1
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Stein CM. Genetic epidemiology of resistance to M. tuberculosis Infection: importance of study design and recent findings. Genes Immun 2023; 24:117-123. [PMID: 37085579 PMCID: PMC10121418 DOI: 10.1038/s41435-023-00204-z] [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: 01/09/2023] [Revised: 04/03/2023] [Accepted: 04/14/2023] [Indexed: 04/23/2023]
Abstract
Resistance to M. tuberculosis, often referred to as "RSTR" in the literature, is being increasingly studied because of its potential relevance as a clinical outcome in vaccine studies. This review starts by addressing the importance of epidemiological characterization of this phenotype, and ongoing challenges in that characterization. Then, this review summarizes the extant genetic and genomic studies of this phenotype, including heritability studies, candidate gene studies, and genome-wide association studies, as well as whole transcriptome studies. Findings from recent studies that used longitudinal characterization of the RSTR phenotype are compared to those using a cross-sectional definition, and the challenges of using tuberculin skin test and interferon-gamma release assay are discussed. Finally, future directions are proposed. Since this is a rapidly evolving area of public health significance, this review will help frame future research questions and study designs.
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Affiliation(s)
- Catherine M Stein
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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2
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Mann M, Brasier AR. Evolution of proteomics technologies for understanding respiratory syncytial virus pathogenesis. Expert Rev Proteomics 2021; 18:379-394. [PMID: 34018899 PMCID: PMC8277732 DOI: 10.1080/14789450.2021.1931130] [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: 03/05/2021] [Accepted: 05/14/2021] [Indexed: 10/21/2022]
Abstract
Introduction: Respiratory syncytial virus (RSV) is a major human pathogen associated with long term morbidity. RSV replication occurs primarily in the epithelium, producing a complex cellular response associated with acute inflammation and long-lived changes in pulmonary function and allergic disease. Proteomics approaches provide important insights into post-transcriptional regulatory processes including alterations in cellular complexes regulating the coordinated innate response and epigenome.Areas covered: Peer-reviewed proteomics studies of host responses to RSV infections and proteomics techniques were analyzed. Methodologies identified include 1)." bottom-up" discovery proteomics, 2). Organellar proteomics by LC-gel fractionation; 3). Dynamic changes in protein interaction networks by LC-MS; and 4). selective reaction monitoring MS. We introduce recent developments in single-cell proteomics, top-down mass spectrometry, and photo-cleavable surfactant chemistries that will have impact on understanding how RSV induces extracellular matrix (ECM) composition and airway remodeling.Expert opinion: RSV replication induces global changes in the cellular proteome, dynamic shifts in nuclear proteins, and remodeling of epigenetic regulatory complexes linked to the innate response. Pathways discovered by proteomics technologies have led to deeper mechanistic understanding of the roles of heat shock proteins, redox response, transcriptional elongation complex remodeling and ECM secretion remodeling in host responses to RSV infections and pathological sequelae.
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Affiliation(s)
- Morgan Mann
- Department of Internal Medicine, University of Wisconsin-Madison School of Medicine and Public Health (SMPH), Madison, WI, USA
| | - Allan R Brasier
- Department of Internal Medicine and Institute for Clinical and Translational Research (ICTR), University of Wisconsin-Madison, Madison, WI, USA
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3
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Tseng YW, Chang CC, Chang YC. Novel Virulence Role of Pneumococcal NanA in Host Inflammation and Cell Death Through the Activation of Inflammasome and the Caspase Pathway. Front Cell Infect Microbiol 2021; 11:613195. [PMID: 33777832 PMCID: PMC7991587 DOI: 10.3389/fcimb.2021.613195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/05/2021] [Indexed: 01/15/2023] Open
Abstract
Streptococcus pneumoniae is one of most deadly Gram-positive bacterium that causes significant mortality and morbidity worldwide. Intense inflammation and cytotoxicity is a hallmark of invasive pneumococcal disease. Pneumococcal NanA has been shown to exaggerate the production of inflammatory cytokines via unmasking of inhibitory Siglec-5 from its sialyl cis-ligands. To further investigate the mechanistic role of NanA and Siglec-5 in pneumococccal diseases, we systemically analyzed genes and signaling pathways differentially regulated in macrophages infected with wild type and NanA-deficient pneumococcus. We found that NanA-mediated desialylation impairs the Siglec-5-TLR-2 interaction and reduces the recruitment of phosphatase SHP-1 to Siglec-5. This dysregulated crosstalk between TLR-2 and inhibitory Siglec-5 exaggerated multiple inflammatory and death signaling pathways and consequently caused excessive inflammation and cytotoxicity in the infected macrophage. Collectively, our results reveal a novel virulence role of NanA in pneumococcal pathogenesis and suggest that targeting NanA activity may ameliorate the pneumococcus-mediated inflammation and cytotoxicity in severe invasive pneumococcal diseases.
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Affiliation(s)
- Yu-Wen Tseng
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chun-Chi Chang
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yung-Chi Chang
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
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4
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Abudukelimu A, Barberis M, Redegeld F, Sahin N, Sharma RP, Westerhoff HV. Complex Stability and an Irrevertible Transition Reverted by Peptide and Fibroblasts in a Dynamic Model of Innate Immunity. Front Immunol 2020; 10:3091. [PMID: 32117197 PMCID: PMC7033641 DOI: 10.3389/fimmu.2019.03091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022] Open
Abstract
We here apply a control analysis and various types of stability analysis to an in silico model of innate immunity that addresses the management of inflammation by a therapeutic peptide. Motivation is the observation, both in silico and in experiments, that this therapy is not robust. Our modeling results demonstrate how (1) the biological phenomena of acute and chronic modes of inflammation may reflect an inherently complex bistability with an irrevertible flip between the two modes, (2) the chronic mode of the model has stable, sometimes unique, steady states, while its acute-mode steady states are stable but not unique, (3) as witnessed by TNF levels, acute inflammation is controlled by multiple processes, whereas its chronic-mode inflammation is only controlled by TNF synthesis and washout, (4) only when the antigen load is close to the acute mode's flipping point, many processes impact very strongly on cells and cytokines, (5) there is no antigen exposure level below which reduction of the antigen load alone initiates a flip back to the acute mode, and (6) adding healthy fibroblasts makes the transition from acute to chronic inflammation revertible, although (7) there is a window of antigen load where such a therapy cannot be effective. This suggests that triple therapies may be essential to overcome chronic inflammation. These may comprise (1) anti-immunoglobulin light chain peptides, (2) a temporarily reduced antigen load, and (3a) fibroblast repopulation or (3b) stem cell strategies.
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Affiliation(s)
- Abulikemu Abudukelimu
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands.,Molecular Cell Physiology, VU University Amsterdam, Amsterdam, Netherlands
| | - Matteo Barberis
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands.,Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom.,Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, United Kingdom
| | - Frank Redegeld
- Division of Pharmacology, Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Nilgun Sahin
- Molecular Cell Physiology, VU University Amsterdam, Amsterdam, Netherlands
| | - Raju P Sharma
- Molecular Cell Physiology, VU University Amsterdam, Amsterdam, Netherlands
| | - Hans V Westerhoff
- Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands.,Molecular Cell Physiology, VU University Amsterdam, Amsterdam, Netherlands.,School for Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom.,Systems Biology Amsterdam, VU University Amsterdam, Amsterdam, Netherlands
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5
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LEVITON A, ALLRED EN, FICHOROVA RN, VANDERVEEN DK, O’SHEA TM, KUBAN K, DAMMANN O. Early Postnatal IGF-1 and IGFBP-1 Blood Levels in Extremely Preterm Infants: Relationships with Indicators of Placental Insufficiency and with Systemic Inflammation. Am J Perinatol 2019; 36:1442-1452. [PMID: 30685870 PMCID: PMC7252600 DOI: 10.1055/s-0038-1677472] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
OBJECTIVE To evaluate to what extent indicators of placenta insufficiency are associated with low concentrations of insulin-like growth factor 1 (IGF-1) and IGF-1-binding protein-1 (IGFBP-1) in neonatal blood, and to what extent the concentrations of these growth factors are associated with concentrations of proteins with inflammatory, neurotrophic, or angiogenic properties. STUDY DESIGN Using multiplex immunoassays, we measured the concentrations of IGF-1 and IGFBP-1, as well as 25 other proteins in blood spots collected weekly from ≥ 880 infants born before the 28th week of gestation, and sought correlates of concentrations in the top and bottom quartiles for gestational age and day the specimen was collected. RESULTS Medically indicated delivery and severe fetal growth restriction (sFGR) were associated with low concentrations of IGF-1 on the first postnatal day and with high concentrations of IGFBP-1 on almost all days. Elevated concentrations of IGF-1 and IGFBP-1 were accompanied by elevated concentrations of many other proteins with inflammatory, neurotrophic, or angiogenic properties. CONCLUSION Disorders associated with impaired placenta implantation and sFGR appear to account for a relative paucity of IGF-1 on the first postnatal day. Elevated concentrations of IGF-1 and especially IGFBP-1 were associated with same-day elevated concentrations of inflammatory, neurotrophic, and angiogenic proteins.
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Affiliation(s)
- Alan LEVITON
- Departments of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Elizabeth N. ALLRED
- Departments of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Raina N. FICHOROVA
- Departments of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Deborah K. VANDERVEEN
- Departments of Ophthalmology, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA
| | - T. Michael O’SHEA
- Department of Pediatrics, University of North Carolina, Chapel Hill, NC
| | - Karl KUBAN
- Division of Neurology, Department of Pediatrics, Boston Medical Center and Boston University, Boston, MA, USA
| | - Olaf DAMMANN
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA, USA,Perinatal Neuropidemiology Unit, Hannover Medical School, Hannover, Germany
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6
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Leviton A, Joseph RM, Fichorova RN, Allred EN, Gerry Taylor H, Michael O'Shea T, Dammann O. Executive Dysfunction Early Postnatal Biomarkers among Children Born Extremely Preterm. J Neuroimmune Pharmacol 2019; 14:188-199. [PMID: 30191383 PMCID: PMC6401360 DOI: 10.1007/s11481-018-9804-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 08/16/2018] [Indexed: 01/12/2023]
Abstract
We evaluated the relationship between blood levels of inflammatory and neurotrophic proteins during the first postnatal month in 692 children born before the 28th week of gestation and executive function limitations among those 10-year olds who had an IQ ≥ 70. The measures of dysfunction were Z-scores ≤ -1 on the Differential Ability Scales-II working memory (WM) assessment) (N = 164), the NEPSY-II (A Developmental NEuroPSYchological Assessment-II) Inhibition-Inhibition assessment) (N = 350), the NEPSY-II Inhibition-Switching assessment) (N = 345), as well as a Z-score ≤ -1 on all three assessments (identified as the executive dysfunction composite (N = 104). Increased risks of the executive dysfunction composite associated with high concentrations of inflammatory proteins (IL-8, TNF-α, and ICAM-1) were modulated by high concentrations of neurotrophic proteins. This pattern of modulation by neurotrophins of increased risk associated with inflammation was also seen for the working memory limitation, but only with high concentrations of IL-8 and TNF-α, and the switching limitation, but only with high concentrations of ICAM-1. We infer that among children born extremely preterm, risks of executive function limitations might be explained by perinatal systemic inflammation in the absence of adequate neurotrophic capability.
