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Badia-Bringué G, Canive M, Vázquez P, Garrido JM, Fernández A, Juste RA, Jiménez JA, González-Recio O, Alonso-Hearn M. Genome-Wide Association Study Reveals Quantitative Trait Loci and Candidate Genes Associated with High Interferon-gamma Production in Holstein Cattle Naturally Infected with Mycobacterium Bovis. Int J Mol Sci 2024; 25:6165. [PMID: 38892353 PMCID: PMC11172856 DOI: 10.3390/ijms25116165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Mycobacterium bovis (Mb) is the causative agent of bovine tuberculosis (bTb). Genetic selection aiming to identify less susceptible animals has been proposed as a complementary measure in ongoing programs toward controlling Mb infection. However, individual animal phenotypes for bTb based on interferon-gamma (IFNɣ) and its use in bovine selective breeding programs have not been explored. In the current study, IFNɣ production was measured using a specific IFNɣ ELISA kit in bovine purified protein derivative (bPPD)-stimulated blood samples collected from Holstein cattle. DNA isolated from the peripheral blood samples collected from the animals included in the study was genotyped with the EuroG Medium Density bead Chip, and the genotypes were imputed to whole-genome sequences. A genome-wide association analysis (GWAS) revealed that the IFNɣ in response to bPPD was associated with a specific genetic profile (heritability = 0.23) and allowed the identification of 163 SNPs, 72 quantitative trait loci (QTLs), 197 candidate genes, and 8 microRNAs (miRNAs) associated with this phenotype. No negative correlations between this phenotype and other phenotypes and traits included in the Spanish breeding program were observed. Taken together, our results define a heritable and distinct immunogenetic profile associated with strong production of IFNɣ in response to Mb.
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Affiliation(s)
- Gerard Badia-Bringué
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - María Canive
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Patricia Vázquez
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Joseba M. Garrido
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain
| | - Ramón A. Juste
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
| | | | - Oscar González-Recio
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain
| | - Marta Alonso-Hearn
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), 48160 Derio, Bizkaia, Spain
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2
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Gentile A, Fulgione A, Auzino B, Iovane V, Gallo D, Garramone R, Iaccarino N, Randazzo A, Iovane G, Cuomo P, Capparelli R, Iannelli D. In vivo biological validation of in silico analysis: A novel approach for predicting the effects of TLR4 exon 3 polymorphisms on brucellosis. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 118:105552. [PMID: 38218390 DOI: 10.1016/j.meegid.2024.105552] [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: 11/30/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/15/2024]
Abstract
The role of the Toll-like receptor 4 (TLR4) is of recognising intracellular and extracellular pathogens and of activating the immune response. This process can be compromised by single nucleotide polymorphisms (SNPs) which might affect the activity of several TLRs. The aim of this study is of ascertaining whether SNPs in the TLR4 of Bubalus bubalis infected by Brucella abortus, compromise the protein functionality. For this purpose, a computational analysis was performed. Next, computational predictions were confirmed by performing genotyping analysis. Finally, NMR-based metabolomics analysis was performed to identify potential biomarkers for brucellosis. The results indicate two SNPs (c. 672 A > C and c. 902 G > C) as risk factor for brucellosis in Bubalus bubalis, and three metabolites (lactate, 3-hydroxybutyrate and acetate) as biological markers for predicting the risk of developing the disease. These metabolites, together with TLR4 structural modifications in the MD2 interaction domain, are a clear signature of the immune system alteration during diverse Gram-negative bacterial infections. This suggests the possibility to extend this study to other pathogens, including Mycobacterium tuberculosis. In conclusion, this study combines multidisciplinary approaches to evaluate the biological and structural effects of SNPs on protein function.
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Affiliation(s)
- Antonio Gentile
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples 80055, Italy
| | - Andrea Fulgione
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples 80055, Italy
| | - Barbara Auzino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples 80055, Italy
| | - Valentina Iovane
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples 80055, Italy
| | - Daniela Gallo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples 80055, Italy
| | - Raffaele Garramone
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples 80055, Italy
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Giuseppe Iovane
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples 80137, Italy
| | - Paola Cuomo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples 80055, Italy
| | - Rosanna Capparelli
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples 80055, Italy.
| | - Domenico Iannelli
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples 80055, Italy
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Gaggioli MR, Jones AG, Panagi I, Washington EJ, Loney RE, Muench JH, Brennan RG, Thurston TLM, Ko DC. A single amino acid in the Salmonella effector SarA/SteE triggers supraphysiological activation of STAT3 for anti-inflammatory target gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580367. [PMID: 38405869 PMCID: PMC10888966 DOI: 10.1101/2024.02.14.580367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Non-typhoidal Salmonella enterica cause an estimated 1 million cases of gastroenteritis annually in the United States. These serovars use secreted protein effectors to mimic and reprogram host cellular functions. We previously discovered that the secreted effector SarA (Salmonella anti-inflammatory response activator; also known as SteE) was required for increased intracellular replication of S. Typhimurium and production of the anti-inflammatory cytokine interleukin-10 (IL-10). SarA facilitates phosphorylation of STAT3 through a region of homology with the host cytokine receptor gp130. Here, we demonstrate that a single amino acid difference between SarA and gp130 is critical for the anti-inflammatory bias of SarA-STAT3 signaling. An isoleucine at the pY+1 position of the YxxQ motif in SarA (which binds the SH2 domain in STAT3) causes increased STAT3 phosphorylation and expression of anti-inflammatory target genes. This isoleucine, completely conserved in ~4000 Salmonella isolates, renders SarA a better substrate for tyrosine phosphorylation by GSK-3. GSK-3 is canonically a serine/threonine kinase that nonetheless undergoes tyrosine autophosphorylation at a motif that has an invariant isoleucine at the pY+1 position. Our results provide a molecular basis for how a Salmonella secreted effector achieves supraphysiological levels of STAT3 activation to control host genes during infection.
