedics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Per Arnell
- Department of Anaesthesia and Intensive Care, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Michael Nekludov
- Department of Anaesthesia, Surgical Services and Intensive Care, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Ole Hyldegaard
- Department of Intensive Care, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Magda Lourda
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Vitor A.P. Martins dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
- LifeGlimmer GmbH, Berlin, Germany
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Steinar Skrede
- Department of Medicine, Division for Infectious Diseases, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Mattias Svensson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
| | - Anna Norrby-Teglund
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institute, Stockholm, Sweden
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7
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Balder Y, Vignoli A, Tenori L, Luchinat C, Saccenti E. Exploration of Blood Lipoprotein and Lipid Fraction Profiles in Healthy Subjects through Integrated Univariate, Multivariate, and Network Analysis Reveals Association of Lipase Activity and Cholesterol Esterification with Sex and Age. Metabolites 2021; 11:metabo11050326. [PMID: 34070169 PMCID: PMC8158518 DOI: 10.3390/metabo11050326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 02/08/2023] Open
Abstract
In this study, we investigated blood lipoprotein and lipid fraction profiles, quantified using nuclear magnetic resonance, in a cohort of 844 healthy blood donors, integrating standard univariate and multivariate analysis with predictive modeling and network analysis. We observed a strong association of lipoprotein and lipid main fraction profiles with sex and age. Our results suggest an age-dependent remodulation of lipase lipoprotein activity in men and a change in the mechanisms controlling the ratio between esterified and non-esterified cholesterol in both men and women.
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Affiliation(s)
- Yasmijn Balder
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands;
| | - Alessia Vignoli
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy; (A.V.); (L.T.); (C.L.)
- Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy; (A.V.); (L.T.); (C.L.)
- Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy; (A.V.); (L.T.); (C.L.)
- Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands;
- Correspondence:
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8
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The INFECT-Project: An International and Multidisciplinary Project on Necrotizing Soft Tissue Infections. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021. [PMID: 33079359 DOI: 10.1007/978-3-030-57616-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
This book describes clinical and microbiologic aspects, pathogenesis, and diagnostics, related to the severe and rapidly spreading necrotizing soft tissue infections. The work has its foundation in a recently completed European Union funded FP7-project called INFECT, which during the period 2013-2018 focused on utilizing a systems medicine approach to increase our understanding of these heterogenous and complex life-threatening infections. In this chapter, the aim and scope as well as key achievements of the INFECT-project are described.
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9
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Systems Biology and Biomarkers in Necrotizing Soft Tissue Infections. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1294:167-186. [PMID: 33079369 DOI: 10.1007/978-3-030-57616-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
In necrotizing soft tissue infection (NSTI) there is a need to identify biomarker sets that can be used for diagnosis and disease management. The INFECT study was designed to obtain such insights through the integration of patient data and results from different clinically relevant experimental models by use of systems biology approaches. This chapter describes the current state of biomarkers in NSTI and how biomarkers are categorized. We introduce the fundamentals of top-down systems biology approaches including analysis tools and we review the use of current methods and systems biology approaches to biomarker discover. Further, we discuss how different "omics" signatures (gene expression, protein, and metabolites) from NSTI patient samples can be used to identify key host and pathogen factors involved in the onset and development of infection, as well as exploring associations to disease outcomes.
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10
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Vignoli A, Tenori L, Luchinat C, Saccenti E. Differential Network Analysis Reveals Molecular Determinants Associated with Blood Pressure and Heart Rate in Healthy Subjects. J Proteome Res 2020; 20:1040-1051. [PMID: 33274633 PMCID: PMC7786375 DOI: 10.1021/acs.jproteome.0c00882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
There
is mounting evidence that subclinical
nonpathological high blood pressure and heart rate during youth and
adulthood steadily increase the risk of developing a cardiovascular
disease at a later stage. For this reason, it is important to understand
the mechanisms underlying the subclinical elevation of blood pressure
and heart rate in healthy, relatively young individuals. In the present
study, we present a network-based metabolomic study of blood plasma
metabolites and lipids measured using nuclear magnetic resonance spectroscopy
on 841 adult healthy blood donor volunteers, which were stratified
for subclinical low and high blood pressure (systolic and diastolic)
and heart rate. Our results indicate a rewiring of metabolic pathways
active in high and low groups, indicating that the subjects with subclinical
high blood pressure and heart rate could present latent cardiometabolic
dysregulations.
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Affiliation(s)
- Alessia Vignoli
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), 50019 Sesto Fiorentino, Italy.,Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), 50019 Sesto Fiorentino, Italy.,Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, 50019 Sesto Fiorentino, Italy
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
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11
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Jahagirdar S, Saccenti E. Evaluation of Single Sample Network Inference Methods for Metabolomics-Based Systems Medicine. J Proteome Res 2020; 20:932-949. [PMID: 33267585 PMCID: PMC7786380 DOI: 10.1021/acs.jproteome.0c00696] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Networks
and network analyses are fundamental tools of systems
biology. Networks are built by inferring pair-wise relationships among
biological entities from a large number of samples such that subject-specific
information is lost. The possibility of constructing these sample
(individual)-specific networks from single molecular profiles might
offer new insights in systems and personalized medicine and as a consequence
is attracting more and more research interest. In this study, we evaluated
and compared LIONESS (Linear Interpolation to Obtain Network Estimates
for Single Samples) and ssPCC (single sample network based on Pearson
correlation) in the metabolomics context of metabolite–metabolite
association networks. We illustrated and explored the characteristics
of these two methods on (i) simulated data, (ii) data generated from
a dynamic metabolic model to simulate real-life observed metabolite
concentration profiles, and (iii) 22 metabolomic data sets and (iv)
we applied single sample network inference to a study case pertaining
to the investigation of necrotizing soft tissue infections to show
how these methods can be applied in metabolomics. We also proposed
some adaptations of the methods that can be used for data exploration.
Overall, despite some limitations, we found single sample networks
to be a promising tool for the analysis of metabolomics data.
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Affiliation(s)
- Sanjeevan Jahagirdar
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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12
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Integration of whole-body [ 18F]FDG PET/MRI with non-targeted metabolomics can provide new insights on tissue-specific insulin resistance in type 2 diabetes. Sci Rep 2020; 10:8343. [PMID: 32433479 PMCID: PMC7239946 DOI: 10.1038/s41598-020-64524-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 03/30/2020] [Indexed: 11/21/2022] Open
Abstract
Alteration of various metabolites has been linked to type 2 diabetes (T2D) and insulin resistance. However, identifying significant associations between metabolites and tissue-specific phenotypes requires a multi-omics approach. In a cohort of 42 subjects with different levels of glucose tolerance (normal, prediabetes and T2D) matched for age and body mass index, we calculated associations between parameters of whole-body positron emission tomography (PET)/magnetic resonance imaging (MRI) during hyperinsulinemic euglycemic clamp and non-targeted metabolomics profiling for subcutaneous adipose tissue (SAT) and plasma. Plasma metabolomics profiling revealed that hepatic fat content was positively associated with tyrosine, and negatively associated with lysoPC(P-16:0). Visceral adipose tissue (VAT) and SAT insulin sensitivity (Ki), were positively associated with several lysophospholipids, while the opposite applied to branched-chain amino acids. The adipose tissue metabolomics revealed a positive association between non-esterified fatty acids and, VAT and liver Ki. Bile acids and carnitines in adipose tissue were inversely associated with VAT Ki. Furthermore, we detected several metabolites that were significantly higher in T2D than normal/prediabetes. In this study we present novel associations between several metabolites from SAT and plasma with the fat fraction, volume and insulin sensitivity of various tissues throughout the body, demonstrating the benefit of an integrative multi-omics approach.
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On the Use of Correlation and MI as a Measure of Metabolite-Metabolite Association for Network Differential Connectivity Analysis. Metabolites 2020; 10:metabo10040171. [PMID: 32344593 PMCID: PMC7241243 DOI: 10.3390/metabo10040171] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/15/2020] [Accepted: 04/22/2020] [Indexed: 02/06/2023] Open
Abstract
Metabolite differential connectivity analysis has been successful in investigating potential molecular mechanisms underlying different conditions in biological systems. Correlation and Mutual Information (MI) are two of the most common measures to quantify association and for building metabolite-metabolite association networks and to calculate differential connectivity. In this study, we investigated the performance of correlation and MI to identify significantly differentially connected metabolites. These association measures were compared on (i) 23 publicly available metabolomic data sets and 7 data sets from other fields, (ii) simulated data with known correlation structures, and (iii) data generated using a dynamic metabolic model to simulate real-life observed metabolite concentration profiles. In all cases, we found more differentially connected metabolites when using correlation indices as a measure for association than MI. We also observed that different MI estimation algorithms resulted in difference in performance when applied to data generated using a dynamic model. We concluded that there is no significant benefit in using MI as a replacement for standard Pearson's or Spearman's correlation when the application is to quantify and detect differentially connected metabolites.
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Systems and Precision Medicine in Necrotizing Soft Tissue Infections. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1294:187-207. [PMID: 33079370 DOI: 10.1007/978-3-030-57616-5_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Necrotizing soft tissue infections (NSTI) are multifactorial and characterized by dysfunctional, time dependent, highly varying hyper- to hypo-inflammatory host responses contributing to disease severity. Furthermore, host-pathogen interactions are diverse and difficult to identify and characterize, due to the many different disease endotypes. There is a need for both refined bedside diagnostics as well as novel targeted treatment options to improve outcome in NSTI. In order to achieve clinically relevant results and to guide preclinical and clinical research the vast amount of fragmented clinical and experimental datasets, which often include omics data at different levels (transcriptomics, proteomics, metabolomics, etc.), need to be organized, harmonized, integrated, and analyzed taking into account the Big Data nature of these datasets. In this chapter, we address these matters from a systems perspective and yet personalized approach. The chapter provides an overview on the increasingly more frequent use of Big Data and Artificial Intelligence (AI) to aggregate and generate knowledge from burgeoning clinical and biochemical information, addresses the challenges to manage this information, and summarizes current efforts to develop robust computer-aided clinical decision support systems so to tackle the serious challenges in NSTI diagnosis, stratification, and optimized tailored therapy.
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