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Affiliation(s)
- Alan Leviton
- Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115-5724, USA.
| | | | - Raina N Fichorova
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Elizabeth N Allred
- Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115-5724, USA
| | - H Gerry Taylor
- Rainbow Babies & Children's Hospital and Case Western Reserve University, Cleveland, OH, USA
| | - T Michael O'Shea
- University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Olaf Dammann
- Tufts University School of Medicine, Boston, MA, 02111, USA
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Hamada A, Torre C, Drancourt M, Ghigo E. Trained Immunity Carried by Non-immune Cells. Front Microbiol 2019; 9:3225. [PMID: 30692968 PMCID: PMC6340064 DOI: 10.3389/fmicb.2018.03225] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/11/2018] [Indexed: 12/21/2022] Open
Abstract
“Trained immunity” is a term proposed by Netea to describe the ability of an organism to develop an exacerbated immunological response to protect against a second infection independent of the adaptative immunity. This immunological memory can last from 1 week to several months and is only described in innate immune cells such as monocytes, macrophages, and natural killer cells. Paradoxically, the lifespan of these cells in the blood is shorter than the duration of trained immunity. This observation suggested that trained immunity could be carried by long lifespan cells such as stem cells and non-immune cells like fibroblasts. It is now evident that in addition to performing their putative function in the development and maintenance of tissue homeostasis, non-immune cells also play an important role in the response to pathogens by producing anti-microbial factors, with long-term inflammation suggesting that non-immune cells can be trained to confer long-lasting immunological memory. This review provides a summary of the current relevant knowledge about the cells which possess immunological memory and discusses the possibility that non-immune cells may carry immunological memory and mechanisms that might be involved.
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Affiliation(s)
- Attoumani Hamada
- IRD, MEPHI, Institut Hospitalier Universitaire Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Cédric Torre
- IRD, MEPHI, Institut Hospitalier Universitaire Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Michel Drancourt
- IRD, MEPHI, Institut Hospitalier Universitaire Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Eric Ghigo
- IRD, MEPHI, Institut Hospitalier Universitaire Méditerranée Infection, Aix-Marseille University, Marseille, France
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8
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Campbell-Tofte J, Vrahatis A, Josefsen K, Mehlsen J, Winther K. Investigating the aetiology of adverse events following HPV vaccination with systems vaccinology. Cell Mol Life Sci 2019; 76:67-87. [PMID: 30324425 PMCID: PMC11105185 DOI: 10.1007/s00018-018-2925-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 09/10/2018] [Accepted: 09/20/2018] [Indexed: 12/18/2022]
Abstract
In contrast to the insidious and poorly immunogenic human papillomavirus (HPV) infections, vaccination with the HPV virus-like particles (vlps) is non-infectious and stimulates a strong neutralizing-antibody response that protects HPV-naïve vaccinees from viral infection and associated cancers. However, controversy about alleged adverse events following immunization (AEFI) with the vlps have led to extensive reductions in vaccine acceptance, with countries like Japan dropping it altogether. The AEFIs are grouped into chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME). In this review, we present a hypothesis that the AEFIs might arise from malfunctions within the immune system when confronted with the unusual antigen. In addition, we outline how the pathophysiology of the AEFIs can be cost-effectively investigated with the holistic principles of systems vaccinology in a two-step process. First, comprehensive immunological profiles of HPV vaccinees exhibiting the AEFIs are generated by integrating the data derived from serological profiling for prominent HPV antibodies and serum cytokines, with data from serum metabolomics, peripheral white blood cells transcriptomics and gut microbiome profiling. Next, the immunological profiles are compared with corresponding profiles generated for matched (a) HPV vaccinees without AEFIs; (b) non-HPV-vaccinated individuals with CFS/ME-like symptoms; and (c) non-HPV-vaccinated individuals without CFS/ME. In these comparisons, any causal links between HPV vaccine and the AEFIs, as well as the underlying molecular basis for the links will be revealed. Such a study should provide an objective basis for evaluating HPV vaccine safety and for identifying biomarkers for individuals at risk of developing AEFI with HPV vaccination.
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Affiliation(s)
| | | | - Knud Josefsen
- Bartholin Institute, Rigshospitalet, Blegdamsvej 9, 2100, Copenhagen Ø, Denmark
| | - Jesper Mehlsen
- Coordinating Research Centre, Bispebjerg and Frederiksberg Hospital, Nordre Fasanvej 57, 2000, Frederiksberg, Denmark
| | - Kaj Winther
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Nørre Allé 51, DK-2200, Copenhagen N, Denmark
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Mulder S, Hamidi H, Kretzler M, Ju W. An integrative systems biology approach for precision medicine in diabetic kidney disease. Diabetes Obes Metab 2018; 20 Suppl 3:6-13. [PMID: 30294956 PMCID: PMC6541014 DOI: 10.1111/dom.13416] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 06/08/2018] [Indexed: 12/12/2022]
Abstract
Current therapeutic approaches are ineffective in many patients with established diabetic kidney disease (DKD), an epidemic affecting one in three patients with diabetes. Early identification of patients at high risk for progression and individualizing therapies have the potential to mitigate kidney complications due to diabetes. To achieve this, a better understanding of the complex pathophysiology of DKD is needed. A system biology approach integrating large-scale omic data is well suited to unravel the molecular mechanisms driving DKD and may offer new perspectives how to personalize therapy. Recent studies indeed show that integrating genome scale data sets generated from prospectively designed clinical cohort studies with model systems using innovative bioinformatics analysis revealed critical molecular pathways in DKD and led to the development of candidate prognostic molecular biomarkers. This review seeks to provide an overview of the recent progress in the application of the integrative systems biology approaches specifically in the field of molecular biomarkers for DKD. We will mainly focus the discussion on how to use integrative system biology approach to first identify patients at high risk of progression, and second to identify patients who may or may not respond to treatment. Challenges and opportunities in applying precision medicine in DKD will also be discussed.
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Affiliation(s)
- Skander Mulder
- University Medical Center Groningen, Groningen, Netherlands
| | - Habib Hamidi
- University of Michigan, Ann Arbor, MI, United States
| | | | - Wenjun Ju
- University of Michigan, Ann Arbor, MI, United States
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Elevations of inflammatory proteins in neonatal blood are associated with obesity and overweight among 2-year-old children born extremely premature. Pediatr Res 2018; 83:1110-1119. [PMID: 29244802 PMCID: PMC6003823 DOI: 10.1038/pr.2017.313] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/22/2017] [Indexed: 01/16/2023]
Abstract
BackgroundChildhood obesity is associated with elevated blood concentrations of inflammation markers. It is not known to what extent inflammation precedes the development of obesity.MethodsIn a cohort of 882 infants born before 28 weeks of gestation, we examined relationships between concentrations of 25 inflammation-related proteins in blood obtained during the first two postnatal weeks and body mass index at 2 years of age.ResultsAmong children delivered for spontaneous indications (n=734), obesity was associated with elevated concentrations of four proteins (IL-1β, IL-6, TNF-R1, and MCP-1) on the first postnatal day; one protein (IL-6) on postnatal day 7; and two proteins (ICAM-3 and VEGF-R1) on postnatal day 14. Among children delivered for maternal or fetal indications (n=148), obesity was associated with elevated concentrations of seven proteins on the 14th postnatal day. In multivariable models in the spontaneous indications subsample, elevated IL-6 on day 1 predicted obesity (odds ratio: 2.9; 95% confidence limits: 1.2, 6.8), whereas elevated VCAM-1 on day 14 predicted overweight at 2 years of age (odds ratio: 2.3; 95% confidence limits: 1.2, 4.3).ConclusionsIn this cohort, neonatal systemic inflammation preceded the onset of obesity, suggesting that inflammation might contribute to the development of obesity.
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11
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Shapiro JA. Living Organisms Author Their Read-Write Genomes in Evolution. BIOLOGY 2017; 6:E42. [PMID: 29211049 PMCID: PMC5745447 DOI: 10.3390/biology6040042] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022]
Abstract
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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12
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Identifying novel transcription factors involved in the inflammatory response by using binding site motif scanning in genomic regions defined by histone acetylation. PLoS One 2017; 12:e0184850. [PMID: 28922390 PMCID: PMC5602638 DOI: 10.1371/journal.pone.0184850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/31/2017] [Indexed: 02/07/2023] Open
Abstract
The innate immune response to pathogenic challenge is a complex, multi-staged process involving thousands of genes. While numerous transcription factors that act as master regulators of this response have been identified, the temporal complexity of gene expression changes in response to pathogen-associated molecular pattern receptor stimulation strongly suggest that additional layers of regulation remain to be uncovered. The evolved pathogen response program in mammalian innate immune cells is understood to reflect a compromise between the probability of clearing the infection and the extent of tissue damage and inflammatory sequelae it causes. Because of that, a key challenge to delineating the regulators that control the temporal inflammatory response is that an innate immune regulator that may confer a selective advantage in the wild may be dispensable in the lab setting. In order to better understand the complete transcriptional response of primary macrophages to the bacterial endotoxin lipopolysaccharide (LPS), we designed a method that integrates temporally resolved gene expression and chromatin-accessibility measurements from mouse macrophages. By correlating changes in transcription factor binding site motif enrichment scores, calculated within regions of accessible chromatin, with the average temporal expression profile of a gene cluster, we screened for transcriptional factors that regulate the cluster. We have validated our predictions of LPS-stimulated transcriptional regulators using ChIP-seq data for three transcription factors with experimentally confirmed functions in innate immunity. In addition, we predict a role in the macrophage LPS response for several novel transcription factors that have not previously been implicated in immune responses. This method is applicable to any experimental situation where temporal gene expression and chromatin-accessibility data are available.
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13
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Allred EN, Dammann O, Fichorova RN, Hooper SR, Hunter SJ, Joseph RM, Kuban K, Leviton A, O'Shea TM, Scott MN. Systemic Inflammation during the First Postnatal Month and the Risk of Attention Deficit Hyperactivity Disorder Characteristics among 10 year-old Children Born Extremely Preterm. J Neuroimmune Pharmacol 2017; 12:531-543. [PMID: 28405874 PMCID: PMC6508968 DOI: 10.1007/s11481-017-9742-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 03/23/2017] [Indexed: 01/19/2023]
Abstract
Although multiple sources link inflammation with attention difficulties, the only human study that evaluated the relationship between systemic inflammation and attention problems assessed attention at age 2 years. Parent and/or teacher completion of the Childhood Symptom Inventory-4 (CSI-4) provided information about characteristics that screen for attention deficit hyperactive disorder (ADHD) among 793 10-year-old children born before the 28th week of gestation who had an IQ ≥ 70. The concentrations of 27 proteins in blood spots obtained during the first postnatal month were measured. 151 children with ADHD behaviors were identified by parent report, while 128 children were identified by teacher report. Top-quartile concentrations of IL-6R, TNF-α, IL-8, VEGF, VEFG-R1, and VEGF-R2 on multiple days were associated with increased risk of ADHD symptoms as assessed by a teacher. Some of this increased risk was modulated by top-quartile concentrations of IL-6R, RANTES, EPO, NT-4, BDNF, bFGF, IGF-1, PIGF, Ang-1, and Ang-2. Systemic inflammation during the first postnatal month among children born extremely preterm appears to increase the risk of teacher-identified ADHD characteristics, and high concentrations of proteins with neurotrophic properties appear capable of modulating this increased risk.
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Affiliation(s)
- Elizabeth N Allred
- Boston Children's Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115-5724, USA
| | - Olaf Dammann
- Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Raina N Fichorova
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Stephen R Hooper
- University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Scott J Hunter
- The University of Chicago Medicine Comer Children's Hospital, Chicago, IL, USA
| | | | - Karl Kuban
- Boston Medical Center and Boston University School of Medicine, Boston, MA, USA
| | - Alan Leviton
- Boston Children's Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, MA, 02115-5724, USA.
| | | | - Megan N Scott
- The University of Chicago Medicine Comer Children's Hospital, Chicago, IL, USA
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14
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Zhao Y, Forst CV, Sayegh CE, Wang IM, Yang X, Zhang B. Molecular and genetic inflammation networks in major human diseases. MOLECULAR BIOSYSTEMS 2017; 12:2318-41. [PMID: 27303926 DOI: 10.1039/c6mb00240d] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
It has been well-recognized that inflammation alongside tissue repair and damage maintaining tissue homeostasis determines the initiation and progression of complex diseases. Albeit with the accomplishment of having captured the most critical inflammation-involved molecules, genetic susceptibilities, epigenetic factors, and environmental factors, our schemata on the role of inflammation in complex diseases remain largely patchy, in part due to the success of reductionism in terms of research methodology per se. Omics data alongside the advances in data integration technologies have enabled reconstruction of molecular and genetic inflammation networks which shed light on the underlying pathophysiology of complex diseases or clinical conditions. Given the proven beneficial role of anti-inflammation in coronary heart disease as well as other complex diseases and immunotherapy as a revolutionary transition in oncology, it becomes timely to review our current understanding of the molecular and genetic inflammation networks underlying major human diseases. In this review, we first briefly discuss the complexity of infectious diseases and then highlight recently uncovered molecular and genetic inflammation networks in other major human diseases including obesity, type II diabetes, coronary heart disease, late onset Alzheimer's disease, Parkinson's disease, and sporadic cancer. The commonality and specificity of these molecular networks are addressed in the context of genetics based on genome-wide association study (GWAS). The double-sword role of inflammation, such as how the aberrant type 1 and/or type 2 immunity leads to chronic and severe clinical conditions, remains open in terms of the inflammasome and the core inflammatome network features. Increasingly available large Omics and clinical data in tandem with systems biology approaches have offered an exciting yet challenging opportunity toward reconstruction of more comprehensive and dynamic molecular and genetic inflammation networks, which hold great promise in transiting network snapshots to video-style multi-scale interplays of disease mechanisms, in turn leading to effective clinical intervention.
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Affiliation(s)
- Yongzhong Zhao
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA. and Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA
| | - Christian V Forst
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA. and Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA
| | - Camil E Sayegh
- Vertex Pharmaceuticals (Canada) Incorporated, 275 Armand-Frappier, Laval, Quebec H7V 4A7, Canada
| | - I-Ming Wang
- Informatics and Analysis, Merck Research Laboratories, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA.
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90025, USA.
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA. and Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA
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15
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Leviton A, Ryan S, Allred EN, Fichorova RN, Michael O'Shea T, Kuban K, Dammann O. Antecedents and early correlates of high and low concentrations of angiogenic proteins in extremely preterm newborns. Clin Chim Acta 2017; 471:1-5. [PMID: 28502557 DOI: 10.1016/j.cca.2017.05.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND To identify the antecedents and very early correlates of low concentrations of angiogenic proteins in the blood of extremely preterm newborns during the first postnatal month. METHODS Using multiplex immunoassays we measured the concentrations of vascular endothelial growth factor A (VEGF), VEGF receptor-1 (VEGFR-1), VEGF receptor-2 (VEGFR-2), placenta growth factor (PIGF), and angiopoietins 1 and 2 (Ang-1, Ang-2), as well as 21 other proteins in blood spots collected on postnatal days 1 (N=1062), 7 (N=1087), 14 (N=989), 21 (N=940) and 28 (N=880) from infants born before the 28th week of gestation. We then sought the protein-concentration correlates of concentrations in the top and bottom quartile for gestational age and day the specimen was collected. RESULTS Children who were delivered for medical indications and those who were severely growth restricted were more likely than others to have low day-1 blood concentrations of VEGF, VEGF-R2, Ang-1, and PIGF. Systemic inflammation accompanied top quartile concentrations of every one of the 6 angiogenic proteins. CONCLUSIONS Low day-1 concentrations of most angiogenic proteins are associated with disorders linked to placenta insufficiency/dysfunction. High concentrations, on the other hand, are associated with systemic inflammation throughout the first postnatal month.
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Affiliation(s)
- Alan Leviton
- Neuroepidemiology Unit, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States.
| | - Stanthia Ryan
- Laboratory of Genital Tract Biology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital Boston MA, Harvard Medical School, Boston, MA, United States
| | - Elizabeth N Allred
- Neuroepidemiology Unit, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Raina N Fichorova
- Laboratory of Genital Tract Biology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital Boston MA, Harvard Medical School, Boston, MA, United States
| | - T Michael O'Shea
- Department of Pediatrics, University of North Carolina, Chapel Hill, NC, United States
| | - Karl Kuban
- Division of Neurology, Department of Pediatrics, Boston Medical Center and Boston University, Boston, MA, United States
| | - Olaf Dammann
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA, United States; Perinatal Neuropidemiology Unit, Hannover Medical School, Hannover, Germany
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16
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Edwards LM. Metabolic systems biology: a brief primer. J Physiol 2017; 595:2849-2855. [PMID: 28028815 DOI: 10.1113/jp272275] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/23/2016] [Indexed: 12/25/2022] Open
Abstract
In the early to mid-20th century, reductionism as a concept in biology was challenged by key thinkers, including Ludwig von Bertalanffy. He proposed that living organisms were specific examples of complex systems and, as such, they should display characteristics including hierarchical organisation and emergent behaviour. Yet the true study of complete biological systems (for example, metabolism) was not possible until technological advances that occurred 60 years later. Technology now exists that permits the measurement of complete levels of the biological hierarchy, for example the genome and transcriptome. The complexity and scale of these data require computational models for their interpretation. The combination of these - systems thinking, high-dimensional data and computation - defines systems biology, typically accompanied by some notion of iterative model refinement. Only sequencing-based technologies, however, offer full coverage. Other 'omics' platforms trade coverage for sensitivity, although the densely connected nature of biological networks suggests that full coverage may not be necessary. Systems biology models are often characterised as either 'bottom-up' (mechanistic) or 'top-down' (statistical). This distinction can mislead, as all models rely on data and all are, to some degree, 'middle-out'. Systems biology has matured as a discipline, and its methods are commonplace in many laboratories. However, many challenges remain, especially those related to large-scale data integration.
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Affiliation(s)
- Lindsay M Edwards
- Respiratory Data Sciences Group, GlaxoSmithKline Medicines Research, Stevenage, Hertfordshire, UK
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17
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Tan Y, Kagan JC. Microbe-inducible trafficking pathways that control Toll-like receptor signaling. Traffic 2017; 18:6-17. [PMID: 27731905 PMCID: PMC5182131 DOI: 10.1111/tra.12454] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 10/07/2016] [Accepted: 10/07/2016] [Indexed: 12/12/2022]
Abstract
The receptors of the mammalian innate immune system are designed for rapid microbial detection, and are located in organelles that are conducive to serve these needs. However, emerging evidence indicates that the sites of microbial detection are not the sites of innate immune signal transduction. Rather, microbial detection triggers the movement of receptors to regions of the cell where factors called sorting adaptors detect active receptors and promote downstream inflammatory responses. These findings highlight the critical role that membrane trafficking pathways play in the initiation of innate immunity to infection. In this review, we describe pathways that promote the microbe-inducible endocytosis of Toll-like receptors (TLRs), and the microbe-inducible movement of TLRs between intracellular compartments. We highlight a new class of proteins called Transporters Associated with the eXecution of Inflammation (TAXI), which have the unique ability to transport TLRs and their microbial ligands to signaling-competent regions of the cell, and we discuss the means by which the subcellular sites of signal transduction are defined.
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Affiliation(s)
- Yunhao Tan
- Harvard Medical School and Division of Gastroenterology, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Jonathan C. Kagan
- Harvard Medical School and Division of Gastroenterology, Boston Children’s Hospital, Boston, MA, 02115, USA
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18
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Wani SA, Sahu AR, Saxena S, Hussain S, Pandey A, Kanchan S, Sahoo AP, Mishra B, Tiwari AK, Mishra BP, Gandham RK, Singh RK. Systems biology approach: Panacea for unravelling host-virus interactions and dynamics of vaccine induced immune response. GENE REPORTS 2016; 5:23-29. [PMID: 32289096 PMCID: PMC7104209 DOI: 10.1016/j.genrep.2016.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/24/2016] [Accepted: 08/01/2016] [Indexed: 12/18/2022]
Abstract
Systems biology is an interdisciplinary research field in life sciences, which involves a comprehensive and quantitative analysis of the interactions between all of the components of biological systems over time. For the past 50 years the discipline of virology has overly focused on the pathogen itself. However, we now know that the host response is equally or more important in defining the eventual pathological outcome of infection. Systems biology has in recent years been increasingly recognised for its importance to infectious disease research. Host-virus interactions can be better understood by taking into account the dynamical molecular networks that constitute a biological system. To decipher the pathobiological mechanisms of any disease requires a deep knowledge of how multiple and concurrent signal-transduction pathways operate and are deregulated. Hence the intricacies of signalling pathways can be dissected only by system level approaches. Deciphering the host virus interactions through system biology approach reviewed High throughput techniques to understand the host pathogen interactions examined Shift from virus-centric perspective to spectrum of virus-host interactions Modeling of host-virus cross talk
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Affiliation(s)
- Sajad Ahmad Wani
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Amit Ranjan Sahu
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Shikha Saxena
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Shahid Hussain
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Aruna Pandey
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Sonam Kanchan
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Aditya Prasad Sahoo
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Bina Mishra
- Division of Biological Products, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Ashok Kumar Tiwari
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Bishnu Prasad Mishra
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
| | - Raj Kumar Singh
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar 243122, India
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Zamora R, Vodovotz Y, Mi Q, Barclay D, Yin J, Horslen S, Rudnick D, Loomes KM, Squires RH. Data-Driven Modeling for Precision Medicine in Pediatric Acute Liver Failure. Mol Med 2016; 22:821-829. [PMID: 27900388 DOI: 10.2119/molmed.2016.00183] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/07/2016] [Indexed: 12/16/2022] Open
Abstract
Absence of early outcome biomarkers for Pediatric Acute Liver Failure (PALF) hinders medical and liver transplant decisions. We sought to define dynamic interactions among circulating inflammatory mediators to gain insights into PALF outcome sub-groups. Serum samples from 101 participants in the PALF study, collected over the first 7 days following enrollment, were assayed for 27 inflammatory mediators. Outcomes (Spontaneous survivors [S, n=61], Non-survivors [NS, n=12], and liver transplant patients [LTx, n=28]) were assessed at 21 days post-enrollment. Dynamic interrelations among mediators were defined using data-driven algorithms. Dynamic Bayesian Network inference identified a common network motif with HMGB1 as a central node in all patient sub-groups. The networks in S and LTx were similar, and differed from NS. Dynamic Network Analysis suggested similar dynamic connectivity in S and LTx, but a more highly-interconnected network in NS that increased with time. A Dynamic Robustness Index calculated to quantify how inflammatory network connectivity changes as a function of correlation stringency differentiated all three patient sub-groups. Our results suggest that increasing inflammatory network connectivity is associated with non-survival in PALF, and may ultimately lead to better patient outcome stratification.
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Affiliation(s)
- Ruben Zamora
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213.,Center for Inflammation and Regenerative Modeling, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219
| | - Yoram Vodovotz
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213.,Center for Inflammation and Regenerative Modeling, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219
| | - Qi Mi
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213
| | - Derek Barclay
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213
| | - Jinling Yin
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213
| | | | | | | | - Robert H Squires
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15213
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20
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Garib FY, Rizopulu AP. T-Regulatory Cells as Part of Strategy of Immune Evasion by Pathogens. BIOCHEMISTRY (MOSCOW) 2016; 80:957-71. [PMID: 26547064 DOI: 10.1134/s0006297915080015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Under physiological conditions, regulatory processes can suppress the immune response after elimination of a pathogen and restore homeostasis through the destruction and suppression of obsolete effector cells of the immune system. The main players in this process are T-regulatory cells (Tregs) and immature dendritic cells, which suppress the immune response by their own products and/or by inducing synthesis of immunosuppressive interleukins IL-10, IL-35, and transforming growth factor (TGF-β) by other cells. This mechanism is also used by widespread "successful" pathogens that are capable of chronically persisting in the human body - herpes virus, hepatitis viruses, human immunodeficiency virus, Mycobacterium tuberculosis, Helicobacter pylori, and others. During coevolution of microbial pathogens and the host immune system, the pathogens developed sophisticated strategies for evading the host defense, so-called immune evasion. In particular, molecular structures of pathogens during the interaction with dendritic cells via activating and inhibitory receptors can change intracellular signal transduction, resulting in block of maturation of dendritic cells. Immature dendritic cells become tolerogenic and cause differentiation of Tregs from the conventional T-cell CD4+. Microbial molecules can also react directly with Tregs through innate immune receptors. Costimulation of Toll-like receptor 5 (TLR5) by flagellin increases the expression of the transcription factor Foxp3, which increases the suppressive activity of Treg cells. From all evasion mechanisms, the induction of immunosuppression by Treg through IL-10, IL-35, and TGF-β appears most effective. This results in the suppression of inflammation and of adaptive immune responses against pathogens, optimizing the conditions for the survival of bacteria and viruses.
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Affiliation(s)
- F Yu Garib
- Lomonosov Moscow State University, Biological Faculty, Moscow, 119991, Russia
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21
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Reviakine I, Jung F, Braune S, Brash JL, Latour R, Gorbet M, van Oeveren W. Stirred, shaken, or stagnant: What goes on at the blood-biomaterial interface. Blood Rev 2016; 31:11-21. [PMID: 27478147 DOI: 10.1016/j.blre.2016.07.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/08/2016] [Accepted: 07/12/2016] [Indexed: 01/15/2023]
Abstract
There is a widely recognized need to improve the performance of vascular implants and external medical devices that come into contact with blood by reducing adverse reactions they cause, such as thrombosis and inflammation. These reactions lead to major adverse cardiovascular events such as heart attacks and strokes. Currently, they are managed therapeutically. This need remains unmet by the biomaterials research community. Recognized stagnation of the blood-biomaterial interface research translates into waning interest from clinicians, funding agencies, and practitioners of adjacent fields. The purpose of this contribution is to stir things up. It follows the 2014 BloodSurf meeting (74th International IUVSTA Workshop on Blood-Biomaterial Interactions), offers reflections on the situation in the field, and a three-pronged strategy integrating different perspectives on the biological mechanisms underlying blood-biomaterial interactions. The success of this strategy depends on reengaging clinicians and on the renewed cooperation of the funding agencies to support long-term efforts.
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Affiliation(s)
- Ilya Reviakine
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
| | - Friedrich Jung
- Institute of Biomaterial Science and Berlin-Brandenburg Centre for Regenerative Therapies (BCRT), Helmholtz Zentrum Geesthacht, Kantstrasse 55, 14513 Teltow, Germany
| | - Steffen Braune
- Institute of Biomaterial Science and Berlin-Brandenburg Centre for Regenerative Therapies (BCRT), Helmholtz Zentrum Geesthacht, Kantstrasse 55, 14513 Teltow, Germany
| | - John L Brash
- Department of Chemical Engineering, School of Biomedical Engineering, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
| | - Robert Latour
- Rhodes Engineering Research Center, Department of Bioengineering, Clemson University, Clemson, SC 29634, USA
| | - Maud Gorbet
- Department of Systems Design Engineering, Biomedical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Wim van Oeveren
- HaemoScan, Stavangerweg 23-23, 9723JC Groningen, The Netherlands
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22
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Martin LB, Burgan SC, Adelman JS, Gervasi SS. Host Competence: An Organismal Trait to Integrate Immunology and Epidemiology. Integr Comp Biol 2016; 56:1225-1237. [DOI: 10.1093/icb/icw064] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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23
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Leviton A, Allred EN, Fichorova RN, Kuban KC, O'Shea TM, Dammann O. Antecedents of inflammation biomarkers in preterm newborns on days 21 and 28. Acta Paediatr 2016; 105:274-80. [PMID: 26610180 DOI: 10.1111/apa.13286] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 10/20/2015] [Accepted: 11/20/2015] [Indexed: 12/31/2022]
Abstract
AIM Most studies of systemic inflammation in very preterm newborns focus on assessments made during the first two weeks. The purpose of this study was to identify some of the antecedents of systemic inflammation evident during postnatal weeks three and four. METHODS We measured the protein concentrations in blood spots collected on postnatal days 21 (N = 176) and 28 (N = 157) from infants born before the 28th week of gestation and sought correlates of measurements in the top quartile. Odds ratios of elevated concentrations were calculated for the most obvious correlates. RESULTS Infants born for maternal and foetal indications were more likely than their peers to have top quartile concentrations of IL-beta, IL-8, TNF-alpha and ICAM-1 on both days 21 and 28. Similarly, infants whose birthweight Z-score was <-2 or between -1 and -2 were also more likely than their peers to have elevated concentrations of these proteins. CONCLUSION Markers of systemic inflammation in the very preterm newborn during the third and fourth postnatal weeks are most strongly associated with maternal and foetal indications for (very preterm) delivery and their common correlate/consequence, foetal growth restriction.
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Affiliation(s)
- Alan Leviton
- Neuroepidemiology Unit Department of Neurology Boston Children's Hospital Harvard Medical School Boston MA USA
| | - Elizabeth N. Allred
- Neuroepidemiology Unit Department of Neurology Boston Children's Hospital Harvard Medical School Boston MA USA
| | - Raina N. Fichorova
- Laboratory of Genital Tract Biology Department of Obstetrics, Gynecology, and Reproductive Biology Brigham and Women's HospitalBoston MA USA
| | - Karl C.K. Kuban
- Division of Neurology Department of Pediatrics Boston Medical Center and Boston University Boston MA USA
| | - T. Michael O'Shea
- Department of Pediatrics Wake Forest University Winston‐Salem NC USA
| | - Olaf Dammann
- Department of Public Health and Community Medicine Tufts University School of Medicine Boston MA USA
- Perinatal Neuropidemiology Unit Hannover Medical School Hannover Germany
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Nakaya HI, Pulendran B. Vaccinology in the era of high-throughput biology. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0146. [PMID: 25964458 DOI: 10.1098/rstb.2014.0146] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Vaccination has been tremendously successful saving lives and preventing infections. However, the development of vaccines against global pandemics such as HIV, malaria and tuberculosis has been obstructed by several challenges. A major challenge is the lack of knowledge about the correlates and mechanisms of protective immunity. Recent advances in the application of systems biological approaches to analyse immune responses to vaccination in humans are beginning to yield new insights about mechanisms of vaccine immunity, and to define molecular signatures, induced rapidly after vaccination, that correlate with and predict vaccine induced immunity. Here, we review these advances and discuss the potential of this systems vaccinology approach in defining novel correlates of protection in clinical trials, and in infection-induced 'experimental challenge models' in humans.
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Affiliation(s)
- Helder I Nakaya
- School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil Emory Vaccine Center and Yerkes National Primate Research Center, Atlanta, GA 30329, USA Department of Pathology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Bali Pulendran
- Emory Vaccine Center and Yerkes National Primate Research Center, Atlanta, GA 30329, USA Department of Pathology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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25
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Leviton A, Allred EN, Fichorova RN, Kuban KCK, Michael O'Shea T, Dammann O. Systemic inflammation on postnatal days 21 and 28 and indicators of brain dysfunction 2years later among children born before the 28th week of gestation. Early Hum Dev 2016; 93:25-32. [PMID: 26735345 PMCID: PMC4733407 DOI: 10.1016/j.earlhumdev.2015.11.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/13/2015] [Accepted: 11/15/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND Systemic inflammation during the first two postnatal weeks in extremely preterm newborns (<28weeks gestation) has been associated with an increased risk of neurodevelopmental dysfunctions. Little is known, however, about the relationship between systemic inflammation during the third and fourth postnatal weeks and subsequent development. METHODS We measured the concentrations of 16 inflammation-related proteins in blood spots collected on postnatal days 21 (N=749) and 28 (N=697) from infants born before the 28th week of gestation and assessed at age 2years. We then sought the developmental correlates of top quartile concentrations for gestational age and day the specimen was collected. Odds ratios and 95% confidence intervals were calculated from regular or multinomial logistic regression models (as appropriate). RESULTS Top quartile concentrations of CRP, IL-1β, IL-6, IL-6R, TNF-R2, IL-8, ICAM-1, and TSH on both days 21 and 28 were associated with ventriculomegaly (when in the NICU) and microcephaly at age 2years. Top quartile concentrations of CRP, SAA, IL-6, TNF-R2, IL-8, and ICAM-1 were associated with mental development index (MDI) of the Bayley-II<55, while top quartile concentrations of CRP, TNF-α (inversely), IL-8, and ICAM-1 were associated with psychomotor development index (PDI)<55 CONCLUSION: Extremely preterm newborns who had systemic inflammation during the third and fourth postnatal weeks were at increased risk of ventriculomegaly during the months after birth, and of microcephaly, and low Bayley Scale scores at 2years old.
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Affiliation(s)
- Alan Leviton
- Neuroepidemiology Unit, Department of Neurology, Boston Children's Hospital, Harvard University, Boston, MA 02115, United States.
| | - Elizabeth N Allred
- Neuroepidemiology Unit, Department of Neurology, Boston Children's Hospital, Harvard University, Boston, MA 02115, United States
| | - Raina N Fichorova
- Laboratory of Genital Tract Biology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Boston, MA 02115, United States
| | - Karl C K Kuban
- Division of Neurology, Department of Pediatrics, Boston Medical Center and Boston University, Boston, MA 02118, United States
| | - T Michael O'Shea
- Department of Pediatrics, Wake Forest University, Winston-Salem, NC 27157, United States
| | - Olaf Dammann
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, United States; Perinatal Neuropidemiology Unit, Hannover Medical School, 30625 Hannover, Germany
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Abstract
While much progress has been made in the fight against the scourge of tuberculosis (TB), we are still some way from reaching the ambitious targets of eliminating it as a global public health problem by the mid twenty-first century. A new and effective vaccine that protects against pulmonary TB disease will be an essential element of any control strategy. Over a dozen vaccines are currently in development, but recent efficacy trial data from one of the most advanced candidates have been disappointing. Limitations of current preclinical animal models exist, together with a lack of a complete understanding of host immunity to TB or robust correlates of disease risk and protection. Therefore, in the context of such obstacles, we discuss the lessons identified from recent efficacy trials, current concepts of biomarkers and correlates of protection, the potential of innovative clinical models such as human challenge and conducting trials in high-incidence settings to evaluate TB vaccines in humans, and the use of systems vaccinology and novel technologies including transcriptomics and metabolomics, that may facilitate their utility.
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Affiliation(s)
| | - Helen McShane
- a The Jenner Institute, University of Oxford , Oxford , UK
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Abstract
This report aims to facilitate the implementation of the Three Rs (replacement, reduction, and refinement) in the use of animal models or procedures involving sepsis and septic shock, an area where there is the potential of high levels of suffering for animals. The emphasis is on refinement because this has the greatest potential for immediate implementation. Specific welfare issues are identified and discussed, and practical measures are proposed to reduce animal use and suffering as well as reducing experimental variability and increasing translatability. The report is based on discussions and submissions from a nonregulatory expert working group consisting of veterinarians, animal technologists, and scientists with expert knowledge relevant to the field.
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Perkins JR, Barrionuevo E, Ranea JA, Blanca M, Cornejo-Garcia JA. Systems biology approaches to enhance our understanding of drug hypersensitivity reactions. Clin Exp Allergy 2015; 44:1461-72. [PMID: 25040150 DOI: 10.1111/cea.12371] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Hypersensitivity drug reactions (HDRs) encompass a wide spectrum of unpredictable clinical entities. They represent an important health problem, affecting people of all ages, and lead to a large strain on the public health system. Here, we summarize experiments that use high-throughput genomics technologies to investigate HDRs. We also introduce the field of systems biology as a relatively recent discipline concerned with the integration and analysis of high-throughput data sets such as DNA microarrays and next-generation sequencing data. We describe previous studies that have applied systems biology techniques to related fields such as allergy and asthma. Finally, we present a number of potential applications of systems biology to the study of HDRs, in order to make the reader aware of the types of analyses that can be performed and the insights that can be gained through their application.
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Affiliation(s)
- J R Perkins
- Research Laboratory, IBIMA-Regional University Hospital of Malaga-UMA, Spain
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Leviton A, Gressens P, Wolkenhauer O, Dammann O. Systems approach to the study of brain damage in the very preterm newborn. Front Syst Neurosci 2015; 9:58. [PMID: 25926780 PMCID: PMC4396381 DOI: 10.3389/fnsys.2015.00058] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 03/26/2015] [Indexed: 12/11/2022] Open
Abstract
Background: A systems approach to the study of brain damage in very preterm newborns has been lacking. Methods: In this perspective piece, we offer encephalopathy of prematurity as an example of the complexity and interrelatedness of brain-damaging molecular processes that can be initiated inflammatory phenomena. Results: Using three transcription factors, nuclear factor-kappa B (NF-κB), Notch-1, and nuclear factor erythroid 2 related factor 2 (NRF2), we show the inter-connectedness of signaling pathways activated by some antecedents of encephalopathy of prematurity. Conclusions: We hope that as biomarkers of exposures and processes leading to brain damage in the most immature newborns become more readily available, those who apply a systems approach to the study of neuroscience can be persuaded to study the pathogenesis of brain disorders in the very preterm newborn.
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Affiliation(s)
- Alan Leviton
- Neuroepidemiology Unit, Boston Children's Hospital Boston, MA, USA ; Department of Neurology, Harvard Medical School Boston, MA, USA
| | - Pierre Gressens
- Inserm, U1141 Paris, France ; Department of Perinatal Imaging and Health, Department of Division of Imaging Sciences and Biomedical Engineering, King's College London, King's Health Partners, St. Thomas' Hospital London, UK
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock Rostock, Germany ; Stellenbosch Institute for Advanced Study (STIAS) Stellenbosch, South Africa
| | - Olaf Dammann
- Department of Public Health and Community Medicine, Tufts University School of Medicine Boston, MA, USA ; Perinatal Epidemiology Unit, Department of Gynecology and Obstetrics, Hannover Medical School Hannover, Germany
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30
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Subramanian N, Torabi-Parizi P, Gottschalk RA, Germain RN, Dutta B. Network representations of immune system complexity. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:13-38. [PMID: 25625853 PMCID: PMC4339634 DOI: 10.1002/wsbm.1288] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 12/09/2014] [Accepted: 12/11/2014] [Indexed: 12/25/2022]
Abstract
The mammalian immune system is a dynamic multiscale system composed of a hierarchically organized set of molecular, cellular, and organismal networks that act in concert to promote effective host defense. These networks range from those involving gene regulatory and protein–protein interactions underlying intracellular signaling pathways and single‐cell responses to increasingly complex networks of in vivo cellular interaction, positioning, and migration that determine the overall immune response of an organism. Immunity is thus not the product of simple signaling events but rather nonlinear behaviors arising from dynamic, feedback‐regulated interactions among many components. One of the major goals of systems immunology is to quantitatively measure these complex multiscale spatial and temporal interactions, permitting development of computational models that can be used to predict responses to perturbation. Recent technological advances permit collection of comprehensive datasets at multiple molecular and cellular levels, while advances in network biology support representation of the relationships of components at each level as physical or functional interaction networks. The latter facilitate effective visualization of patterns and recognition of emergent properties arising from the many interactions of genes, molecules, and cells of the immune system. We illustrate the power of integrating ‘omics’ and network modeling approaches for unbiased reconstruction of signaling and transcriptional networks with a focus on applications involving the innate immune system. We further discuss future possibilities for reconstruction of increasingly complex cellular‐ and organism‐level networks and development of sophisticated computational tools for prediction of emergent immune behavior arising from the concerted action of these networks. WIREs Syst Biol Med 2015, 7:13–38. doi: 10.1002/wsbm.1288 This article is categorized under:
Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Macromolecular Interactions, Methods
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Affiliation(s)
- Naeha Subramanian
- Institute for Systems Biology, Seattle, WA, USA; Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Kuban KCK, O'Shea TM, Allred EN, Paneth N, Hirtz D, Fichorova RN, Leviton A. Systemic inflammation and cerebral palsy risk in extremely preterm infants. J Child Neurol 2014; 29:1692-8. [PMID: 24646503 PMCID: PMC4167987 DOI: 10.1177/0883073813513335] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The authors hypothesized that among extremely preterm infants, elevated concentrations of inflammation-related proteins in neonatal blood are associated with cerebral palsy at 24 months. In 939 infants born before 28 weeks gestation, the authors measured blood concentrations of 25 proteins on postnatal days 1, 7, and 14 and evaluated associations between elevated protein concentrations and cerebral palsy diagnosis. Protein elevations within 3 days of birth were not associated with cerebral palsy. Elevations of tumor necrosis factor-α, tumor necrosis factor-α-receptor-1, interleukin-8, and intercellular adhesion molecule-1 on at least 2 days were associated with diparesis. Recurrent-persistent elevations of interleukin-6, E-selectin, or insulin-like growth factor binding protein-1 were associated with hemiparesis. Diparesis and hemiparesis were more likely among infants who had at least 4 of 9 protein elevations that previously have been associated with cognitive impairment and microcephaly. Repeated elevations of inflammation-related proteins during the first 2 postnatal weeks are associated with increased risk of cerebral palsy.
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Affiliation(s)
- Karl C K Kuban
- Department of Pediatrics, Boston Medical Center, Boston, MA, USA
| | - T Michael O'Shea
- Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Elizabeth N Allred
- Harvard Medical School, Boston, MA, USA Boston Children's Hospital, Boston, MA, USA Harvard School of Public Health, Boston, MA, USA
| | - Nigel Paneth
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA
| | - Deborah Hirtz
- National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Raina N Fichorova
- Harvard Medical School, Boston, MA, USA Department of Obstetrics Gynecology & Reproductive Biology, Brigham and Women's Hospital, Boston, MA, USA
| | - Alan Leviton
- Harvard Medical School, Boston, MA, USA Boston Children's Hospital, Boston, MA, USA
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Abstract
Systems-level analysis of biological processes strives to comprehensively and quantitatively evaluate the interactions between the relevant molecular components over time, thereby enabling development of models that can be employed to ultimately predict behavior. Rapid development in measurement technologies (omics), when combined with the accessible nature of the cellular constituents themselves, is allowing the field of innate immunity to take significant strides toward this lofty goal. In this review, we survey exciting results derived from systems biology analyses of the immune system, ranging from gene regulatory networks to influenza pathogenesis and systems vaccinology.
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Aevermann BD, Pickett BE, Kumar S, Klem EB, Agnihothram S, Askovich PS, Bankhead A, Bolles M, Carter V, Chang J, Clauss TRW, Dash P, Diercks AH, Eisfeld AJ, Ellis A, Fan S, Ferris MT, Gralinski LE, Green RR, Gritsenko MA, Hatta M, Heegel RA, Jacobs JM, Jeng S, Josset L, Kaiser SM, Kelly S, Law GL, Li C, Li J, Long C, Luna ML, Matzke M, McDermott J, Menachery V, Metz TO, Mitchell H, Monroe ME, Navarro G, Neumann G, Podyminogin RL, Purvine SO, Rosenberger CM, Sanders CJ, Schepmoes AA, Shukla AK, Sims A, Sova P, Tam VC, Tchitchek N, Thomas PG, Tilton SC, Totura A, Wang J, Webb-Robertson BJ, Wen J, Weiss JM, Yang F, Yount B, Zhang Q, McWeeney S, Smith RD, Waters KM, Kawaoka Y, Baric R, Aderem A, Katze MG, Scheuermann RH. A comprehensive collection of systems biology data characterizing the host response to viral infection. Sci Data 2014; 1:140033. [PMID: 25977790 PMCID: PMC4410982 DOI: 10.1038/sdata.2014.33] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 08/15/2014] [Indexed: 12/13/2022] Open
Abstract
The Systems Biology for Infectious Diseases Research program was established by
the U.S. National Institute of Allergy and Infectious Diseases to investigate
host-pathogen interactions at a systems level. This program generated 47
transcriptomic and proteomic datasets from 30 studies that investigate
in vivo and in vitro host responses to
viral infections. Human pathogens in the Orthomyxoviridae and
Coronaviridae families, especially pandemic H1N1 and avian
H5N1 influenza A viruses and severe acute respiratory syndrome coronavirus
(SARS-CoV), were investigated. Study validation was demonstrated via
experimental quality control measures and meta-analysis of independent
experiments performed under similar conditions. Primary assay results are
archived at the GEO and PeptideAtlas public repositories, while processed
statistical results together with standardized metadata are publically available
at the Influenza Research Database (www.fludb.org) and the Virus Pathogen
Resource (www.viprbrc.org). By comparing data from mutant versus wild-type
virus and host strains, RNA versus protein differential expression, and
infection with genetically similar strains, these data can be used to further
investigate genetic and physiological determinants of host responses to viral
infection.
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Affiliation(s)
| | | | - Sanjeev Kumar
- Northrop Grumman Information Systems, Health IT , Rockville, MD 20850, USA
| | - Edward B Klem
- Northrop Grumman Information Systems, Health IT , Rockville, MD 20850, USA
| | - Sudhakar Agnihothram
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | | | - Armand Bankhead
- Oregon Clinical & Translational Research Institute , Portland, Oregon 97239-3098, USA ; Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health Sciences University , Portland, Oregon 97239-3098, USA
| | - Meagen Bolles
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA
| | - Victoria Carter
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Jean Chang
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Therese R W Clauss
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Pradyot Dash
- Department of Immunology, St. Jude Children's Research Hospital , Memphis, TN 38105-3678, USA
| | - Alan H Diercks
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Amie J Eisfeld
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Amy Ellis
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Shufang Fan
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7264, USA
| | - Lisa E Gralinski
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA
| | - Richard R Green
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Masato Hatta
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Robert A Heegel
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Jon M Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Sophia Jeng
- Oregon Clinical & Translational Research Institute , Portland, Oregon 97239-3098, USA
| | - Laurence Josset
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Shari M Kaiser
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Sara Kelly
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - G Lynn Law
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Chengjun Li
- Division of Animal influenza, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Harbin, Heilongjiang Province 150001, China
| | - Jiangning Li
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Casey Long
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | - Maria L Luna
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Melissa Matzke
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Jason McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Vineet Menachery
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Hugh Mitchell
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Garnet Navarro
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Gabriele Neumann
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | | | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , Richland, WA 99354, USA
| | | | - Catherine J Sanders
- Department of Immunology, St. Jude Children's Research Hospital , Memphis, TN 38105-3678, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Anil K Shukla
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Amy Sims
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | - Pavel Sova
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Vincent C Tam
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Nicolas Tchitchek
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital , Memphis, TN 38105-3678, USA
| | - Susan C Tilton
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Allison Totura
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA
| | - Jing Wang
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | | | - Ji Wen
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Jeffrey M Weiss
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA
| | - Feng Yang
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Boyd Yount
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA
| | - Qibin Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Shannon McWeeney
- Oregon Clinical & Translational Research Institute , Portland, Oregon 97239-3098, USA ; Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health Sciences University , Portland, Oregon 97239-3098, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory , Richland, WA 99352, USA
| | - Yoshihiro Kawaoka
- School of Veterinary Medicine, Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison , Madison, WI 53706, USA
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill , Chapel Hill, NC 27599-7400, USA ; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599-7290, USA
| | - Alan Aderem
- Seattle Biomedical Research Institute , Seattle, WA 98109, USA
| | - Michael G Katze
- Department of Microbiology, University of Washington , Seattle, WA 98195, USA ; Washington National Primate Research Center, University of Washington , Seattle, WA 98195, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute , La Jolla, CA 92037, USA ; Department of Pathology, University of California , San Diego, CA 92093, USA
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Busslinger M, Tarakhovsky A. Epigenetic control of immunity. Cold Spring Harb Perspect Biol 2014; 6:6/6/a019307. [PMID: 24890513 DOI: 10.1101/cshperspect.a019307] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Immunity relies on the heterogeneity of immune cells and their ability to respond to pathogen challenges. In the adaptive immune system, lymphocytes display a highly diverse antigen receptor repertoire that matches the vast diversity of pathogens. In the innate immune system, the cell's heterogeneity and phenotypic plasticity enable flexible responses to changes in tissue homeostasis caused by infection or damage. The immune responses are calibrated by the graded activity of immune cells that can vary from yeast-like proliferation to lifetime dormancy. This article describes key epigenetic processes that contribute to the function of immune cells during health and disease.
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Affiliation(s)
- Meinrad Busslinger
- Research Institute of Molecular Pathology, Vienna Biocenter, A-1030 Vienna, Austria
| | - Alexander Tarakhovsky
- Laboratory of Lymphocyte Signaling, The Rockefeller University, New York, New York 10021
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35
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Blankley S, Graham CM, Howes A, Bloom CI, Berry MPR, Chaussabel D, Pascual V, Banchereau J, Lipman M, O’Garra A. Identification of the key differential transcriptional responses of human whole blood following TLR2 or TLR4 ligation in-vitro. PLoS One 2014; 9:e97702. [PMID: 24842522 PMCID: PMC4026482 DOI: 10.1371/journal.pone.0097702] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 04/23/2014] [Indexed: 01/01/2023] Open
Abstract
The use of human whole blood for transcriptomic analysis has potential advantages over the use of isolated immune cells for studying the transcriptional response to pathogens and their products. Whole blood stimulation can be carried out in a laboratory without the expertise or equipment to isolate immune cells from blood, with the added advantage of being able to undertake experiments using very small volumes of blood. Toll like receptors (TLRs) are a family of pattern recognition receptors which recognise highly conserved microbial products. Using the TLR2 ligand (Pam3CSK4) and the TLR4 ligand (LPS), human whole blood was stimulated for 0, 1, 3, 6, 12 or 24 hours at which times mRNA was isolated and a comparative microarray was undertaken. A common NFκB transcriptional programme was identified following both TLR2 and TLR4 ligation which peaked at between 3 to 6 hours including upregulation of many of the NFκB family members. In contrast an interferon transcriptional response was observed following TLR4 but not TLR2 ligation as early as 1 hour post stimulation and peaking at 6 hours. These results recapitulate the findings observed in previously published studies using isolated murine and human myeloid cells indicating that in vitro stimulated human whole blood can be used to interrogate the early transcriptional kinetic response of innate cells to TLR ligands. Our study demonstrates that a transcriptomic analysis of mRNA isolated from human whole blood can delineate both the temporal response and the key transcriptional differences following TLR2 and TLR4 ligation.