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Affiliation(s)
- Margaret R. Gaggioli
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Angela G. Jones
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Ioanna Panagi
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Erica J. Washington
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Rachel E. Loney
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | | | - Richard G. Brennan
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Teresa L. M. Thurston
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Dennis C. Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
- Lead contact
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4
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Badia-Bringué G, Canive M, Vázquez P, Garrido JM, Fernández A, Juste RA, Jiménez JA, González-Recio O, Alonso-Hearn M. Association between High Interferon-Gamma Production in Avian Tuberculin-Stimulated Blood from Mycobacterium avium subsp. paratuberculosis-Infected Cattle and Candidate Genes Implicated in Necroptosis. Microorganisms 2023; 11:1817. [PMID: 37512987 PMCID: PMC10384200 DOI: 10.3390/microorganisms11071817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/07/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
The mechanisms underlying host resistance to Mycobacterium avium subsp. paratuberculosis (MAP) infection are largely unknown. In the current study, we hypothesize that cows with an ability to produce higher levels of interferon-gamma (IFNɣ) might control MAP infection more successfully. To test this hypothesis, IFNɣ production was measured using a specific IFNɣ ELISA kit in avian purified protein derivative (aPPD)-stimulated blood samples collected from 152 Holstein cattle. DNA isolated from peripheral blood samples of the animals included in the study was genotyped with the EuroG Medium-Density Bead Chip, and the genotypes were imputed to whole-genome sequencing. A genome-wide association analysis (GWAS) revealed that high levels of IFNɣ in response to the aPPD were associated with a specific genetic profile (heritability = 0.64) and allowed the identification of 71 SNPs, 40 quantitative trait loci (QTL), and 104 candidate genes. A functional analysis using the 104 candidate genes revealed a significant enrichment of genes involved in the innate immune response and, more specifically, in necroptosis. Taken together, our results define a heritable and distinct immunogenetic profile associated with the production of high IFNɣ levels and with the capacity of the host to lyse MAP-infected macrophages by necroptosis.
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Affiliation(s)
- Gerard Badia-Bringué
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain
- Doctoral Program in Molecular Biology and Biomedicine, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), 48940 Leioa, Spain
| | - María Canive
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain
| | - Patricia Vázquez
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain
| | - Joseba M Garrido
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | - Ramón A Juste
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain
| | | | - Oscar González-Recio
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | - Marta Alonso-Hearn
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain
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5
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Neira-Goulart M, de Sá NBR, Ribeiro-Alves M, Perazzo H, Geraldo KM, Ribeiro MPD, Cardoso SW, Grinsztejn B, Veloso VG, Rodrigues Gomes L, Cazote ADS, de Almeida DV, Giacoia-Gripp CBW, Côrtes FH, Morgado MG. Inflammasome genes polymorphisms are associated with progression to mechanical ventilation and death in a cohort of hospitalized COVID-19 patients in a reference hospital in Rio de Janeiro, Brazil. Gene 2023; 865:147325. [PMID: 36870425 PMCID: PMC9979696 DOI: 10.1016/j.gene.2023.147325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/23/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
COVID-19 has a broad spectrum of clinical manifestations. We assessed the impact of single nucleotide polymorphisms (SNPs) of inflammasome genesas risk factors for progression toCOVID-19 critical outcomes, such as mechanical ventilation support (MVS) or death.The study included 451 hospitalized individuals followed up at the INI/FIOCRUZ, Rio de Janeiro, Brazil, from 06/2020 to 03/2021. SNPs genotyping was determined by Real-Time PCR. We analyzed risk factors for progression to MVS (n = 174[38.6 %]) or death (n = 175[38.8 %])as a result of COVID-19 by Cox proportional hazardmodels.Slower progression toMVSwas associated with allele G (aHR = 0.66;P = 0.005) or the genotype G/G (aHR = 0.391;P = 0.006) in the NLRP3 rs10754558 or the allele G (aHR = 0.309;P = 0.004) in the IL1βrs1143634, while C allele in the NLRP3 rs4612666 (aHR = 2.342;P = 0.006) or in the rs10754558 (aHR = 2.957;P = 0.005) were associated with faster progression to death. Slower progression to death was associated to allele G (aHR = 0.563;P = 0.006) or the genotype A/G (aHR = 0.537;P = 0.005) in the CARD8 rs6509365; the genotype A/C in the IFI16 rs1101996 (aHR = 0.569;P = 0.011); the genotype T/T (aHR = 0.394;P = 0.004) or allele T (aHR = 0.68;P = 0.006) in the NLRP3 rs4612666, and the genotype G/G (aHR = 0.326;P = 0.005) or allele G (aHR = 0,68;P = 0.014) in the NLRP3 rs10754558. Our results suggest that inflammasome genetic variations might influence the critical clinical course of COVID-19.
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Affiliation(s)
- Milena Neira-Goulart
- Laboratory of AIDS & Molecular Immunology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
| | | | - Marcelo Ribeiro-Alves
- Laboratory of Clinical Research on STD/AIDS, National Institute of Infectology Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Hugo Perazzo
- Laboratory of Clinical Research on STD/AIDS, National Institute of Infectology Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Kim Mattos Geraldo
- