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Rump K, Unterberg M, Bergmann L, Bankfalvi A, Menon A, Schäfer S, Scherag A, Bazzi Z, Siffert W, Peters J, Adamzik M. AQP5-1364A/C polymorphism and the AQP5 expression influence sepsis survival and immune cell migration: a prospective laboratory and patient study. J Transl Med 2016; 14:321. [PMID: 27871297 PMCID: PMC5117689 DOI: 10.1186/s12967-016-1079-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 11/08/2016] [Indexed: 12/12/2022] Open
Abstract
Background The C-allele of the aquaporin (AQP5) -1364A/C polymorphism is associated with decreased AQP5 expression but increased 30-day survival in patients with severe sepsis. AQP5 expression might affect survival via an impact on cell migration. Consequently, we tested the hypothesis that (1) Aqp5 knockout (KO) compared to wild type (WT) mice show an increased survival following lipopolysaccharide (LPS) administration, and that (2) AQP5 expression and the AQP5 -1364A/C polymorphism alters immune cell migration. Methods We investigated Aqp5-KO and wild type mice after intraperitoneal injection of either E.coli lipopolysaccharide (LPS, serotype O127:B8, 20 mg/kg) or saline. Furthermore, neutrophils of volunteers with the AA-AQP5 or AC/CC-AQP5- genotype were incubated with 10−8 M Chemotactic peptide (fMLP) and their migration was assessed by a filter migration assay. Additionally, AQP5 expression after fMLP incubation was analyzed by RT-PCR and Western blot. Moreover, migration of AQP5 overexpressing Jurkat cells was studied after SDF-1α-stimulation. We used exact Wilcoxon–Mann–Whitney tests; exact Wilcoxon signed-rank tests and the Kaplan–Meier estimator for statistical analysis. Results Fifty-six percent of Aqp5-KO but only 22% of WT mice survived following LPS-injection. WT mice showed increased neutrophil migration into peritoneum and lung compared to Aqp5-KO mice. Target-oriented migration of neutrophils was seen after 0.5 h in AA-genotype cells but only after 1.5 h in AC/CC-genotype cells, with a threefold lower migrating cell count. AQP5 overexpressing Jurkat cells showed a 2.4 times stronger migration compared to native Jurkat cells. Conclusion The AQP5 genotype may influence survival following LPS by altering neutrophil cell migration. Trial registration DRKS00010437. Retrospectively registered 26 April 2016 Electronic supplementary material The online version of this article (doi:10.1186/s12967-016-1079-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katharina Rump
- Klinik für Anästhesiologie, Intensivmedizin und Schmerztherapie, Universitätsklinikum Knappschaftskrankenhaus Bochum-Langendreer, In der Schornau 55, 45882, Bochum, Germany. .,Institut für Pharmakogenetik, Universität Duisburg-Essen, Duisburg, Germany. .,Klinik für Anästhesiologie und Intensivmedizin, Universitätsklinikum and Universität Duisburg-Essen, Essen, Germany.
| | - Matthias Unterberg
- Klinik für Anästhesiologie, Intensivmedizin und Schmerztherapie, Universitätsklinikum Knappschaftskrankenhaus Bochum-Langendreer, In der Schornau 55, 45882, Bochum, Germany
| | - Lars Bergmann
- Klinik für Anästhesiologie, Intensivmedizin und Schmerztherapie, Universitätsklinikum Knappschaftskrankenhaus Bochum-Langendreer, In der Schornau 55, 45882, Bochum, Germany
| | - Agnes Bankfalvi
- Institut für Pathologie, Universitätsklinikum and Universität Duisburg-Essen, Essen, Germany
| | - Anil Menon
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, Cincinnati, OH, USA
| | - Simon Schäfer
- Klinik für Anästhesiologie und Intensivmedizin, Universitätsklinikum and Universität Duisburg-Essen, Essen, Germany.,Klinik für Anästhesiologie, LMU, Munich, Germany
| | - André Scherag
- Clinical Epidemiology, Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Zainab Bazzi
- Klinik für Anästhesiologie, Intensivmedizin und Schmerztherapie, Universitätsklinikum Knappschaftskrankenhaus Bochum-Langendreer, In der Schornau 55, 45882, Bochum, Germany
| | - Winfried Siffert
- Institut für Pharmakogenetik, Universität Duisburg-Essen, Duisburg, Germany
| | - Jürgen Peters
- Klinik für Anästhesiologie und Intensivmedizin, Universitätsklinikum and Universität Duisburg-Essen, Essen, Germany
| | - Michael Adamzik
- Klinik für Anästhesiologie, Intensivmedizin und Schmerztherapie, Universitätsklinikum Knappschaftskrankenhaus Bochum-Langendreer, In der Schornau 55, 45882, Bochum, Germany.,Klinik für Anästhesiologie und Intensivmedizin, Universitätsklinikum and Universität Duisburg-Essen, Essen, Germany
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102
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Bustamante M, Standl M, Bassat Q, Vilor-Tejedor N, Medina-Gomez C, Bonilla C, Ahluwalia TS, Bacelis J, Bradfield JP, Tiesler CMT, Rivadeneira F, Ring S, Vissing NH, Fink NR, Jugessur A, Mentch FD, Ballester F, Kriebel J, Kiefte-de Jong JC, Wolsk HM, Llop S, Thiering E, Beth SA, Timpson NJ, Andersen J, Schulz H, Jaddoe VWV, Evans DM, Waage J, Hakonarson H, Grant SFA, Jacobsson B, Bønnelykke K, Bisgaard H, Davey Smith G, Moll HA, Heinrich J, Estivill X, Sunyer J. A genome-wide association meta-analysis of diarrhoeal disease in young children identifies FUT2 locus and provides plausible biological pathways. Hum Mol Genet 2016; 25:4127-4142. [PMID: 27559109 PMCID: PMC5291237 DOI: 10.1093/hmg/ddw264] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 07/21/2016] [Accepted: 07/28/2016] [Indexed: 02/02/2023] Open
Abstract
More than a million childhood diarrhoeal episodes occur worldwide each year, and in developed countries a considerable part of them are caused by viral infections. In this study, we aimed to search for genetic variants associated with diarrhoeal disease in young children by meta-analyzing genome-wide association studies, and to elucidate plausible biological mechanisms. The study was conducted in the context of the Early Genetics and Lifecourse Epidemiology (EAGLE) consortium. Data about diarrhoeal disease in two time windows (around 1 year of age and around 2 years of age) was obtained via parental questionnaires, doctor interviews or medical records. Standard quality control and statistical tests were applied to the 1000 Genomes imputed genotypic data. The meta-analysis (N = 5758) followed by replication (N = 3784) identified a genome-wide significant association between rs8111874 and diarrhoea at age 1 year. Conditional analysis suggested that the causal variant could be rs601338 (W154X) in the FUT2 gene. Children with the A allele, which results in a truncated FUT2 protein, had lower risk of diarrhoea. FUT2 participates in the production of histo-blood group antigens and has previously been implicated in the susceptibility to infections, including Rotavirus and Norovirus Gene-set enrichment analysis suggested pathways related to the histo-blood group antigen production, and the regulation of ion transport and blood pressure. Among others, the gastrointestinal tract, and the immune and neuro-secretory systems were detected as relevant organs. In summary, this genome-wide association meta-analysis suggests the implication of the FUT2 gene in diarrhoeal disease in young children from the general population.
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Affiliation(s)
- Mariona Bustamante
- ISGlobal, Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Pompeu Fabra University (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Marie Standl
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Quique Bassat
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Natalia Vilor-Tejedor
- ISGlobal, Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Pompeu Fabra University (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Carolina Medina-Gomez
- The Generation R Study Group, Erasmus MC, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Carolina Bonilla
- MRC/University of Bristol Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Tarunveer S Ahluwalia
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Bacelis
- Department of Obstetrics and Gynecology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jonathan P Bradfield
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Carla M T Tiesler
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Ludwig-Maximilians-University of Munich, Dr. von Hauner Children's Hospital, Division of Metabolic Diseases and Nutritional Medicine, Munich, Germany
| | - Fernando Rivadeneira
- The Generation R Study Group, Erasmus MC, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Susan Ring
- MRC/University of Bristol Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Nadja H Vissing
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Nadia R Fink
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Area of Health Data and Digitalisation, Institute of Public Health, Oslo, Norway
| | - Frank D Mentch
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ferran Ballester
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, València, Spain
| | - Jennifer Kriebel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Jessica C Kiefte-de Jong
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, Rotterdam, The Netherlands
- Leiden University College, The Hague, The Netherlands
| | - Helene M Wolsk
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Sabrina Llop
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, València, Spain
| | - Elisabeth Thiering
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Ludwig-Maximilians-University of Munich, Dr. von Hauner Children's Hospital, Division of Metabolic Diseases and Nutritional Medicine, Munich, Germany
| | - Systke A Beth
- The Generation R Study Group, Erasmus MC, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, Rotterdam, The Netherlands
| | - Nicholas J Timpson
- MRC/University of Bristol Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Josefine Andersen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Holger Schulz
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, Rotterdam, The Netherlands
| | - David M Evans
- MRC/University of Bristol Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Johannes Waage
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Struan F A Grant
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Endocrinology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Area of Health Data and Digitalisation, Institute of Public Health, Oslo, Norway
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - George Davey Smith
- MRC/University of Bristol Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Henriette A Moll
- Department of Pediatrics, Erasmus MC, Rotterdam, The Netherlands
| | - Joachim Heinrich
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Inner City Clinic, University Hospital of Munich (LMU), Munich, Germany
| | - Xavier Estivill
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Pompeu Fabra University (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
- Experimental Genetics, Sidra Medical and Research Centre, Doha, Qatar
| | - Jordi Sunyer
- ISGlobal, Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Pompeu Fabra University (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
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103
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Taudien S, Lausser L, Giamarellos-Bourboulis EJ, Sponholz C, Schöneweck F, Felder M, Schirra LR, Schmid F, Gogos C, Groth S, Petersen BS, Franke A, Lieb W, Huse K, Zipfel PF, Kurzai O, Moepps B, Gierschik P, Bauer M, Scherag A, Kestler HA, Platzer M. Genetic Factors of the Disease Course After Sepsis: Rare Deleterious Variants Are Predictive. EBioMedicine 2016; 12:227-238. [PMID: 27639823 PMCID: PMC5078585 DOI: 10.1016/j.ebiom.2016.08.037] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/19/2016] [Accepted: 08/24/2016] [Indexed: 12/20/2022] Open
Abstract
Sepsis is a life-threatening organ dysfunction caused by dysregulated host response to infection. For its clinical course, host genetic factors are important and rare genomic variants are suspected to contribute. We sequenced the exomes of 59 Greek and 15 German patients with bacterial sepsis divided into two groups with extremely different disease courses. Variant analysis was focusing on rare deleterious single nucleotide variants (SNVs). We identified significant differences in the number of rare deleterious SNVs per patient between the ethnic groups. Classification experiments based on the data of the Greek patients allowed discrimination between the disease courses with estimated sensitivity and specificity > 75%. By application of the trained model to the German patients we observed comparable discriminatory properties despite lower population-specific rare SNV load. Furthermore, rare SNVs in genes of cell signaling and innate immunity related pathways were identified as classifiers discriminating between the sepsis courses. Sepsis patients with favorable disease course after sepsis, even in the case of unfavorable preconditions, seem to be affected more often by rare deleterious SNVs in cell signaling and innate immunity related pathways, suggesting a protective role of impairments in these processes against a poor disease course. Rare SNV load is higher in the Greek vs. German population. Subsets of rare deleterious SNVs are predictive for the disease course after sepsis. Patients with favorable disease course seem to carry protective deleterious variants in sepsis related pathways.
Sepsis is a life-threatening disease caused by improper response to infection. Only little is known about the role of genetic factors. From > 4000 patients we selected the most extreme cases showing either a favorable or adverse disease course. We determined rare (< 1/200) protein-damaging genetic variants, as they may have a large effect. Using a computational model that includes knowledge on genes we can predict the disease course with > 75% accuracy. Surprisingly, favorable courses can be expected if defense mechanisms are damaged and prevented from overshooting. This underlines the relevance of rare variants for better understanding of sepsis and may offer new treatment options.