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Affiliation(s)
- Simon Blankley
- Division of Immunoregulation, MRC National Institute for Medical Research, London, United Kingdom
- * E-mail:
| | - Christine M. Graham
- Division of Immunoregulation, MRC National Institute for Medical Research, London, United Kingdom
| | - Ashleigh Howes
- Division of Immunoregulation, MRC National Institute for Medical Research, London, United Kingdom
| | - Chloe I. Bloom
- Division of Immunoregulation, MRC National Institute for Medical Research, London, United Kingdom
| | - Matthew P. R. Berry
- Division of Immunoregulation, MRC National Institute for Medical Research, London, United Kingdom
- Department of Respiratory Medicine, Imperial College Healthcare NHS trust, London, United Kingdom
| | - Damien Chaussabel
- Baylor Institute for Immunology Research/ANRS Center for Human Vaccines, INSERM, Dallas, Texas, United States of America
- Systems Immunology, Benaroya Research Institute, Seattle, Washington, United States of America
| | - Virginia Pascual
- Baylor Institute for Immunology Research/ANRS Center for Human Vaccines, INSERM, Dallas, Texas, United States of America
| | - Jacques Banchereau
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, United States of America
| | - Marc Lipman
- Department of Respiratory Medicine, Royal Free London NHS Foundation Trust, University College London, London, United Kingdom
| | - Anne O’Garra
- Division of Immunoregulation, MRC National Institute for Medical Research, London, United Kingdom
- Department of Medicine, National Heart and Lung Institute, Imperial College, London, United Kingdom
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36
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Blankley S, Berry MPR, Graham CM, Bloom CI, Lipman M, O'Garra A. The application of transcriptional blood signatures to enhance our understanding of the host response to infection: the example of tuberculosis. Philos Trans R Soc Lond B Biol Sci 2014; 369:20130427. [PMID: 24821914 PMCID: PMC4024221 DOI: 10.1098/rstb.2013.0427] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Despite advances in antimicrobials, vaccination and public health measures, infectious diseases remain a leading cause of morbidity and mortality worldwide. With the increase in antimicrobial resistance and the emergence of new pathogens, there remains a need for new and more accurate diagnostics, the ability to monitor adequate treatment response as well as the ability to predict prognosis for an individual. Transcriptional approaches using blood signatures have enabled a better understanding of the host response to diseases, leading not only to new avenues of basic research, but also to the identification of potential biomarkers for use in diagnosis, prognosis and treatment monitoring.
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Affiliation(s)
- Simon Blankley
- Division of Immunoregulation, MRC National Institute for Medical Research, , London NW7 1AA, UK
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37
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Monti M, Cozzolino M, Cozzolino F, Vitiello G, Tedesco R, Flagiello A, Pucci P. Puzzle of protein complexesin vivo: a present and future challenge for functional proteomics. Expert Rev Proteomics 2014; 6:159-69. [DOI: 10.1586/epr.09.7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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38
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Gibbs DL, Gralinski L, Baric RS, McWeeney SK. Multi-omic network signatures of disease. Front Genet 2014; 4:309. [PMID: 24432028 PMCID: PMC3882664 DOI: 10.3389/fgene.2013.00309] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 12/19/2013] [Indexed: 12/12/2022] Open
Abstract
To better understand dynamic disease processes, integrated multi-omic methods are needed, yet comparing different types of omic data remains difficult. Integrative solutions benefit experimenters by eliminating potential biases that come with single omic analysis. We have developed the methods needed to explore whether a relationship exists between co-expression network models built from transcriptomic and proteomic data types, and whether this relationship can be used to improve the disease signature discovery process. A naïve, correlation based method is utilized for comparison. Using publicly available infectious disease time series data, we analyzed the related co-expression structure of the transcriptome and proteome in response to SARS-CoV infection in mice. Transcript and peptide expression data was filtered using quality scores and subset by taking the intersection on mapped Entrez IDs. Using this data set, independent co-expression networks were built. The networks were integrated by constructing a bipartite module graph based on module member overlap, module summary correlation, and correlation to phenotypes of interest. Compared to the module level results, the naïve approach is hindered by a lack of correlation across data types, less significant enrichment results, and little functional overlap across data types. Our module graph approach avoids these problems, resulting in an integrated omic signature of disease progression, which allows prioritization across data types for down-stream experiment planning. Integrated modules exhibited related functional enrichments and could suggest novel interactions in response to infection. These disease and platform-independent methods can be used to realize the full potential of multi-omic network signatures. The data (experiment SM001) are publically available through the NIAID Systems Virology (https://www.systemsvirology.org) and PNNL (http://omics.pnl.gov) web portals. Phenotype data is found in the supplementary information. The ProCoNA package is available as part of Bioconductor 2.13.
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Affiliation(s)
- David L Gibbs
- McWeeney Lab, Division of Bioinformatics and Computational Biology, Oregon Health & Science University Portland, OR, USA
| | - Lisa Gralinski
- Baric Lab, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Ralph S Baric
- Baric Lab, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Shannon K McWeeney
- McWeeney Lab, Division of Bioinformatics and Computational Biology, Oregon Health & Science University Portland, OR, USA ; McWeeney Lab, OHSU Knight Cancer Institute, Oregon Health & Science University Portland, OR, USA
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39
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Human systems immunology: hypothesis-based modeling and unbiased data-driven approaches. Semin Immunol 2013; 25:193-200. [PMID: 23375135 PMCID: PMC3836867 DOI: 10.1016/j.smim.2012.11.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 11/08/2012] [Indexed: 11/23/2022]
Abstract
Systems immunology is an emerging paradigm that aims at a more systematic and quantitative understanding of the immune system. Two major approaches have been utilized to date in this field: unbiased data-driven modeling to comprehensively identify molecular and cellular components of a system and their interactions; and hypothesis-based quantitative modeling to understand the operating principles of a system by extracting a minimal set of variables and rules underlying them. In this review, we describe applications of the two approaches to the study of viral infections and autoimmune diseases in humans, and discuss possible ways by which these two approaches can synergize when applied to human immunology.
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40
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Abstract
Recent advances in the enzymology of transcription and chromatin regulation have led to the discovery of proteins that play a prominent role in cell differentiation and the maintenance of specialized cell functions. Knowledge about post-synthetic DNA and histone modifications as well as information about the rules that guide the formation of multimolecular chromatin-bound complexes have helped to delineate gene-regulating pathways and describe how these pathways are altered in various pathological conditions. The present review focuses on the emerging area of therapeutic interference with chromatin function for the purpose of cancer treatment and immunomodulation.
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Affiliation(s)
- Rab Prinjha
- Epinova DPU, Immuno-Inflammation Therapy Area, Medicines Research Centre, GlaxoSmithKline, Stevenage SG1 2NY, United Kingdom
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41
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Abstract
OBJECTIVES To familiarize clinicians with advances in computational disease modeling applied to trauma and sepsis. DATA SOURCES PubMed search and review of relevant medical literature. SUMMARY Definitions, key methods, and applications of computational modeling to trauma and sepsis are reviewed. CONCLUSIONS Computational modeling of inflammation and organ dysfunction at the cellular, organ, whole-organism, and population levels has suggested a positive feedback cycle of inflammation → damage → inflammation that manifests via organ-specific inflammatory switching networks. This structure may manifest as multicompartment "tipping points" that drive multiple organ dysfunction. This process may be amenable to rational inflammation reprogramming.
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42
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Contrasted evolutionary histories of two Toll-like receptors (Tlr4 and Tlr7) in wild rodents (MURINAE). BMC Evol Biol 2013; 13:194. [PMID: 24028551 PMCID: PMC3848458 DOI: 10.1186/1471-2148-13-194] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 09/06/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND In vertebrates, it has been repeatedly demonstrated that genes encoding proteins involved in pathogen-recognition by adaptive immunity (e.g. MHC) are subject to intensive diversifying selection. On the other hand, the role and the type of selection processes shaping the evolution of innate-immunity genes are currently far less clear. In this study we analysed the natural variation and the evolutionary processes acting on two genes involved in the innate-immunity recognition of Microbe-Associated Molecular Patterns (MAMPs). RESULTS We sequenced genes encoding Toll-like receptor 4 (Tlr4) and 7 (Tlr7), two of the key bacterial- and viral-sensing receptors of innate immunity, across 23 species within the subfamily Murinae. Although we have shown that the phylogeny of both Tlr genes is largely congruent with the phylogeny of rodents based on a comparably sized non-immune sequence dataset, we also identified several potentially important discrepancies. The sequence analyses revealed that major parts of both Tlrs are evolving under strong purifying selection, likely due to functional constraints. Yet, also several signatures of positive selection have been found in both genes, with more intense signal in the bacterial-sensing Tlr4 than in the viral-sensing Tlr7. 92% and 100% of sites evolving under positive selection in Tlr4 and Tlr7, respectively, were located in the extracellular domain. Directly in the Ligand-Binding Region (LBR) of TLR4 we identified two rapidly evolving amino acid residues and one site under positive selection, all three likely involved in species-specific recognition of lipopolysaccharide of gram-negative bacteria. In contrast, all putative sites of LBRTLR7 involved in the detection of viral nucleic acids were highly conserved across rodents. Interspecific differences in the predicted 3D-structure of the LBR of both Tlrs were not related to phylogenetic history, while analyses of protein charges clearly discriminated Rattini and Murini clades. CONCLUSIONS In consequence of the constraints given by the receptor protein function purifying selection has been a dominant force in evolution of Tlrs. Nevertheless, our results show that episodic diversifying parasite-mediated selection has shaped the present species-specific variability in rodent Tlrs. The intensity of diversifying selection was higher in Tlr4 than in Tlr7, presumably due to structural properties of their ligands.
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43
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Fair JM, Rivas AL. Systems Biology and Ratio-Based, Real-Time Disease Surveillance. Transbound Emerg Dis 2013; 62:437-45. [PMID: 24024609 DOI: 10.1111/tbed.12162] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Indexed: 12/21/2022]
Abstract
Most infectious disease surveillance methods are not well fit for early detection. To address such limitation, here we evaluated a ratio- and Systems Biology-based method that does not require prior knowledge on the identity of an infective agent. Using a reference group of birds experimentally infected with West Nile virus (WNV) and a problem group of unknown health status (except that they were WNV-negative and displayed inflammation), both groups were followed over 22 days and tested with a system that analyses blood leucocyte ratios. To test the ability of the method to discriminate small data sets, both the reference group (n = 5) and the problem group (n = 4) were small. The questions of interest were as follows: (i) whether individuals presenting inflammation (disease-positive or D+) can be distinguished from non-inflamed (disease-negative or D-) birds, (ii) whether two or more D+ stages can be detected and (iii) whether sample size influences detection. Within the problem group, the ratio-based method distinguished the following: (i) three (one D- and two D+) data classes; (ii) two (early and late) inflammatory stages; (iii) fast versus regular or slow responders; and (iv) individuals that recovered from those that remained inflamed. Because ratios differed in larger magnitudes (up to 48 times larger) than percentages, it is suggested that data patterns are likely to be recognized when disease surveillance methods are designed to measure inflammation and utilize ratios.
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Affiliation(s)
- J M Fair
- Los Alamos National Laboratory, Biosecurity & Public Health, Los Alamos, NM, USA
| | - A L Rivas
- Center for Global Health, School of Medicine, University of New Mexico, Albuquerque, NM, USA
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Abstract
Immunity to respiratory virus infection is governed by complex biological networks that influence disease progression and pathogenesis. Systems biology provides an opportunity to explore and understand these multifaceted interactions based on integration and modeling of multiple biological parameters. In this review, we describe new and refined systems-based approaches used to model, identify, and validate novel targets within complex networks following influenza and coronavirus infection. In addition, we propose avenues for extension and expansion that can revolutionize our understanding of infectious disease processes. Together, we hope to provide a window into the unique and expansive opportunity presented by systems biology to understand complex disease processes within the context of infectious diseases.
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Affiliation(s)
- Vineet D. Menachery
- Department of EpidemiologyUniversity of North Carolina at Chapel HillChapel HillNCUSA
| | - Ralph S. Baric
- Department of EpidemiologyUniversity of North Carolina at Chapel HillChapel HillNCUSA
- Department of Microbiology and ImmunologyUniversity of North Carolina at Chapel HillChapel HillNCUSA
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45
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Deffur A, Mulder NJ, Wilkinson RJ. Co-infection with Mycobacterium tuberculosis and human immunodeficiency virus: an overview and motivation for systems approaches. Pathog Dis 2013; 69:101-13. [PMID: 23821533 DOI: 10.1111/2049-632x.12060] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 06/17/2013] [Accepted: 06/20/2013] [Indexed: 12/13/2022] Open
Abstract
Tuberculosis is a devastating disease that accounts for a high proportion of infectious disease morbidity and mortality worldwide. HIV-1 co-infection exacerbates tuberculosis. Enhanced understanding of the host-pathogen relationship in HIV-1 and Mycobacterium tuberculosis co-infection is required. While reductionist approaches have yielded many valuable insights into disease pathogenesis, systems approaches are required that develop data-driven models able to predict emergent properties of this complex co-infection system in order to develop novel therapeutic approaches and to improve diagnostics. Here, we provide a pathogenesis-focused overview of HIV-TB co-infection followed by an introduction to systems approaches and concrete examples of how such approaches are useful.
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Affiliation(s)
- Armin Deffur
- Clinical Infectious Diseases Research Initiative, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Department of Medicine, University of Cape Town, Cape Town, South Africa
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Combined in silico, in vivo, and in vitro studies shed insights into the acute inflammatory response in middle-aged mice. PLoS One 2013; 8:e67419. [PMID: 23844008 PMCID: PMC3699569 DOI: 10.1371/journal.pone.0067419] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 05/17/2013] [Indexed: 11/19/2022] Open
Abstract
We combined in silico, in vivo, and in vitro studies to gain insights into age-dependent changes in acute inflammation in response to bacterial endotoxin (LPS). Time-course cytokine, chemokine, and NO2−/NO3− data from “middle-aged” (6–8 months old) C57BL/6 mice were used to re-parameterize a mechanistic mathematical model of acute inflammation originally calibrated for “young” (2–3 months old) mice. These studies suggested that macrophages from middle-aged mice are more susceptible to cell death, as well as producing higher levels of pro-inflammatory cytokines, vs. macrophages from young mice. In support of the in silico-derived hypotheses, resident peritoneal cells from endotoxemic middle-aged mice exhibited reduced viability and produced elevated levels of TNF-α, IL-6, IL-10, and KC/CXCL1 as compared to cells from young mice. Our studies demonstrate the utility of a combined in silico, in vivo, and in vitro approach to the study of acute inflammation in shock states, and suggest hypotheses with regard to the changes in the cytokine milieu that accompany aging.
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Li S, Nakaya HI, Kazmin DA, Oh JZ, Pulendran B. Systems biological approaches to measure and understand vaccine immunity in humans. Semin Immunol 2013; 25:209-18. [PMID: 23796714 DOI: 10.1016/j.smim.2013.05.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 05/09/2013] [Indexed: 02/01/2023]
Abstract
Recent studies have demonstrated the utility of using systems approaches to identify molecular signatures that can be used to predict vaccine immunity in humans. Such approaches are now being used extensively in vaccinology, and are beginning to yield novel insights about the molecular networks driving vaccine immunity. In this review, we present a broad review of the methodologies involved in these studies, and discuss the promise and challenges involved in this emerging field of "systems vaccinology."
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Affiliation(s)
- Shuzhao Li
- Emory Vaccine Center, Yerkes National Primate Research Center, 954 Gatewood Road, Atlanta, GA 30329, USA
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48
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Zhao Y, Brasier AR. Applications of selected reaction monitoring (SRM)-mass spectrometry (MS) for quantitative measurement of signaling pathways. Methods 2013; 61:313-22. [PMID: 23410677 PMCID: PMC3763905 DOI: 10.1016/j.ymeth.2013.02.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 01/30/2013] [Accepted: 02/01/2013] [Indexed: 01/12/2023] Open
Abstract
Quantitative measurement of the major regulatory proteins in signaling networks poses several technical challenges, including low abundance, the presence of post-translational modifications (PTMs), and the lack of suitable affinity detection reagents. Using the innate immune response (IIR) as a model signaling pathway, we illustrate the approach of stable isotope dilution (SID)-selected reaction monitoring (SRM)-mass spectrometry (MS) assays for quantification of low abundance signaling proteins. A work flow for SID-SRM-MS assay development is established for proteins with experimentally observed MS spectra and for those without. Using the interferon response factor (IRF)-3 transcription factor as an example, we illustrate the steps in high responding signature peptide identification, SID-SRM-MS assay optimization, and evaluation. SRM assays for normalization of IIR abundance to invariant housekeeping proteins are presented. We provide an example of SID-SRM assay development for post-translational modification (PTM) detection using an activating phospho-Ser modified NF-κB/RelA transcription factor, and describe challenges inherent in PTM-SID-SRM-MS assay development. Application of highly qualified quantitative, SID-SRM-MS assays will enable a systems-level approach to understanding the dynamics and kinetics of signaling in host cells, such as the IIR.
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Affiliation(s)
- Yingxin Zhao
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX, USA
- Departments of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Translational Science, University of Texas Medical Branch, Galveston, TX, USA
| | - Allan R. Brasier
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX, USA
- Departments of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Translational Science, University of Texas Medical Branch, Galveston, TX, USA
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49
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Zhao Y, Tian B, Edeh CB, Brasier AR. Quantitation of the dynamic profiles of the innate immune response using multiplex selected reaction monitoring-mass spectrometry. Mol Cell Proteomics 2013; 12:1513-29. [PMID: 23418394 PMCID: PMC3675810 DOI: 10.1074/mcp.m112.023465] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 01/23/2013] [Indexed: 11/06/2022] Open
Abstract
The innate immune response (IIR) is a coordinated intracellular signaling network activated by the presence of pathogen-associated molecular patterns that limits pathogen spread and induces adaptive immunity. Although the precise temporal activation of the various arms of the IIR is a critical factor in the outcome of a disease, currently there are no quantitative multiplex methods for its measurement. In this study, we investigate the temporal activation pattern of the IIR in response to intracellular double-stranded RNA stimulation using a quantitative 10-plex stable isotope dilution-selected reaction monitoring-MS assay. We were able to observe rapid activation of both NF-κB and IRF3 signaling arms, with IRF3 demonstrating a transient response, whereas NF-κB underwent a delayed secondary amplification phase. Our measurements of the NF-κB-IκBα negative feedback loop indicate that about 20% of IκBα in the unstimulated cell is located within the nucleus and represents a population that is rapidly degraded in response to double-stranded RNA. Later in the time course of stimulation, the nuclear IκBα pool is repopulated first prior to its cytoplasmic accumulation. Examination of the IRF3 pathway components shows that double-stranded RNA induces initial consumption of the RIG-I PRR and the IRF3 kinase (TBK1). Stable isotope dilution-selected reaction monitoring-MS measurements after siRNA-mediated IRF3 or RelA knockdown suggests that a low nuclear threshold of NF-κB is required for inducing target gene expression, and that there is cross-inhibition of the NF-κB and IRF3 signaling arms. Finally, we were able to measure delayed noncanonical NF-κB activation by quantifying the abundance of the processed (52 kDa) NF-κB2 subunit in the nucleus. We conclude that quantitative proteomics measurement of the individual signaling arms of the IIR in response to system perturbations is significantly enabled by stable isotope dilution-selected reaction monitoring-MS-based quantification, and that this technique will reveal novel insights into the dynamics and connectivity of the IIR.
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Affiliation(s)
- Yingxin Zhao
- From the ‡Institute for Translational Sciences, University of Texas Medical Branch, Galveston, Texas 77555
- §Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas 77555
- ¶Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas 77555
| | - Bing Tian
- ¶Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas 77555
| | - Chukwudi B. Edeh
- ¶Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas 77555
| | - Allan R. Brasier
- From the ‡Institute for Translational Sciences, University of Texas Medical Branch, Galveston, Texas 77555
- §Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas 77555
- ¶Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas 77555
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50
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Zhang W, Zou X. Systematic analysis of the mechanisms of virus-triggered type I IFN signaling pathways through mathematical modeling. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2013; 10:771-779. [PMID: 24091409 DOI: 10.1109/tcbb.2013.31] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Based on biological experimental data, we developed a mathematical model of the virus-triggered signaling pathways that lead to induction of type I IFNs and systematically analyzed the mechanisms of the cellular antiviral innate immune responses, including the negative feedback regulation of ISG56 and the positive feedback regulation of IFNs. We found that the time between 5 and 48 hours after viral infection is vital for the control and/or elimination of the virus from the host cells and demonstrated that the ISG56-induced inhibition of MITA activation is stronger than the ISG56-induced inhibition of TBK1 activation. The global parameter sensitivity analysis suggests that the positive feedback regulation of IFNs is very important in the innate antiviral system. Furthermore, the robustness of the innate immune signaling network was demonstrated using a new robustness index. These results can help us understand the mechanisms of the virus-induced innate immune response at a system level and provide instruction for further biological experiments.
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