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Affiliation(s)
- Stefan Taudien
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Ludwig Lausser
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany; Institute of Medical Systems Biology, Ulm University, Germany
| | - Evangelos J Giamarellos-Bourboulis
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Christoph Sponholz
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany; Department of Anaesthesiology and Intensive Care Therapy, Jena University Hospital, Jena, Germany
| | - Franziska Schöneweck
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Research group Clinical Epidemiology, CSCC, Jena University Hospital, Jena, Germany
| | - Marius Felder
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | | | - Florian Schmid
- Institute of Medical Systems Biology, Ulm University, Germany
| | - Charalambos Gogos
- Department of Internal Medicine, University of Patras, Medical School, Greece
| | - Susann Groth
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Britt-Sabina Petersen
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Klaus Huse
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Peter F Zipfel
- Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany; Friedrich Schiller University Jena, Jena, Germany
| | - Oliver Kurzai
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Septomics Research Center Jena, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany
| | - Barbara Moepps
- Institute of Pharmacology and Toxicology, Ulm University Medical Center, Ulm, Germany
| | - Peter Gierschik
- Institute of Pharmacology and Toxicology, Ulm University Medical Center, Ulm, Germany
| | - Michael Bauer
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Department of Anaesthesiology and Intensive Care Therapy, Jena University Hospital, Jena, Germany
| | - André Scherag
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Research group Clinical Epidemiology, CSCC, Jena University Hospital, Jena, Germany
| | - Hans A Kestler
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany; Institute of Medical Systems Biology, Ulm University, Germany; Friedrich Schiller University Jena, Jena, Germany.
| | - Matthias Platzer
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany.
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104
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Genetic Factors of the Disease Course after Sepsis: A Genome-Wide Study for 28Day Mortality. EBioMedicine 2016; 12:239-246. [PMID: 27639821 PMCID: PMC5078589 DOI: 10.1016/j.ebiom.2016.08.043] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/26/2016] [Accepted: 08/27/2016] [Indexed: 12/30/2022] Open
Abstract
Sepsis is the dysregulated host response to an infection which leads to life-threatening organ dysfunction that varies by host genomic factors. We conducted a genome-wide association study (GWAS) in 740 adult septic patients and focused on 28 day mortality as outcome. Variants with suggestive evidence for an association (p ≤ 10− 5) were validated in two additional GWA studies (n = 3470) and gene coding regions related to the variants were assessed in an independent exome sequencing study (n = 74). In the discovery GWAS, we identified 243 autosomal variants which clustered in 14 loci (p ≤ 10− 5). The best association signal (rs117983287; p = 8.16 × 10− 8) was observed for a missense variant located at chromosome 9q21.2 in the VPS13A gene. VPS13A was further supported by additional GWAS (p = 0.03) and sequencing data (p = 0.04). Furthermore, CRISPLD2 (p = 5.99 × 10− 6) and a region on chromosome 13q21.33 (p = 3.34 × 10− 7) were supported by both our data and external biological evidence. We found 14 loci with suggestive evidence for an association with 28 day mortality and found supportive, converging evidence for three of them in independent data sets. Elucidating the underlying biological mechanisms of VPS13A, CRISPLD2, and the chromosome 13 locus should be a focus of future research activities. A low frequency missense variant in VPS13A on chromosome 9q21.2 was associated with 28 day mortality after sepsis A frequent intronic variant in CRISPLD2 was also supported and was reported to be associated with procalcitonin levels Similarly supported was an intergenic frequent variant on chromosome13q21.33 – a region related to chronic kidney disease
Sepsis is the dysregulated host response to an infection which leads to life-threatening organ dysfunction that is known to vary by host genomic factors. However, the detection of genetic variants related to sepsis outcomes has been challenging so far. We conducted a discovery genome-wide association study (GWAS) in 740 adult patients with sepsis looking for variants that vary with 28 day mortality. We followed-up our best findings by additional GWAS and exome sequencing data in 3544 adult patients and report three regions including the genes VPS13A and CRISPLD2 that were supported by our data and external biological evidence.
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105
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Denlinger LC, Schell K, Angelini G, Green D, Guadarrama A, Prabhu U, Coursin DB, Hogan K, Bertics PJ. A novel assay to detect nucleotide receptor P2X7 genetic polymorphisms influencing numerous innate immune functions. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/09680519040100020101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The importance of accessory signaling pathways amplifying endotoxin responses has recently been highlighted by genetic studies describing LPS-hyporesponsive individuals despite carrying the common allele for TLR4. The nucleotide receptor P2X7 modulates the production of numerous LPS-stimulated inflammatory mediators. We have recently described the largest phenotypic screen known for genetic polymorphisms associated with the nucleotide receptor P2X7, a global regulator of leukocyte function. This required the development of a novel monocyte pore assay with numerous advantages over previous methods and with the potential to facilitate rapid (< 3 h), multiplex analysis of clinical samples. This paper addresses aspects pertinent to the development of the monocyte pore assay, briefly summarizes our results suggestingthat P2X7 alleles modulate LPSstimulated cytokine production, and discusses a model wherein P2X7 may serve as an amplification loop of innate immunity.
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Affiliation(s)
- Loren C. Denlinger
- Department of Medicine, University of Wisconsin Medical School, Madison, Wisconsin, USA, , Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison Wisconsin, USA
| | - Kathleen Schell
- Comprehensive Cancer Center, University of Wisconsin Medical School, Madison, Wisconsin, USA
| | - Giuditta Angelini
- Department of Anesthesiology, University of Wisconsin Medical School, Madison, Wisconsin, USA
| | - Dawn Green
- Department of Anesthesiology, University of Wisconsin Medical School, Madison, Wisconsin, USA
| | - Arturo Guadarrama
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison Wisconsin, USA
| | - Usha Prabhu
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison Wisconsin, USA
| | - Douglas B. Coursin
- Department of Medicine, University of Wisconsin Medical School, Madison, Wisconsin, USA, Department of Anesthesiology, University of Wisconsin Medical School, Madison, Wisconsin, USA
| | - Kirk Hogan
- Department of Anesthesiology, University of Wisconsin Medical School, Madison, Wisconsin, USA
| | - Paul J. Bertics
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison Wisconsin, USA, Comprehensive Cancer Center, University of Wisconsin Medical School, Madison, Wisconsin, USA
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Suarez De La Rica A, Gilsanz F, Maseda E. Epidemiologic trends of sepsis in western countries. ANNALS OF TRANSLATIONAL MEDICINE 2016; 4:325. [PMID: 27713883 DOI: 10.21037/atm.2016.08.59] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Since the American College of Chest Physicians (ACCP) and the Society of Critical care Medicine (SCCM) published the first consensus definition of syndromes related to sepsis in 1992, the knowledge of epidemiology of sepsis has clearly improved, although no prospective studies have been performed to analyse the incidence of sepsis in general population. There are differences in epidemiologic trends in sepsis between western countries and low-income and middle-income countries. In the United States (US), most of epidemiologic studies have been based on large, administrative databases, reporting an increase in the incidence of severe sepsis over years. In general, studies describing epidemiology of sepsis outside the US use clinical definitions and intensive care unit (ICU) observational cohort designs instead of administrative databases and definitions. Incidence of sepsis has increased over years, probably due to progressive aging of population, the existence of more comorbidities and maybe the liberal use of sepsis codification, by including patients with less severity. Notwithstanding, mortality due to sepsis is clearly decreasing over years, probably to improvement in ICU care, although absolute mortality is growing on account of the raise in incidence. Risk factors for sepsis are the two ends of life, male sex, US black race, presence of comorbidities and certain genetic variants. Respiratory tract infections are the most common source of sepsis, and, nowadays, Gram-positive infections are more frequent that Gram-negative sepsis in most prospective studies.
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Affiliation(s)
- Alejandro Suarez De La Rica
- Department of Anesthesiology and Surgical Critical Care, Surgical Intensive Care Unit, Hospital Universitario La Paz, Madrid, Spain
| | - Fernando Gilsanz
- Department of Anesthesiology and Surgical Critical Care, Surgical Intensive Care Unit, Hospital Universitario La Paz, Madrid, Spain
| | - Emilio Maseda
- Department of Anesthesiology and Surgical Critical Care, Surgical Intensive Care Unit, Hospital Universitario La Paz, Madrid, Spain
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Prucha M, Zazula R, Russwurm S. Immunotherapy of Sepsis: Blind Alley or Call for Personalized Assessment? Arch Immunol Ther Exp (Warsz) 2016; 65:37-49. [PMID: 27554587 DOI: 10.1007/s00005-016-0415-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/14/2016] [Indexed: 01/20/2023]
Abstract
Sepsis is the most frequent cause of death in noncoronary intensive care units. In the past 10 years, progress has been made in the early identification of septic patients and their treatment. These improvements in support and therapy mean that mortality is gradually decreasing, however, the rate of death from sepsis remains unacceptably high. Immunotherapy is not currently part of the routine treatment of sepsis. Despite experimental successes, the administration of agents to block the effect of sepsis mediators failed to show evidence for improved outcome in a multitude of clinical trials. The following survey summarizes the current knowledge and results of clinical trials on the immunotherapy of sepsis and describes the limitations of our knowledge of the pathogenesis of sepsis. Administration of immunomodulatory drugs should be linked to the current immune status assessed by both clinical and molecular patterns. Thus, a careful daily review of the patient's immune status needs to be introduced into routine clinical practice giving the opportunity for effective and tailored use of immunomodulatory therapy.
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Affiliation(s)
- Miroslav Prucha
- Department of Clinical Biochemistry, Hematology and Immunology, Hospital Na Homolce, Prague, Czech Republic.
| | - Roman Zazula
- Department of Anesthesiology and Intensive Care, First Faculty of Medicine, Charles University in Prague and Thomayer Hospital, Prague, Czech Republic
| | - Stefan Russwurm
- Department of Anesthesiology and Intensive Care, University Hospital, Jena, Germany
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108
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Ahnert P, Creutz P, Scholz M, Schütte H, Engel C, Hossain H, Chakraborty T, Bauer M, Kiehntopf M, Völker U, Hammerschmidt S, Loeffler M, Suttorp N. PROGRESS - prospective observational study on hospitalized community acquired pneumonia. BMC Pulm Med 2016; 16:108. [PMID: 27535544 PMCID: PMC4987996 DOI: 10.1186/s12890-016-0255-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/03/2016] [Indexed: 12/23/2022] Open
Abstract
Background Community acquired pneumonia (CAP) is a high incidence disease resulting in about 260,000 hospital admissions per year in Germany, more than myocardial infarction or stroke. Worldwide, CAP is the most frequent infectious disease with high lethality ranging from 1.2 % in those 20–29 years old to over 10 % in patients older than 70 years, even in industrial nations. CAP poses numerous medical challenges, which the PROGRESS (Pneumonia Research Network on Genetic Resistance and Susceptibility for the Evolution of Severe Sepsis) network aims to tackle: Operationalization of disease severity throughout the course of disease, outcome prediction for hospitalized patients and prediction of transitions from uncomplicated CAP to severe CAP, and finally, to CAP with sepsis and organ failure as a life-threatening condition. It is a major aim of PROGRESS to understand and predict patient heterogeneity regarding outcome in the hospital and to develop novel treatment concepts. Methods PROGRESS was designed as a clinical, observational, multi-center study of patients with CAP requiring hospitalization. More than 1600 patients selected for low burden of co-morbidities have been enrolled, aiming at a total of 3000. Course of disease, along with therapy, was closely monitored by daily assessments and long-term follow-up. Daily blood samples allow in depth molecular-genetic characterization of patients. We established a well-organized workflow for sample logistics and a comprehensive data management system to collect and manage data from more than 50 study centers in Germany and Austria. Samples are stored in a central biobank and clinical data are stored in a central data base which also integrates all data from molecular assessments. Discussion With the PROGRESS study, we established a comprehensive data base of high quality clinical and molecular data allowing investigation of pressing research questions regarding CAP. In-depth molecular characterization will contribute to the discovery of disease mechanisms and establishment of diagnostic and predictive biomarkers. A strength of PROGRESS is the focus on younger patients with low burden of co-morbidities, allowing a more direct look at host biology with less confounding. As a resulting limitation, insights from PROGRESS will require validation in representative patient cohorts to assess clinical utility. Trial registration The PROGRESS study was retrospectively registered on May 24th, 2016 with ClinicalTrials.gov: NCT02782013
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Affiliation(s)
- Peter Ahnert
- Institute for Medical Informatics, Statistics, and Epidemiology (IMISE), Medical Faculty, University of Leipzig, Haertelstr. 16-18, 04107, Leipzig, Germany.
| | - Petra Creutz
- Department of Infectious Disease and Respiratory Medicine, Charité - University Medicine Berlin, Campus Virchowklinikum, Augustenburgerplatz 1, 13353, Berlin, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics, and Epidemiology (IMISE), Medical Faculty, University of Leipzig, Haertelstr. 16-18, 04107, Leipzig, Germany
| | - Hartwig Schütte
- Department of Pulmonary Medicine, Ernst von Bergmann Hospital, Charlottenstr. 72, 14467, Potsdam, Germany
| | - Christoph Engel
- Institute for Medical Informatics, Statistics, and Epidemiology (IMISE), Medical Faculty, University of Leipzig, Haertelstr. 16-18, 04107, Leipzig, Germany
| | - Hamid Hossain
- Institute of Medical Microbiology, Justus-Liebig University Giessen, Schubertstr. 81, 35392, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus-Liebig University Giessen, Schubertstr. 81, 35392, Giessen, Germany
| | - Michael Bauer
- Department of Anesthesiology and Intensive Medicine, Jena University Hospital, Erlanger Allee 101, 07747, Jena, Germany
| | - Michael Kiehntopf
- Integrated Biobank Jena (IBBJ) and Institute of Clinical Chemistry and Laboratory Diagnostics, Jena University Hospital, Erlanger Allee 101, 07747, Jena, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, Ernst-Moritz-Arndt University Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17487, Greifswald, Germany
| | - Sven Hammerschmidt
- Interfaculty Institute for Genetics and Functional Genomics, Department Genetics of Microorganisms, Ernst-Moritz-Arndt University Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, 17487, Greifswald, Germany
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics, and Epidemiology (IMISE), Medical Faculty, University of Leipzig, Haertelstr. 16-18, 04107, Leipzig, Germany
| | - Norbert Suttorp
- Department of Infectious Disease and Respiratory Medicine, Charité - University Medicine Berlin, Campus Virchowklinikum, Augustenburgerplatz 1, 13353, Berlin, Germany
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109
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Sipahi T, Pocan H, Akar N. Effect of Various Genetic Polymorphisms on the Incidence and Outcome of Severe Sepsis. Clin Appl Thromb Hemost 2016; 12:47-54. [PMID: 16444434 DOI: 10.1177/107602960601200108] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Several genetic polymorphisms have been identified in patients with sepsis and severe sepsis, such as the tumor necrosis factor-α (TNF-α) and TNF-β genes, the interleukin-1 (IL-1) family, the IL-6, the IL-10, the CD-14, the Toll-like receptors, plasminogen activator inhibitor type 1, and the factor V 1691G-A mutations. In this study, the relationship between the TNF-α 308G/A, the IL-6-174 G/C, the PAI-1, the FVL, the EPCR, and the Cathepsin G (Ars 125 Ser) polymorphisms and the development and outcome of sepsis in pediatric patients was studied. TNF-α 308 G/A, PAI-1 4G/4G, and EPCR mutations influence the risk of severe sepsis in children. IL-6 174 G/C, FVL, and Cathepsin G (Ars 125 Ser) did not influence the incidence and mortality of severe sepsis.
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Affiliation(s)
- Tansu Sipahi
- Department of Pediatric Hematology, Fatih University, Faculty of Medicine, Ankara, Turkey.
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110
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Infection control in colon surgery. Langenbecks Arch Surg 2016; 401:581-97. [DOI: 10.1007/s00423-016-1467-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 06/16/2016] [Indexed: 01/27/2023]
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111
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Polymorphism in a lincRNA Associates with a Doubled Risk of Pneumococcal Bacteremia in Kenyan Children. Am J Hum Genet 2016; 98:1092-1100. [PMID: 27236921 PMCID: PMC4908194 DOI: 10.1016/j.ajhg.2016.03.025] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 03/28/2016] [Indexed: 12/31/2022] Open
Abstract
Bacteremia (bacterial bloodstream infection) is a major cause of illness and death in sub-Saharan Africa but little is known about the role of human genetics in susceptibility. We conducted a genome-wide association study of bacteremia susceptibility in more than 5,000 Kenyan children as part of the Wellcome Trust Case Control Consortium 2 (WTCCC2). Both the blood-culture-proven bacteremia case subjects and healthy infants as controls were recruited from Kilifi, on the east coast of Kenya. Streptococcus pneumoniae is the most common cause of bacteremia in Kilifi and was thus the focus of this study. We identified an association between polymorphisms in a long intergenic non-coding RNA (lincRNA) gene (AC011288.2) and pneumococcal bacteremia and replicated the results in the same population (p combined = 1.69 × 10(-9); OR = 2.47, 95% CI = 1.84-3.31). The susceptibility allele is African specific, derived rather than ancestral, and occurs at low frequency (2.7% in control subjects and 6.4% in case subjects). Our further studies showed AC011288.2 expression only in neutrophils, a cell type that is known to play a major role in pneumococcal clearance. Identification of this novel association will further focus research on the role of lincRNAs in human infectious disease.
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112
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Nagalla S, Bray PF. Personalized medicine in thrombosis: back to the future. Blood 2016; 127:2665-71. [PMID: 26847245 PMCID: PMC4891951 DOI: 10.1182/blood-2015-11-634832] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 01/31/2016] [Indexed: 01/26/2023] Open
Abstract
Most physicians believe they practiced personalized medicine prior to the genomics era that followed the sequencing of the human genome. The focus of personalized medicine has been primarily genomic medicine, wherein it is hoped that the nucleotide dissimilarities among different individuals would provide clinicians with more precise understanding of physiology, more refined diagnoses, better disease risk assessment, earlier detection and monitoring, and tailored treatments to the individual patient. However, to date, the "genomic bench" has not worked itself to the clinical thrombosis bedside. In fact, traditional plasma-based hemostasis-thrombosis laboratory testing, by assessing functional pathways of coagulation, may better help manage venous thrombotic disease than a single DNA variant with a small effect size. There are some new and exciting discoveries in the genetics of platelet reactivity pertaining to atherothrombotic disease. Despite a plethora of genetic/genomic data on platelet reactivity, there are relatively little actionable pharmacogenetic data with antiplatelet agents. Nevertheless, it is crucial for genome-wide DNA/RNA sequencing to continue in research settings for causal gene discovery, pharmacogenetic purposes, and gene-gene and gene-environment interactions. The potential of genomics to advance medicine will require integration of personal data that are obtained in the patient history: environmental exposures, diet, social data, etc. Furthermore, without the ritual of obtaining this information, we will have depersonalized medicine, which lacks the precision needed for the research required to eventually incorporate genomics into routine, optimal, and value-added clinical care.
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Affiliation(s)
- Srikanth Nagalla
- The Cardeza Foundation for Hematologic Research and the Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
| | - Paul F Bray
- The Cardeza Foundation for Hematologic Research and the Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA
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113
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Abstract
PURPOSE OF REVIEW The review will update readers on research examining the influence of genetic variation and epigenetics on the immune system and whether genetic variation influences the outcome of critically ill children. RECENT FINDINGS Although there have been few recent studies examining the role of genetic variation in the severity of disease or outcome in critically ill children, studies in critically ill adults have been informative. For example, genetic variations in the genes coding for various components of the immune response, such as the Toll-like receptor 1, interleukin-1RA, proprotein convertase subtilisin/kexin type 9, adoponectin, nuclear factor erythroid 2-related factor 2, elafin, sphingosine 1-phosphate receptor 3, and sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1 have been associated with various outcomes in critically ill adult populations. Many of the variants demonstrate functional consequences in the protein levels or activities. In critically ill children, there is an association with increased ICU length of stay in children with septic shock with one of the Toll-like receptor 1 variants. SUMMARY The degree of influence of host genetic variation in the outcome in critically ill children remains a much understudied area of research. However, it remains important because it may not only help identify children at risk for worse outcomes but it may provide insight into mechanisms of critical illnesses and novel therapies.
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114
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Simon L, Chen E, Edelstein L, Kong X, Bhatlekar S, Rigoutsos I, Bray P, Shaw C. Integrative Multi-omic Analysis of Human Platelet eQTLs Reveals Alternative Start Site in Mitofusin 2. Am J Hum Genet 2016; 98:883-897. [PMID: 27132591 DOI: 10.1016/j.ajhg.2016.03.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/11/2016] [Indexed: 02/07/2023] Open
Abstract
Platelets play a central role in ischemic cardiovascular events. Cardiovascular disease (CVD) is a major cause of death worldwide. Numerous genome-wide association studies (GWASs) have identified loci associated with CVD risk. However, our understanding of how these variants contribute to disease is limited. Using data from the platelet RNA and expression 1 (PRAX1) study, we analyzed cis expression quantitative trait loci (eQTLs) in platelets from 154 normal human subjects. We confirmed these results in silico by performing allele-specific expression (ASE) analysis, which demonstrated that the allelic directionality of eQTLs and ASE patterns correlate significantly. Comparison of platelet eQTLs with data from the Genotype-Tissue Expression (GTEx) project revealed that a number of platelet eQTLs are platelet specific and that platelet eQTL peaks localize to the gene body at a higher rate than eQTLs from other tissues. Upon integration with data from previously published GWASs, we found that the trait-associated variant rs1474868 coincides with the eQTL peak for mitofusin 2 (MFN2). Additional experimental and computational analyses revealed that this eQTL is linked to an unannotated alternate MFN2 start site preferentially expressed in platelets. Integration of phenotype data from the PRAX1 study showed that MFN2 expression levels were significantly associated with platelet count. This study links the variant rs1474868 to a platelet-specific regulatory role for MFN2 and demonstrates the utility of integrating multi-omic data with eQTL analysis in disease-relevant tissues for interpreting GWAS results.
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115
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Jaeger M, Stappers MHT, Joosten LAB, Gyssens IC, Netea MG. Genetic variation in pattern recognition receptors: functional consequences and susceptibility to infectious disease. Future Microbiol 2016; 10:989-1008. [PMID: 26059622 DOI: 10.2217/fmb.15.37] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Cells of the innate immune system are equipped with surface and cytoplasmic receptors for microorganisms called pattern recognition receptors (PRRs). PRRs recognize specific pathogen-associated molecular patterns and as such are crucial for the activation of the immune system. Currently, five different classes of PRRs have been described: Toll-like receptors, C-type lectin receptors, nucleotide-binding oligomerization domain-like receptors, retinoic acid-inducible gene I-like receptors and absent in melanoma 2-like receptors. Following their discovery, many sequence variants in PRR genes have been uncovered and shown to be implicated in human infectious diseases. In this review, we will discuss the effect of genetic variation in PRRs and their signaling pathways on susceptibility to infectious diseases in humans.
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Affiliation(s)
- Martin Jaeger
- Department of Internal Medicine, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Mark H T Stappers
- Department of Internal Medicine, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, The Netherlands.,Department of Medical Microbiology & Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.,Faculty of Medicine, Research group of Immunology & Biochemistry, Hasselt University, Hasselt, Belgium
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Inge C Gyssens
- Department of Internal Medicine, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, The Netherlands.,Department of Medical Microbiology & Infectious Diseases, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.,Faculty of Medicine, Research group of Immunology & Biochemistry, Hasselt University, Hasselt, Belgium
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, The Netherlands
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116
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Yerges-Armstrong LM, Chai S, O'Connell JR, Curran JE, Blangero J, Mitchell BD, Shuldiner AR, Damcott CM. Gene Expression Differences Between Offspring of Long-Lived Individuals and Controls in Candidate Longevity Regions: Evidence for PAPSS2 as a Longevity Gene. J Gerontol A Biol Sci Med Sci 2016; 71:1295-9. [PMID: 26896383 DOI: 10.1093/gerona/glv212] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 11/04/2015] [Indexed: 11/13/2022] Open
Abstract
Although there is compelling evidence for a genetic contribution to longevity, identification of specific genes that robustly associate with longevity has been a challenge. In order to identify longevity-enhancing genes, we measured differential gene expression between offspring of long-lived Amish (older than 90 years; cases, n = 128) and spouses of these offspring (controls, n = 121) and correlated differentially expressed transcripts with locations of longevity-associated variants detected in a prior genome-wide association study (GWAS) of survival to age 90. Expression of one of these transcripts, 3'-phosphoadenosine 5'-phosphosulfate synthase 2 (PAPSS2), was significantly higher in offspring versus controls (4×10(-4)) and this association was replicated using quantitative real-time polymerase chain reaction. PAPSS2, a sulfation enzyme located on chromosome 10, is ~80kb upstream of the PAPSS2 transcription start site. We found evidence of cis-expression for the originally reported GWAS SNP and PAPSS2 Monogenic conditions linked to PAPSS2 include andrenocortical androgen excess resulting in premature pubarche and skeletal dysplasias, both of which have premature aging features. In summary, these findings provide novel evidence for PAPSS2 as a longevity locus and illustrate the value of harnessing multiple "-omic" approaches to identify longevity candidates.
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Affiliation(s)
- Laura M Yerges-Armstrong
- Program for Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore
| | - Sumbul Chai
- Program for Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore
| | - Jeffery R O'Connell
- Program for Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore
| | - Joanne E Curran
- SouthTexas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville
| | - John Blangero
- SouthTexas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville
| | - Braxton D Mitchell
- Program for Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore. Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Maryland
| | - Alan R Shuldiner
- Program for Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore. Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Maryland
| | - Coleen M Damcott
- Program for Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore.
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117
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Shah SS, Rockett KA, Jallow M, Sisay-Joof F, Bojang KA, Pinder M, Jeffreys A, Craik R, Hubbart C, Wellems TE, Kwiatkowski DP. Heterogeneous alleles comprising G6PD deficiency trait in West Africa exert contrasting effects on two major clinical presentations of severe malaria. Malar J 2016; 15:13. [PMID: 26738565 PMCID: PMC4704392 DOI: 10.1186/s12936-015-1045-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 12/09/2015] [Indexed: 11/11/2022] Open
Abstract
Background Glucose-6-phosphate dehydrogenase (G6PD) deficiency exhibits considerable allelic heterogeneity which manifests with variable biochemical and clinical penetrance. It has long been thought that G6PD deficiency confers partial protection against severe malaria, however prior genetic association studies have disagreed with regard to the strength and specificity of a protective effect, which might reflect differences in the host genetic background, environmental influences, or in the specific clinical phenotypes considered. Methods A case-control association study of severe malaria was conducted in The Gambia, a region in West Africa where there is considerable allelic heterogeneity underlying expression of G6PD deficiency trait, evaluating the three major nonsynonymous polymorphisms known to be associated with enzyme deficiency (A968G, T542A, and C202T) in a cohort of 3836 controls and 2379 severe malaria cases. Results Each deficiency allele exhibited a similar trend toward protection against severe malaria overall (15–26 % reduced risk); however, in stratifying severe malaria to two of its constituent clinical subphenotypes, severe malarial anaemia (SMA) and cerebral malaria (CM), the three deficiency alleles exhibited trends of opposing effect, with risk conferred to SMA and protection with respect to CM. To assess the overall effect of G6PD deficiency trait, deficiency alleles found across all three loci were pooled. G6PD deficiency trait was found to be significantly associated with protection from severe malaria overall (OR 0.83 [0.75–0.92], \documentclass[12pt]{minimal}
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\begin{document}$$P = 0.0006$$\end{document}P=0.0006), but this was limited to CM (OR 0.73 [0.61–0.87], \documentclass[12pt]{minimal}
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\begin{document}$$P = 0.0005$$\end{document}P=0.0005), with a trend toward increased risk for SMA, especially in fully-deficient individuals (OR 1.43 [0.99–2.08], \documentclass[12pt]{minimal}
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\begin{document}$$P = 0.056$$\end{document}P=0.056). Sex-stratified testing largely comported with these results, with evidence suggesting that protection by G6PD deficiency trait is conferred to both males and females, though susceptibility to SMA may be restricted to fully-deficient male hemizygotes. Conclusions In a part of Africa where multiple alleles contribute to expression of G6PD deficiency trait, these findings clarify and extend previous work done in populations where a single variant predominates, and taken together suggest a causal role for G6PD deficiency trait itself with respect to severe malaria, with opposing effects seen on two major clinical subphenotypes.
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Affiliation(s)
- Shivang S Shah
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. .,Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Kirk A Rockett
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Muminatou Jallow
- Medical Research Council Laboratories, Banjul, Fajara, The Gambia.
| | - Fatou Sisay-Joof
- Medical Research Council Laboratories, Banjul, Fajara, The Gambia.
| | - Kalifa A Bojang
- Medical Research Council Laboratories, Banjul, Fajara, The Gambia.
| | - Margaret Pinder
- Medical Research Council Laboratories, Banjul, Fajara, The Gambia.
| | - Anna Jeffreys
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Rachel Craik
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Christina Hubbart
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Thomas E Wellems
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Dominic P Kwiatkowski
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. .,Wellcome Trust Sanger Institute, Hinxton, UK.
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Abstract
Sepsis is a major cause of neonatal morbidity and mortality, especially in vulnerable preterm populations. Immature immune defenses, and environmental and maternal factors contribute to this risk, with as many as a third of very preterm infants experiencing sepsis during their stay in the neonatal intensive care unit (NICU). Epidemiologic and twin studies have suggested that there is a genetic contribution to sepsis predilection. Several investigators have conducted candidate gene association studies on variants of specific interest and potential functional significance in neonatal sepsis. In this review, we describe details of studies that have evaluated genetic susceptibility in neonatal sepsis, and summarize findings from a review of candidate gene association studies.
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Affiliation(s)
- Lakshmi Srinivasan
- Department of Pediatrics, The Children's Hospital of Philadelphia, The University of Pennsylvania, Philadelphia, PA.
| | - Haresh Kirpalani
- Department of Pediatrics, The Children's Hospital of Philadelphia, The University of Pennsylvania, Philadelphia, PA
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Logunova N, Korotetskaya M, Polshakov V, Apt A. The QTL within the H2 Complex Involved in the Control of Tuberculosis Infection in Mice Is the Classical Class II H2-Ab1 Gene. PLoS Genet 2015; 11:e1005672. [PMID: 26618355 PMCID: PMC4664271 DOI: 10.1371/journal.pgen.1005672] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 10/26/2015] [Indexed: 12/27/2022] Open
Abstract
The level of susceptibility to tuberculosis (TB) infection depends upon allelic variations in numerous interacting genes. In our mouse model system, the whole-genome quantitative trait loci (QTLs) scan revealed three QTLs involved in TB control on chromosomes 3, 9, and in the vicinity of the H2 complex on chromosome 17. For the present study, we have established a panel of new congenic, MHC-recombinant mouse strains bearing differential small segments of chromosome 17 transferred from the TB-susceptible I/St (H2j) strain onto the genetic background of TB-resistant C57BL/6 (B6) mice (H2b). This allowed narrowing the QTL interval to 17Ch: 33, 77–34, 34 Mb, containing 36 protein-encoding genes. Cloning and sequencing of the H2j allelic variants of these genes demonstrated profound polymorphic variations compare to the H2b haplotype. In two recombinant strains, B6.I-249.1.15.100 and B6.I-249.1.15.139, recombination breakpoints occurred in different sites of the H2-Aβ 1 gene (beta-chain of the Class II heterodimer H2-A), providing polymorphic variations in the domain β1 of the Aβ-chain. These variations were sufficient to produce different TB-relevant phenotypes: the more susceptible B6.I-249.1.15.100 strain demonstrated shorter survival time, more rapid body weight loss, higher mycobacterial loads in the lungs and more severe lung histopathology compared to the more resistant B6.I-249.1.15.139 strain. CD4+ T cells recognized mycobacterial antigens exclusively in the context of the H2-A Class II molecule, and the level of IFN-γ-producing CD4+ T cells in the lungs was significantly higher in the resistant strain. Thus, we directly demonstrated for the first time that the classical H2- Ab1 Class II gene is involved in TB control. Molecular modeling of the H2-Aj product predicts that amino acid (AA) substitutions in the Aβ-chain modify the motif of the peptide–MHC binding groove. Moreover, unique AA substitutions in both α- and β-chains of the H2-Aj molecule might affect its interactions with the T-cell receptor (TCR). Many genes of the host regulate interactions with Mycobacterium tuberculosis and determine the level of susceptibility to, and severity of, tuberculosis (TB). Identification of these genes and their alleles is continuing and contributes new knowledge about the host-pathogen interactions. So far, forward genetic approaches (from phenotype to gene) have identified several chromosomal segments involved in genetic control of TB in mice (quantitative trait loci—QTL), but only one particular gene, Ipr1, has been identified. Here, we report the identification of a second TB-controlling gene. On the basis of a pair of mouse inbred strains with polar susceptibility to TB infection (susceptible I/St and more resistant C57BL/6) we established a panel of recombinant strains carrying small segments of Chromosome 17 from I/St on the genetic background of C57BL/6. A combination of genetic mapping, gene sequencing, TB phenotypes assessment and immunological approaches demonstrates that the H2-Ab1 gene encoding the beta-chain of the Class II heterodimer H2-A determines susceptibility to TB infection. The importance of allelic polymorphisms in Class II genes encoding antigen-presenting molecules in susceptibility to infection has been suspected. This is the first prove of this role obtained by the methods of classical forward genetics.
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Affiliation(s)
- Nadezhda Logunova
- Laboratory for Immunogenetics, Central Institute for Tuberculosis, Moscow, Russia
- * E-mail: (NL); (AA)
| | - Maria Korotetskaya
- Laboratory for Immunogenetics, Central Institute for Tuberculosis, Moscow, Russia
| | - Vladimir Polshakov
- Center for Magnetic Tomography & Spectroscopy, School of Fundamental Medicine, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexander Apt
- Laboratory for Immunogenetics, Central Institute for Tuberculosis, Moscow, Russia
- Department of Immunology, School of Biology, M. V. Lomonosov Moscow State University, Moscow, Russia
- * E-mail: (NL); (AA)
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Human genetic basis of interindividual variability in the course of infection. Proc Natl Acad Sci U S A 2015; 112:E7118-27. [PMID: 26621739 DOI: 10.1073/pnas.1521644112] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The key problem in human infectious diseases was posed at the turn of the 20th century: their pathogenesis. For almost any given virus, bacterium, fungus, or parasite, life-threatening clinical disease develops in only a small minority of infected individuals. Solving this infection enigma is important clinically, for diagnosis, prognosis, prevention, and treatment. Some microbes will inevitably remain refractory to, or escape vaccination, or chemotherapy, or both. The solution also is important biologically, because the emergence and evolution of eukaryotes alongside more rapidly evolving prokaryotes, archaea, and viruses posed immunological challenges of an ecological and evolutionary nature. We need to study these challenges in natural, as opposed to experimental, conditions, and also at the molecular and cellular levels. According to the human genetic theory of infectious diseases, inborn variants underlie life-threatening infectious diseases. Here I review the history of the field of human genetics of infectious diseases from the turn of the 19th century to the second half of the 20th century. This paper thus sets the scene, providing the background information required to understand and appreciate the more recently described monogenic forms of resistance or predisposition to specific infections discussed in a second paper in this issue.
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121
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Patarčić I, Gelemanović A, Kirin M, Kolčić I, Theodoratou E, Baillie KJ, de Jong MD, Rudan I, Campbell H, Polašek O. The role of host genetic factors in respiratory tract infectious diseases: systematic review, meta-analyses and field synopsis. Sci Rep 2015; 5:16119. [PMID: 26524966 PMCID: PMC4630784 DOI: 10.1038/srep16119] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 10/09/2015] [Indexed: 12/17/2022] Open
Abstract
Host genetic factors have frequently been implicated in respiratory infectious diseases, often with inconsistent results in replication studies. We identified 386 studies from the total of 24,823 studies identified in a systematic search of four bibliographic databases. We performed meta-analyses of studies on tuberculosis, influenza, respiratory syncytial virus, SARS-Coronavirus and pneumonia. One single-nucleotide polymorphism from IL4 gene was significant for pooled respiratory infections (rs2070874; 1.66 [1.29–2.14]). We also detected an association of TLR2 gene with tuberculosis (rs5743708; 3.19 [2.03–5.02]). Subset analyses identified CCL2 as an additional risk factor for tuberculosis (rs1024611; OR = 0.79 [0.72–0.88]). The IL4-TLR2-CCL2 axis could be a highly interesting target for translation towards clinical use. However, this conclusion is based on low credibility of evidence - almost 95% of all identified studies had strong risk of bias or confounding. Future studies must build upon larger-scale collaborations, but also strictly adhere to the highest evidence-based principles in study design, in order to reduce research waste and provide clinically translatable evidence.
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Affiliation(s)
- Inga Patarčić
- Department of Public Health, University of Split School of Medicine, Split, Croatia
| | - Andrea Gelemanović
- Department of Public Health, University of Split School of Medicine, Split, Croatia
| | - Mirna Kirin
- Department of Public Health, University of Split School of Medicine, Split, Croatia
| | - Ivana Kolčić
- Department of Public Health, University of Split School of Medicine, Split, Croatia
| | - Evropi Theodoratou
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics , University of Edinburgh, Edinburgh, UK
| | - Kenneth J Baillie
- Roslin Institute, University of Edinburgh, Midlothian, UK.,Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Menno D de Jong
- Department of Medical Microbiology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics , University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics , University of Edinburgh, Edinburgh, UK
| | - Ozren Polašek
- Department of Public Health, University of Split School of Medicine, Split, Croatia.,Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics , University of Edinburgh, Edinburgh, UK
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122
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Sponholz C, Kramer M, Schöneweck F, Menzel U, Inanloo Rahatloo K, Giamarellos-Bourboulis EJ, Papavassileiou V, Lymberopoulou K, Pavlaki M, Koutelidakis I, Perdios I, Scherag A, Bauer M, Platzer M, Huse K. Polymorphisms of cystathionine beta-synthase gene are associated with susceptibility to sepsis. Eur J Hum Genet 2015; 24:1041-8. [PMID: 26508567 DOI: 10.1038/ejhg.2015.231] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 09/14/2015] [Accepted: 09/29/2015] [Indexed: 11/09/2022] Open
Abstract
Sepsis is the systemic inflammatory host response to infection. Cystathionine beta-synthase (CBS)-dependent homocysteine (Hcy) pathway was demonstrated to affect disease severity and mortality in patients with severe sepsis/septic shock. Independent studies identified a single-nucleotide polymorphism (SNP, rs6586282, hg19 chr21:g.44478497C>T) in intron 14 of the CBS-coding gene (CBS) associated with Hcy plasma levels. We aimed to describe the association of this SNP and variants of a splice donor-affecting variable-number tandem repeat (VNTR, NG_008938.1:g.22763_22793[16_22]) 243 bp downstream of rs6586282 with severe human sepsis. We analyzed the VNTR structure and genotyped variants of rs6586282 and a neighboring SNP (rs34758144, hg19 chr21:g.44478582G>A) in two case-control studies including patients with severe sepsis/septic shock from Germany (n=168) and Greece (n=237). In both studies, we consistently observed an association of CBS VNTR alleles with sepsis susceptibility. Risk linearly increased with number of tandem repeats (per allele odds ratio in the adjusted analysis 1.34; 95% confidence interval (CI)=1.17-1.55; P<0.001). Association had also been shown for rs34758144 whose risk allele is in linkage disequilibrium with one long VNTR allele (19 repeat). In contrast, we observed no evidence for an effect on 28-day survival in patients with severe sepsis/septic shock (per allele hazard ratio in the adjusted analysis for VNTR 1.10; 95% CI=0.95-1.28; P=0.20). In a minigene approach, we demonstrated alternative splicing in distinct VNTR alleles, which, however, was independent of the number of tandem units. In conclusion, there is no ordinary conjunction between human CBS and severe sepsis/septic shock, but CBS genotypes are involved in disease susceptibility.
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Affiliation(s)
- Christoph Sponholz
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.,Genome Analysis, Leibniz Institute for Age Research-Fritz Lipmann Institute, Jena, Germany.,Department of Anaesthesiology and Intensive Care Therapy, Jena University Hospital, Jena, Germany
| | - Marcel Kramer
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.,Genome Analysis, Leibniz Institute for Age Research-Fritz Lipmann Institute, Jena, Germany
| | - Franziska Schöneweck
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.,Research group Clinical Epidemiology, CSCC, Jena University Hospital, Jena, Germany
| | - Uwe Menzel
- Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Jena, Germany
| | - Kolsoum Inanloo Rahatloo
- Genome Analysis, Leibniz Institute for Age Research-Fritz Lipmann Institute, Jena, Germany.,School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Evangelos J Giamarellos-Bourboulis
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.,4th Department of Internal Medicine, University of Athens, Medical School, Athens, Greece
| | | | - Korina Lymberopoulou
- 2nd Department of Internal Medicine, Sismanogleion General Hospital, Athens, Greece
| | - Maria Pavlaki
- Department of Internal Medicine, Argos General Hospital, Argos, Greece
| | - Ioannis Koutelidakis
- 2nd Department of Surgery, University of Thessaloniki, Medical School, Thessaloniki, Greece
| | - Ioannis Perdios
- 1st Department of Internal Medicine, 'G. Gennimatas' General Hospital, Athens, Greece
| | - André Scherag
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.,Research group Clinical Epidemiology, CSCC, Jena University Hospital, Jena, Germany
| | - Michael Bauer
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.,Department of Anaesthesiology and Intensive Care Therapy, Jena University Hospital, Jena, Germany
| | - Matthias Platzer
- Genome Analysis, Leibniz Institute for Age Research-Fritz Lipmann Institute, Jena, Germany
| | - Klaus Huse
- Genome Analysis, Leibniz Institute for Age Research-Fritz Lipmann Institute, Jena, Germany
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123
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Sauer MED, Salomão H, Ramos GB, D'Espindula HRS, Rodrigues RSA, Macedo WC, Sindeaux RHM, Mira MT. Genetics of leprosy: Expected-and unexpected-developments and perspectives. Clin Dermatol 2015; 34:96-104. [PMID: 26773629 DOI: 10.1016/j.clindermatol.2015.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A solid body of evidence produced over decades of intense research supports the hypothesis that leprosy phenotypes are largely dependent on the genetic characteristics of the host. The early evidence of a major gene effect controlling susceptibility to leprosy came from studies of familial aggregation, twins, and complex segregation analysis. Later, linkage and association analysis, first applied to the investigation of candidate genes and chromosomal regions and more recently, to genome-wide scans, have revealed several HLA and non-HLA gene variants as risk factors for leprosy phenotypes such as disease per se, its clinical forms, and leprosy reactions. In addition, powerful, hypothesis-free strategies such as genome-wide association studies have led to an exciting, unexpected development: Leprosy susceptibility genes seem to be shared with Crohn's and Parkinson's disease. Today, a major challenge is to find the exact variants causing the biological effect underlying the genetic associations. New technologies, such as Next Generation Sequencing-that allows, for the first time, the cost- and time-effective sequencing of a complete human genome-hold the promise to reveal such variants; thus, strategies can be developed to study the functional impact of these variants in the context of infection, hopefully leading to the development of new targets for leprosy treatment and prevention.
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Affiliation(s)
- Monica E D Sauer
- Group for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifical Catholic University of Paraná, Curitiba, Paraná, Brazil
| | - Heloisa Salomão
- Group for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifical Catholic University of Paraná, Curitiba, Paraná, Brazil
| | - Geovana B Ramos
- Group for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifical Catholic University of Paraná, Curitiba, Paraná, Brazil
| | - Helena R S D'Espindula
- Group for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifical Catholic University of Paraná, Curitiba, Paraná, Brazil
| | - Rafael S A Rodrigues
- Group for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifical Catholic University of Paraná, Curitiba, Paraná, Brazil
| | - Wilian C Macedo
- Group for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifical Catholic University of Paraná, Curitiba, Paraná, Brazil
| | - Renata H M Sindeaux
- School of Health and Biological Sciences, Pontifical Catholic University of Paraná, Curitiba, Paraná, Brazil
| | - Marcelo T Mira
- Group for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifical Catholic University of Paraná, Curitiba, Paraná, Brazil; School of Health and Biological Sciences, Pontifical Catholic University of Paraná, Curitiba, Paraná, Brazil.
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124
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Mathias B, Lipori G, Moldawer LL, Efron PA. Integrating "big data" into surgical practice. Surgery 2015; 159:371-4. [PMID: 26603852 DOI: 10.1016/j.surg.2015.08.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 08/12/2015] [Indexed: 12/19/2022]
Abstract
'Big data' is the next frontier of medicine. We now have the ability to generate and analyze large quantities of healthcare data. Although interpreting and integrating this information into clinical practice poses many challenges, the potential benefits of personalized medicine are seemingly without limit.
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Affiliation(s)
- Brittany Mathias
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL
| | - Gigi Lipori
- University of Florida Health and Shands Hospital, Gainesville, FL
| | - Lyle L Moldawer
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL
| | - Philip A Efron
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL.
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125
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Role of innate immunity in primary graft dysfunction after lung transplantation. Curr Opin Organ Transplant 2015; 18:518-23. [PMID: 23995372 DOI: 10.1097/mot.0b013e3283651994] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Primary graft dysfunction (PGD), a form of acute lung injury after lung transplantation, has a significant impact on clinical outcomes after lung transplantation. This potentially reversible graft impairment occurs after ischemia-reperfusion injury. This review describes the expanding body of literature evaluating the central role of innate immune activation, nonadaptive responses and dysregulation in the development of PGD after lung transplant. RECENT FINDINGS The innate immune system, highlighted by Toll-like receptor pathways and neutrophil migration and influx, plays an important role in the initiation and propagation of ischemia-reperfusion injury. Recent plasma biomarker and gene association studies have identified several genes and proteins composing innate immune pathways to be associated with PGDs. Long pentraxin-3 and Toll-like receptors, as well as inflammasomes and Toll-interacting protein, are associated with the development of PGD after lung transplantation. SUMMARY Innate immune pathways are involved in the development of PGD and may provide attractive targets for therapies. It may be possible to prevent or treat PGD, as well as to allow pre-transplant PGD risk stratification. To improve understanding of the mechanisms behind clinical risk factors for PGD will require further in-depth correlation of donor-specific and recipient-related triggers of nonadaptive immune responses.
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126
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Gilchrist JJ, MacLennan CA, Hill AVS. Genetic susceptibility to invasive Salmonella disease. Nat Rev Immunol 2015; 15:452-63. [PMID: 26109132 DOI: 10.1038/nri3858] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Invasive Salmonella disease, in the form of enteric fever and invasive non-typhoidal Salmonella (iNTS) disease, causes substantial morbidity and mortality in children and adults in the developing world. The study of genetic variations in humans and mice that influence susceptibility of the host to Salmonella infection provides important insights into immunity to Salmonella. In this Review, we discuss data that have helped to elucidate the host genetic determinants of human enteric fever and iNTS disease, alongside data from the mouse model of Salmonella infection. Considered together, these studies provide a detailed picture of the immunobiology of human invasive Salmonella disease.
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Affiliation(s)
- James J Gilchrist
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, UK
| | - Calman A MacLennan
- 1] Jenner Institute, Nuffield Department of Medicine, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford, OX3 7DQ, UK. [2] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Adrian V S Hill
- 1] Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, UK. [2] Jenner Institute, Nuffield Department of Medicine, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford, OX3 7DQ, UK
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127
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Sauer MED, Salomão H, Ramos GB, D'Espindula HRS, Rodrigues RSA, Macedo WC, Sindeaux RHM, Mira MT. Genetics of leprosy: expected and unexpected developments and perspectives. Clin Dermatol 2015; 33:99-107. [PMID: 25432815 DOI: 10.1016/j.clindermatol.2014.10.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A solid body of evidence produced over decades of intense research supports the hypothesis that leprosy phenotypes are largely dependent on the genetic characteristics of the host. The early evidence of a major gene effect controlling susceptibility to leprosy came from studies of familial aggregation, twins, and Complex Segregation Analysis. Later, linkage and association analysis, first applied to the investigation of candidate genes and chromosomal regions and more recently, to genome-wide scans, have revealed several leukocyte antigen complex and nonleukocyte antigen complex gene variants as risk factors for leprosy phenotypes such as disease per se, its clinical forms and leprosy reactions. In addition, powerful, hypothesis-free strategies such as Genome-Wide Association Studies have led to an exciting, unexpected development: Leprosy susceptibility genes seem to be shared with Crohn's and Parkinson's diseases. Today, a major challenge is to find the exact variants causing the biological effect underlying the genetic associations. New technologies, such as Next Generation Sequencing that allows, for the first time, the cost and time-effective sequencing of a complete human genome, hold the promise to reveal such variants. Strategies can be developed to study the functional effect of these variants in the context of infection, hopefully leading to the development of new targets for leprosy treatment and prevention.
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Affiliation(s)
- Monica E D Sauer
- Group for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifical Catholic University of Paraná, Curitiba, Paraná, Brazil
| | - Heloisa Salomão
- Group for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifical Catholic University of Paraná, Curitiba, Paraná, Brazil
| | - Geovana B Ramos
- Group for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifical Catholic University of Paraná, Curitiba, Paraná, Brazil
| | - Helena R S D'Espindula
- Group for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifical Catholic University of Paraná, Curitiba, Paraná, Brazil
| | - Rafael S A Rodrigues
- Group for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifical Catholic University of Paraná, Curitiba, Paraná, Brazil
| | - Wilian C Macedo
- Group for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifical Catholic University of Paraná, Curitiba, Paraná, Brazil
| | - Renata H M Sindeaux
- School of Health and Biological Sciences, Pontifical Catholic University of Paraná, Curitiba, Paraná, Brazil
| | - Marcelo T Mira
- Group for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifical Catholic University of Paraná, Curitiba, Paraná, Brazil; School of Health and Biological Sciences, Pontifical Catholic University of Paraná, Curitiba, Paraná, Brazil.
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128
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Abstract
Host- and pathogen-derived lipids share clearance mechanisms that pinpoint PCSK9 as a plausible target for the treatment of some patients with sepsis (Walley et al., this issue).
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Affiliation(s)
- Claudia dos Santos
- Department of Medicine, St. Michael's Hospital, University of Toronto, Toronto, Ontario M5B 1W8, Canada. Department of Critical Care Medicine and the Keenan Research Centre for Biomedical Science of the Li Ka Shing Knowledge Institute, St. Michael's Hospital, University of Toronto, Toronto, Ontario M5B 1W8, Canada
| | - John C Marshall
- Department of Critical Care Medicine and the Keenan Research Centre for Biomedical Science of the Li Ka Shing Knowledge Institute, St. Michael's Hospital, University of Toronto, Toronto, Ontario M5B 1W8, Canada. Department of Surgery, St. Michael's Hospital, University of Toronto, Toronto, Ontario M5B 1W8, Canada.
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129
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Bulat-Kardum LJ, Etokebe GE, Lederer P, Balen S, Dembic Z. Genetic Polymorphisms in the Toll-like Receptor 10, Interleukin (IL)17A and IL17F Genes Differently Affect the Risk for Tuberculosis in Croatian Population. Scand J Immunol 2015; 82:63-9. [DOI: 10.1111/sji.12300] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 03/29/2015] [Indexed: 02/04/2023]
Affiliation(s)
- L. J. Bulat-Kardum
- Molecular Genetics Laboratory; Department of Oral Biology; Dental Faculty; University of Oslo; Oslo Norway
- Department of Pulmology; Clinic for Internal Medicine; Clinical Hospital Center Rijeka; School of Medicine; University of Rijeka; Rijeka Croatia
| | - G. E. Etokebe
- Molecular Genetics Laboratory; Department of Oral Biology; Dental Faculty; University of Oslo; Oslo Norway
| | - P. Lederer
- Molecular Genetics Laboratory; Department of Oral Biology; Dental Faculty; University of Oslo; Oslo Norway
| | - S. Balen
- Clinical Institute for Transfusion Medicine; Clinical Hospital Center Rijeka; School of Medicine; University of Rijeka; Rijeka Croatia
| | - Z. Dembic
- Molecular Genetics Laboratory; Department of Oral Biology; Dental Faculty; University of Oslo; Oslo Norway
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130
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Lin X, Stenvang J, Rasmussen MH, Zhu S, Jensen NF, Tarpgaard LS, Yang G, Belling K, Andersen CL, Li J, Bolund L, Brünner N. The potential role of Alu Y in the development of resistance to SN38 (Irinotecan) or oxaliplatin in colorectal cancer. BMC Genomics 2015; 16:404. [PMID: 25997618 PMCID: PMC4440512 DOI: 10.1186/s12864-015-1552-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Accepted: 04/17/2015] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Irinotecan (SN38) and oxaliplatin are chemotherapeutic agents used in the treatment of colorectal cancer. However, the frequent development of resistance to these drugs represents a considerable challenge in the clinic. Alus as retrotransposons comprise 11% of the human genome. Genomic toxicity induced by carcinogens or drugs can reactivate Alus by altering DNA methylation. Whether or not reactivation of Alus occurs in SN38 and oxaliplatin resistance remains unknown. RESULTS We applied reduced representation bisulfite sequencing (RRBS) to investigate the DNA methylome in SN38 or oxaliplatin resistant colorectal cancer cell line models. Moreover, we extended the RRBS analysis to tumor tissue from 14 patients with colorectal cancer who either did or did not benefit from capecitabine + oxaliplatin treatment. For the clinical samples, we applied a concept of 'DNA methylation entropy' to estimate the diversity of DNA methylation states of the identified resistance phenotype-associated methylation loci observed in the cell line models. We identified different loci being characteristic for the different resistant cell lines. Interestingly, 53% of the identified loci were Alu sequences- especially the Alu Y subfamily. Furthermore, we identified an enrichment of Alu Y sequences that likely results from increased integration of new copies of Alu Y sequence in the drug-resistant cell lines. In the clinical samples, SOX1 and other SOX gene family members were shown to display variable DNA methylation states in their gene regions. The Alu Y sequences showed remarkable variation in DNA methylation states across the clinical samples. CONCLUSION Our findings imply a crucial role of Alu Y in colorectal cancer drug resistance. Our study underscores the complexity of colorectal cancer aggravated by mobility of Alu elements and stresses the importance of personalized strategies, using a systematic and dynamic view, for effective cancer therapy.
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Affiliation(s)
- Xue Lin
- Department of Biomedicine, University of Aarhus, the Bartholin Building, DK-8000, Aarhus C, Denmark.
| | - Jan Stenvang
- Department of Veterinary Disease Biology, Section of Molecular Disease Biology, Faculty of Health and Medical Sciences, Copenhagen University, Strandboulevarden 49, Copenhagen, Denmark.
| | - Mads Heilskov Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgårdsvej 100, DK-8200, Aarhus N, Denmark.
| | - Shida Zhu
- BGI (Beijing Genomics Institute), Shenzhen, 518083, China.
| | - Niels Frank Jensen
- Department of Veterinary Disease Biology, Section of Molecular Disease Biology, Faculty of Health and Medical Sciences, Copenhagen University, Strandboulevarden 49, Copenhagen, Denmark.
| | - Line S Tarpgaard
- Department of Oncology, Odense University Hospital, Sdr. Boulevard 29, DK-5000, Odense C, Denmark.
| | - Guangxia Yang
- BGI (Beijing Genomics Institute), Shenzhen, 518083, China.
| | - Kirstine Belling
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800, Lyngby, Denmark.
| | - Claus Lindbjerg Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgårdsvej 100, DK-8200, Aarhus N, Denmark.
| | - Jian Li
- Department of Biomedicine, University of Aarhus, the Bartholin Building, DK-8000, Aarhus C, Denmark.
- BGI (Beijing Genomics Institute), Shenzhen, 518083, China.
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing, 210096, China.
| | - Lars Bolund
- Department of Biomedicine, University of Aarhus, the Bartholin Building, DK-8000, Aarhus C, Denmark.
- BGI (Beijing Genomics Institute), Shenzhen, 518083, China.
| | - Nils Brünner
- Department of Veterinary Disease Biology, Section of Molecular Disease Biology, Faculty of Health and Medical Sciences, Copenhagen University, Strandboulevarden 49, Copenhagen, Denmark.
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Mills TC, Chapman S, Hutton P, Gordon AC, Bion J, Chiche JD, Holloway PAH, Stüber F, Garrard CS, Hinds CJ, Hill AVS, Rautanen A. Variants in the Mannose-binding Lectin Gene MBL2 do not Associate With Sepsis Susceptibility or Survival in a Large European Cohort. Clin Infect Dis 2015; 61:695-703. [PMID: 25969530 PMCID: PMC4530723 DOI: 10.1093/cid/civ378] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/05/2015] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Sepsis is an increasingly common condition, which continues to be associated with unacceptably high mortality. A large number of association studies have investigated susceptibility to, or mortality from, sepsis for variants in the functionally important immune-related gene MBL2. These studies have largely been underpowered and contradictory. METHODS We genotyped and analyzed 4 important MBL2 single nucleotide polymorphisms (SNPs; rs5030737, rs1800450, rs1800451, and rs7096206) in 1839 European community-acquired pneumonia (CAP) and peritonitis sepsis cases, and 477 controls from the United Kingdom. We analyzed the following predefined subgroups and outcomes: 28-day and 6 month mortality from sepsis due to CAP or peritonitis combined, 28-day mortality from CAP sepsis, peritonitis sepsis, pneumococcal sepsis or sepsis in younger patients, and susceptibility to CAP sepsis or pneumococcal sepsis in the United Kingdom. RESULTS There were no significant associations (all P-values were greater than .05 after correction for multiple testing) between MBL2 genotypes and any of our predefined analyses. CONCLUSIONS In this large, well-defined cohort of immune competent adult patients, no associations between MBL2 genotype and sepsis susceptibility or outcome were identified.
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Affiliation(s)
- Tara C Mills
- Wellcome Trust Centre for Human Genetics, University of Oxford
| | - Stephen Chapman
- Wellcome Trust Centre for Human Genetics, University of Oxford
| | | | - Anthony C Gordon
- Section of Anaesthetics, Pain Medicine and Intensive Care, Imperial College London
| | - Julian Bion
- School of Clinical and Experimental Medicine, University of Birmingham, United Kingdom
| | | | - Paul A H Holloway
- Section of Anaesthetics, Pain Medicine and Intensive Care, Imperial College London
| | - Frank Stüber
- Department of Anaesthesiology and Pain Medicine, Bern University Hospital and University of Bern, Switzerland
| | | | - Charles J Hinds
- Barts and The London School of Medicine Queen Mary University of London, United Kingdom
| | - Adrian V S Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford
| | - Anna Rautanen
- Wellcome Trust Centre for Human Genetics, University of Oxford
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Eisen DP. Editorial Commentary: Shall We Disregard Mannose-Binding Lectin Modification in the Future Because We Cannot Prevent Sepsis With This Molecule? Clin Infect Dis 2015; 61:704-6. [DOI: 10.1093/cid/civ380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 05/01/2015] [Indexed: 01/02/2023] Open
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Identification of a nonsynonymous polymorphism in the SVEP1 gene associated with altered clinical outcomes in septic shock. Crit Care Med 2015; 43:101-8. [PMID: 25188548 DOI: 10.1097/ccm.0000000000000604] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Mortality from septic shock is highly heritable. The identification of causal genetic factors is insufficient. To discover key contributors, we first identified nonsynonymous single-nucleotide polymorphisms in conserved genomic regions that are predicted to have significant effects on protein function. We then test the hypothesis that these nonsynonymous single-nucleotide polymorphisms across the genome alter clinical outcome of septic shock. DESIGN Genetic-association study plus in vitro experiment using primary cells plus in silico analysis using genomic DNA and protein database. SETTING Twenty-seven ICUs at academic teaching centers in Canada, Australia, and the United States. PATIENTS Patients with septic shock of European ancestry (n = 520). INTERVENTIONS Patients with septic shock were genotyped for 843 nonsynonymous single-nucleotide polymorphisms in conserved regions of the genome and are predicted to have damaging effects from the protein sequence. MEASUREMENTS AND MAIN RESULTS The primary outcome variable was 28-day mortality. Secondary outcome variables were organ dysfunction. Productions of adhesion molecules including interleukin-8, growth-regulated oncogene-α, monocyte chemoattractant protein-1, and monocyte chemoattractant protein-3 were measured in human umbilical vein endothelial cells after SVEP1 gene silencing by RNA interference. Patients with septic shock having the SVEP1 C allele of nonsynonymous single-nucleotide polymorphism, SVEP1 c.2080A>C (p. Gln581His, rs10817033), had a significant increase in the hazard of death over the 28 days (hazard ratio, 1.72; 95% CI, 1.31-2.26; p = 9.7 × 10-5) and increased organ dysfunction and needed more organ support (p < 0.05). Silencing SVEP1 significantly increased interleukin-8, growth-regulated oncogene-α, monocyte chemoattractant protein-1, monocyte chemoattractant protein-3 production in human umbilical vein endothelial cells under lipopolysaccharide stimulation (p < 0.01). CONCLUSIONS C allele of SVEP1 c.2080A>C (p. Gln581His) single-nucleotide polymorphism, a non-synonymous single-nucleotide polymorphism in conserved regions and predicted to have damaging effects on protein structure, was associated with increased 28-day mortality and organ dysfunction of septic shock. SVEP1 appears to regulate molecules of the leukocyte adhesion pathway.
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Finding a needle in the haystack: leveraging bioinformatics to identify a functional genetic risk factor for sepsis death. Crit Care Med 2015; 43:242-3. [PMID: 25514715 DOI: 10.1097/ccm.0000000000000664] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Nakada TA, Boyd JH, Russell JA, Aguirre-Hernández R, Wilkinson MD, Thair SA, Nakada E, McConechy MK, Fjell CD, Walley KR. VPS13D Gene Variant Is Associated with Altered IL-6 Production and Mortality in Septic Shock. J Innate Immun 2015; 7:545-53. [PMID: 25896417 DOI: 10.1159/000381265] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 02/26/2015] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Genetic variations contribute to septic shock mortality. To discover a novel locus, we performed in vitro genome-wide association studies (GWAS) and further tested the result in a cohort of septic shock patients. METHODS Two in vitro GWAS using a quantitative trait locus analysis of stimulated IL-6 production in lymphoblastoid cells from 60 individuals of European ancestry were performed. VPS13D rs6685273 was genotyped in European ancestry patients (n = 498). The VPS13D gene was silenced in vitro. RESULTS Two GWAS using lymphoblastoid cells identified the locus of VPS13D rs6685273 that was significant in the same direction in both GWAS. The VPS13D rs6685273 C allele was associated with increased IL-6 production. Patients with septic shock who had the VPS13D rs6685273 CC genotype had an increased 28-day mortality (p = 0.023) and more organ failure (p < 0.05) compared to the CT/TT genotypes. VPS13D in vitro gene silencing in the HeLa cell line increased IL-6 production. Furthermore, the rs6685273 genotype was associated with differential VPS13D splice variant expression. CONCLUSIONS The VPS13D rs6685273 C allele was associated with increased IL-6 production in vitro. The patients with the VPS13D rs6685273 CC genotype had increased 28-day mortality and increased organ failure. VPS13D appears to regulate IL-6 production.
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Affiliation(s)
- Taka-aki Nakada
- Critical Care Research Laboratories, Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, B.C., Canada
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Health-related quality of life following pediatric critical illness. Intensive Care Med 2015; 41:1235-46. [PMID: 25851391 DOI: 10.1007/s00134-015-3780-7] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 03/25/2015] [Indexed: 12/21/2022]
Abstract
PURPOSE The aims of this focused review of the literature on children surviving critical illness were to (1) determine whether health-related quality of life (HRQL) represents a clinically meaningful outcome measure for children surviving critical illness and (2) evaluate the HRQL measures implemented in pediatric critical care studies to date. METHODS This was a focused review of the literature from 1980 to 2015 based on a search of EMBASE/PubMed, MEDLINE and PsycInfo assessing trends and determinants of HRQL outcomes in children surviving critical illness. We also evaluated the psychometric properties of the HRQL instruments used in the studies identified by examining each measure's reported reliability, validity and sensitivity to clinical change. RESULTS The literature search identified 253 pediatric articles for potential inclusion in the review, among which data from 78 studies were ultimately selected for inclusion. Of the 22 measures utilized in the studies reviewed, only four demonstrated excellent psychometric properties for use in pediatric critical care trials. Trends in HRQL identified in the studies reviewed suggest significant ongoing morbidity for children surviving critical illness. Key determinants of poor HRQL outcomes include reason for PICU admission (sepsis, meningoencephalitis, trauma), antecedents (chronic comorbid conditions), treatments received (prolonged cardiopulmonary resuscitation, long-stay patients, invasive technology), psychological outcomes (post-traumatic stress disorder, parent anxiety/depression) and social and environmental characteristics (low socioeconomic status, parental education and functioning). CONCLUSIONS Validated pediatric HRQL instruments are now available. Significant impact on HRQL has been demonstrated in acute and acute on chronic critical illness. Future pediatric critical care interventional trials should include both mortality as well as long-term HRQL measurements to truly ascertain the full impact of critical illness in children.
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Franks Z, Carlisle M, Rondina MT. Current challenges in understanding immune cell functions during septic syndromes. BMC Immunol 2015; 16:11. [PMID: 25887317 PMCID: PMC4374283 DOI: 10.1186/s12865-015-0073-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 02/05/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Sepsis is a dynamic infectious disease syndrome characterized by dysregulated inflammatory responses. RESULTS Despite decades of research, improvements in the treatment of sepsis have been modest. These limited advances are likely due, in part, to multiple factors, including substantial heterogeneity in septic syndromes, significant knowledge gaps in our understanding of how immune cells function in sepsis, and limitations in animal models that accurately recapitulate the human septic milieu. The goal of this brief review is to describe current challenges in understanding immune cell functions during sepsis. We also provide a framework to guide scientists and clinicians in research and patient care as they strive to better understand dysregulated cell responses during sepsis. CONCLUSIONS Additional, well-designed translational studies in sepsis are critical for enhancing our understanding of the role of immune cells in sepsis.
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Affiliation(s)
- Zechariah Franks
- Program in Molecular Medicine, Salt Lake City, 84112, , Utah, USA.
| | | | - Matthew T Rondina
- Program in Molecular Medicine, Salt Lake City, 84112, , Utah, USA.
- Division of General Internal Medicine, University of Utah School of Medicine, Salt Lake City, 84112, , Utah, USA.
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Erranz MB, Wilhelm BJ, Riquelme VR, Cruces RP. [Genetic predisposition and Pediatric Acute Respiratory Distress Syndrome: New tools for genetic study]. REVISTA CHILENA DE PEDIATRIA 2015; 86:73-79. [PMID: 26235685 DOI: 10.1016/j.rchipe.2015.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/02/2015] [Indexed: 06/04/2023]
Abstract
Acute respiratory distress syndrome (ARDS) is the most severe form of respiratory failure. Theoretically, any acute lung condition can lead to ARDS, but only a small percentage of individuals actually develop the disease. On this basis, genetic factors have been implicated in the risk of developing ARDS. Based on the pathophysiology of this disease, many candidate genes have been evaluated as potential modifiers in patient, as well as in animal models, of ARDS. Recent experimental data and clinical studies suggest that variations of genes involved in key processes of tissue, cellular and molecular lung damage may influence susceptibility and prognosis of ARDS. However, the pathogenesis of pediatric ARDS is complex, and therefore, it can be expected that many genes might contribute. Genetic variations such as single nucleotide polymorphisms and copy-number variations are likely associated with susceptibility to ARDS in children with primary lung injury. Genome-wide association (GWA) studies can objectively examine these variations, and help identify important new genes and pathogenetic pathways for future analysis. This approach might also have diagnostic and therapeutic implications, such as predicting patient risk or developing a personalized therapeutic approach to this serious syndrome.
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Affiliation(s)
- M Benjamín Erranz
- Centro de Medicina Regenerativa, Facultad de Medicina Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - B Jan Wilhelm
- Departamento de Pediatría, Facultad de Medicina Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
| | - V Raquel Riquelme
- Unidad de Paciente Crítico Pediátrica, Hospital El Carmen de Maipú, Santiago, Chile
| | - R Pablo Cruces
- Unidad de Paciente Crítico Pediátrica, Hospital El Carmen de Maipú, Santiago, Chile; Centro de Investigación de Medicina Veterinaria, Escuela de Medicina Veterinaria, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Santiago, Chile.
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Carter R, Wolf J, van Opijnen T, Muller M, Obert C, Burnham C, Mann B, Li Y, Hayden RT, Pestina T, Persons D, Camilli A, Flynn PM, Tuomanen EI, Rosch JW. Genomic analyses of pneumococci from children with sickle cell disease expose host-specific bacterial adaptations and deficits in current interventions. Cell Host Microbe 2015; 15:587-599. [PMID: 24832453 DOI: 10.1016/j.chom.2014.04.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 02/10/2014] [Accepted: 03/20/2014] [Indexed: 10/25/2022]
Abstract
Sickle cell disease (SCD) patients are at high risk of contracting pneumococcal infection. To address this risk, they receive pneumococcal vaccines, and antibiotic prophylaxis and treatment. To assess the impact of SCD and these interventions on pneumococcal genetic architecture, we examined the genomes of more than 300 pneumococcal isolates from SCD patients over 20 years. Modern SCD strains retained invasive capacity but shifted away from the serotypes used in vaccines. These strains had specific genetic changes related to antibiotic resistance, capsule biosynthesis, metabolism, and metal transport. A murine SCD model coupled with Tn-seq mutagenesis identified 60 noncapsular pneumococcal genes under differential selective pressure in SCD, which correlated with aspects of SCD pathophysiology. Further, virulence determinants in the SCD context were distinct from the general population, and protective capacity of potential antigens was lost over time in SCD. This highlights the importance of understanding bacterial pathogenesis in the context of high-risk individuals.
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Affiliation(s)
- Robert Carter
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Joshua Wolf
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Tim van Opijnen
- Tufts University School of Medicine, Department of Molecular Biology and Microbiology, 136 Harrison Avenue, Boston, MA 02111-1817 USA
| | - Martha Muller
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Caroline Obert
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Corinna Burnham
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Beth Mann
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Yimei Li
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Randall T Hayden
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Tamara Pestina
- Department of Experimental Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Derek Persons
- Department of Experimental Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Andrew Camilli
- Tufts University School of Medicine, Department of Molecular Biology and Microbiology, 136 Harrison Avenue, Boston, MA 02111-1817 USA.,Howard Hughes Medical Institute, Department of Molecular Biology and Microbiology, 136 Harrison Avenue, Boston, MA 02111-1817 USA
| | - Patricia M Flynn
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Elaine I Tuomanen
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Jason W Rosch
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
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Uhel F, Tadié JM, Le Tulzo Y. Choc septique : mécanismes du décès. MEDECINE INTENSIVE REANIMATION 2015. [DOI: 10.1007/s13546-015-1019-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Rautanen A, Mills TC, Gordon AC, Hutton P, Steffens M, Nuamah R, Chiche JD, Parks T, Chapman SJ, Davenport EE, Elliott KS, Bion J, Lichtner P, Meitinger T, Wienker TF, Caulfield MJ, Mein C, Bloos F, Bobek I, Cotogni P, Sramek V, Sarapuu S, Kobilay M, Ranieri VM, Rello J, Sirgo G, Weiss YG, Russwurm S, Schneider EM, Reinhart K, Holloway PAH, Knight JC, Garrard CS, Russell JA, Walley KR, Stüber F, Hill AVS, Hinds CJ. Genome-wide association study of survival from sepsis due to pneumonia: an observational cohort study. THE LANCET. RESPIRATORY MEDICINE 2015; 3:53-60. [PMID: 25533491 PMCID: PMC4314768 DOI: 10.1016/s2213-2600(14)70290-5] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Sepsis continues to be a major cause of death, disability, and health-care expenditure worldwide. Despite evidence suggesting that host genetics can influence sepsis outcomes, no specific loci have yet been convincingly replicated. The aim of this study was to identify genetic variants that influence sepsis survival. METHODS We did a genome-wide association study in three independent cohorts of white adult patients admitted to intensive care units with sepsis, severe sepsis, or septic shock (as defined by the International Consensus Criteria) due to pneumonia or intra-abdominal infection (cohorts 1-3, n=2534 patients). The primary outcome was 28 day survival. Results for the cohort of patients with sepsis due to pneumonia were combined in a meta-analysis of 1553 patients from all three cohorts, of whom 359 died within 28 days of admission to the intensive-care unit. The most significantly associated single nucleotide polymorphisms (SNPs) were genotyped in a further 538 white patients with sepsis due to pneumonia (cohort 4), of whom 106 died. FINDINGS In the genome-wide meta-analysis of three independent pneumonia cohorts (cohorts 1-3), common variants in the FER gene were strongly associated with survival (p=9·7 × 10(-8)). Further genotyping of the top associated SNP (rs4957796) in the additional cohort (cohort 4) resulted in a combined p value of 5·6 × 10(-8) (odds ratio 0·56, 95% CI 0·45-0·69). In a time-to-event analysis, each allele reduced the mortality over 28 days by 44% (hazard ratio for death 0·56, 95% CI 0·45-0·69; likelihood ratio test p=3·4 × 10(-9), after adjustment for age and stratification by cohort). Mortality was 9·5% in patients carrying the CC genotype, 15·2% in those carrying the TC genotype, and 25·3% in those carrying the TT genotype. No significant genetic associations were identified when patients with sepsis due to pneumonia and intra-abdominal infection were combined. INTERPRETATION We have identified common variants in the FER gene that associate with a reduced risk of death from sepsis due to pneumonia. The FER gene and associated molecular pathways are potential novel targets for therapy or prevention and candidates for the development of biomarkers for risk stratification. FUNDING European Commission and the Wellcome Trust.
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Affiliation(s)
- Anna Rautanen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Tara C Mills
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | - Michael Steffens
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE) of the University of Bonn, Bonn, Germany
| | - Rosamond Nuamah
- William Harvey Research Institute, Barts and The London School of Medicine Queen Mary University of London, London, UK
| | | | - Tom Parks
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stephen J Chapman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Emma E Davenport
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Julian Bion
- School of Clinical and Experimental Medicine, University of Birmingham, Birmingham, UK
| | - Peter Lichtner
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Technische Universität München, Institute of Human Genetics, Munich, Germany
| | - Thomas F Wienker
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE) of the University of Bonn, Bonn, Germany
| | - Mark J Caulfield
- William Harvey Research Institute, Barts and The London School of Medicine Queen Mary University of London, London, UK
| | - Charles Mein
- William Harvey Research Institute, Barts and The London School of Medicine Queen Mary University of London, London, UK
| | - Frank Bloos
- Jena University Hospital and Center for Sepsis Control and Care, Jena, Germany
| | - Ilona Bobek
- National Health Service Centre, Budapest, Hungary
| | | | | | | | | | | | - Jordi Rello
- CIBERES, Vall d'Hebron Institute of Research, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Gonzalo Sirgo
- Joan XXIII University Hospital, Pere Virgili Health Institute, University Rovirai Virgili, Tarragona, Spain
| | | | | | - E Marion Schneider
- Section of Experimental Anesthesiology, University Hospital, Ulm, Germany
| | - Konrad Reinhart
- Jena University Hospital and Center for Sepsis Control and Care, Jena, Germany
| | | | - Julian C Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | | | - Frank Stüber
- Department of Anaesthesiology and Pain Medicine, Bern University Hospital, and University of Bern, Switzerland
| | - Adrian V S Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Charles J Hinds
- William Harvey Research Institute, Barts and The London School of Medicine Queen Mary University of London, London, UK
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143
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Gendiagnostische Forschung an Kindern in Österreich. Monatsschr Kinderheilkd 2014. [DOI: 10.1007/s00112-014-3245-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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144
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Prucha M, Bellingan G, Zazula R. Sepsis biomarkers. Clin Chim Acta 2014; 440:97-103. [PMID: 25447700 DOI: 10.1016/j.cca.2014.11.012] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 11/05/2014] [Accepted: 11/11/2014] [Indexed: 02/06/2023]
Abstract
Sepsis is the most frequent cause of death in non-coronary intensive care units (ICUs). In the past 10 years, progress has been made in the early identification of septic patients and in their treatment and these improvements in support and therapy mean that the mortality is gradually decreasing but it still remains unacceptably high. Leaving clinical diagnosis aside, the laboratory diagnostics represent a complex range of investigations that can place significant demands on the system given the speed of response required. There are hundreds of biomarkers which could be potentially used for diagnosis and prognosis in septic patients. The main attributes of successful markers would be high sensitivity, specificity, possibility of bed-side monitoring, and financial accessibility. Only a fraction is used in routine clinical practice because many lack sufficient sensitivity or specificity. The following review gives a short overview of the current epidemiology of sepsis, its pathogenesis and state-of-the-art knowledge on the use of specific biochemical, hematological and immunological parameters in its diagnostics. Prospective approaches towards discovery of new diagnostic biomarkers have been shortly mentioned.
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Affiliation(s)
- Miroslav Prucha
- Department of Clinical Biochemistry, Hematology and Immunology, Hospital Na Homolce, Prague, Czech Republic.
| | - Geoff Bellingan
- University College London Hospitals, 235 Euston Rd, London NW1 2PG, United Kingdom(1)
| | - Roman Zazula
- Department of Anesthesiology and Intensive Care, First Faculty of Medicine, Charles University in Prague and Thomayer Hospital, Prague, Czech Republic
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Siddique I, Brimble KS, Walkin L, Summers A, Brenchley P, Herrick S, Margetts PJ. Genetic Polymorphisms and Peritoneal Membrane Function. Perit Dial Int 2014; 35:517-29. [PMID: 25395500 DOI: 10.3747/pdi.2014.00049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/18/2014] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Outcomes for peritoneal dialysis (PD) patients are affected by the characteristics of the peritoneal membrane, which may be determined by genetic variants. We carried out a systematic review of the literature to identify studies which assessed the association between genetic polymorphisms, peritoneal membrane solute transport, and clinical outcomes for PD patients. METHODS The National Library of Medicine was searched using a variety of strategies. Studies which met our inclusion criteria were reviewed and data abstracted. Our outcomes of interest included: high transport status peritoneal membrane, risk for peritonitis, encapsulating peritoneal sclerosis (EPS), patient and technique survival. We combined data from studies which evaluated the same genetic polymorphism and the same outcome. RESULTS We evaluated 18 relevant studies. All studies used a candidate gene approach. Gene polymorphisms in the interleukin (IL)-6 gene were associated with peritoneal membrane solute transport in several studies in different ethnic populations. Associations with solute transport and polymorphisms in endothelial nitric oxide synthase and receptor for advanced glycation end product genes were also identified. There was evidence of a genetic predisposition for peritonitis found in 2 studies, and for EPS in 1 study. Survival was found to be associated with a polymorphism in vascular endothelial growth factor and technique failure was associated with a polymorphism in the IL-1 receptor antagonist. CONCLUSIONS There is evidence that characteristics of the peritoneal membrane and clinical outcomes for PD patients have genetic determinants. The most consistent association was between IL-6 gene polymorphisms and peritoneal membrane solute transport.
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Affiliation(s)
| | | | - Louise Walkin
- Faculty of MHS, University of Manchester, United Kingdom
| | | | | | - Sarah Herrick
- Faculty of MHS, University of Manchester, United Kingdom
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Meyer CG, Thye T. Host genetic studies in adult pulmonary tuberculosis. Semin Immunol 2014; 26:445-53. [PMID: 25307123 DOI: 10.1016/j.smim.2014.09.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 09/16/2014] [Accepted: 09/21/2014] [Indexed: 01/08/2023]
Abstract
Early observations, candidate gene studies and, more recently, genome-wide association studies have shown that susceptibility to tuberculosis has a host genetic component. Because the value of candidate gene studies has been doubted due to major limitations such as lack of sufficient power and small study groups, lack of reproducibility in independent groups and, often, ambiguous or even contrasting results in attempts of replication, much hope and expectancy has been put on the progress the genome-wide association approach has created. However, much less than initially expected became clear by the results obtained in genome-wide studies, emphasizing the need of increasing sample sizes, e.g. through meta-analyses, and of increasing the density of genetic variants studied across the human genome. A further reason why a rather low number of associated genetic variants were identified to date in infectious diseases in general and tuberculosis in particular might be the fact that selection acts strongly in diseases that affect the reproductive success. As in most genome-wide association studies performed so far, significant signals, often most likely surrogate marker only, have been found in non-coding regions of genomes, the identification of truly causative genetic variation and of the functionality of associated factors needs urgent attention. In the following we briefly discuss genetic studies in tuberculosis and describe new technologies that are currently employed in the search for responsible genetic elements involved in tuberculosis susceptibility.
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Affiliation(s)
- Christian G Meyer
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany.
| | - Thorsten Thye
- Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359 Hamburg, Germany
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147
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Meyer NJ. Beyond single-nucleotide polymorphisms: genetics, genomics, and other 'omic approaches to acute respiratory distress syndrome. Clin Chest Med 2014; 35:673-84. [PMID: 25453417 DOI: 10.1016/j.ccm.2014.08.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This article summarizes the contributions of high-throughput genomic, proteomic, metabolomic, and gene expression investigations to the understanding of inherited or acquired risk for acute respiratory distress syndrome (ARDS). Although not yet widely applied to a complex trait like ARDS, these techniques are now routinely used to study a variety of disease states. Omic applications hold great promise for identifying novel factors that may contribute to ARDS pathophysiology or may be appropriate for further development as biomarkers or surrogates in clinical studies. Opportunities and challenges of different techniques are discussed, and examples of successful applications in non-ARDS fields are used to illustrate the potential use of each technique.
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Affiliation(s)
- Nuala J Meyer
- Pulmonary, Allergy, and Critical Care Medicine, University of Pennsylvania, Perelman School of Medicine, 3600 Spruce Street, 5039 Maloney Building, Philadelphia, PA 19104, USA.
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148
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Randolph AG, Yip WK, Falkenstein-Hagander K, Weiss ST, Janssen R, Keisling S, Bont L. Vitamin D-binding protein haplotype is associated with hospitalization for RSV bronchiolitis. Clin Exp Allergy 2014; 44:231-7. [PMID: 24447085 DOI: 10.1111/cea.12247] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 11/20/2013] [Accepted: 11/26/2013] [Indexed: 12/19/2022]
Abstract
BACKGROUND Between 75 000 and 125 000 U.S. infants are hospitalized for respiratory syncytial virus (RSV) bronchiolitis every year. Up to half will be diagnosed with asthma in later childhood. Vitamin D deficiency has been associated with susceptibility to asthma and respiratory infections. Measured vitamin D is largely bound to vitamin D-binding protein (VDBP); VDBP levels are influenced by its gene (GC) haplotype. OBJECTIVE We assessed the relationship between polymorphisms rs7041 and rs4588, which define haplotypes GC1s, GC1f, and GC2, and RSV bronchiolitis susceptibility and subsequent asthma. METHODS We retrospectively recruited 198 otherwise healthy children (93% White) hospitalized for severe RSV bronchiolitis in Boston and 333 parents into a follow-up study to assess asthma diagnosis. Data were analysed using family-based genetic association tests. We independently validated our results in 465 White children hospitalized with RSV bronchiolitis and 930 White population controls from the Netherlands. RESULTS The rs7041_C allele (denoting haplotype GC1s) was overtransmitted (P = 0.02, additive model) in the entire Boston cohort, in Whites (P = 0.03), and especially in children subsequently diagnosed with asthma (P = 0.006). The GC1f haplotype was undertransmitted in the asthma subgroups (all races and White, both P < 0.05). The rs7041_C allele was also more frequent in the RSV bronchiolitis group compared with controls (OR 1.12, 95% CI 1.02, 1.4, P = 0.03) in the Netherlands, especially in mechanically ventilated patients (P = 0.009). CONCLUSION AND CLINICAL RELEVANCE GC1s haplotype carriage may increase the risk of RSV bronchiolitis in infancy and subsequent asthma development. The GC1s haplotype is associated with higher VDBP levels, resulting in less freely available vitamin D. KEY MESSAGES Vitamin D-binding protein (VDBP) haplotypes influence free vitamin D levels. We report an association between a VDBP haplotype and hospitalization for RSV bronchiolitis in infancy in two independent cohorts.
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Affiliation(s)
- A G Randolph
- Department of Anesthesia, Perioperative and Pain Medicine, Boston Children's Hospital, Boston, MA, USA; Channing, Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
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149
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Gusenleitner D, Auerbach SS, Melia T, Gómez HF, Sherr DH, Monti S. Genomic models of short-term exposure accurately predict long-term chemical carcinogenicity and identify putative mechanisms of action. PLoS One 2014; 9:e102579. [PMID: 25058030 PMCID: PMC4109923 DOI: 10.1371/journal.pone.0102579] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 06/20/2014] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Despite an overall decrease in incidence of and mortality from cancer, about 40% of Americans will be diagnosed with the disease in their lifetime, and around 20% will die of it. Current approaches to test carcinogenic chemicals adopt the 2-year rodent bioassay, which is costly and time-consuming. As a result, fewer than 2% of the chemicals on the market have actually been tested. However, evidence accumulated to date suggests that gene expression profiles from model organisms exposed to chemical compounds reflect underlying mechanisms of action, and that these toxicogenomic models could be used in the prediction of chemical carcinogenicity. RESULTS In this study, we used a rat-based microarray dataset from the NTP DrugMatrix Database to test the ability of toxicogenomics to model carcinogenicity. We analyzed 1,221 gene-expression profiles obtained from rats treated with 127 well-characterized compounds, including genotoxic and non-genotoxic carcinogens. We built a classifier that predicts a chemical's carcinogenic potential with an AUC of 0.78, and validated it on an independent dataset from the Japanese Toxicogenomics Project consisting of 2,065 profiles from 72 compounds. Finally, we identified differentially expressed genes associated with chemical carcinogenesis, and developed novel data-driven approaches for the molecular characterization of the response to chemical stressors. CONCLUSION Here, we validate a toxicogenomic approach to predict carcinogenicity and provide strong evidence that, with a larger set of compounds, we should be able to improve the sensitivity and specificity of the predictions. We found that the prediction of carcinogenicity is tissue-dependent and that the results also confirm and expand upon previous studies implicating DNA damage, the peroxisome proliferator-activated receptor, the aryl hydrocarbon receptor, and regenerative pathology in the response to carcinogen exposure.
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Affiliation(s)
- Daniel Gusenleitner
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- Department of Computational Biomedicine, Boston University Medical Campus, Boston, Massachusetts, United States of America
| | - Scott S. Auerbach
- Biomolecular Screening Branch, Division of the National Toxicology Program at the National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, North Carolina, United States of America
| | - Tisha Melia
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Harold F. Gómez
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - David H. Sherr
- Department of Environmental Health, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Stefano Monti
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- Department of Computational Biomedicine, Boston University Medical Campus, Boston, Massachusetts, United States of America
- * E-mail:
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150
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Russell CD, Griffiths SJ, Baillie JK, Haas J. Stratified infection medicine: a call to arms. THE LANCET. INFECTIOUS DISEASES 2014; 14:451. [PMID: 24849724 DOI: 10.1016/s1473-3099(14)70774-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Clark D Russell
- Division of Pathway Medicine, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK.
| | - Samantha J Griffiths
- Division of Pathway Medicine, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | | | - Juergen Haas
- Division of Pathway Medicine, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
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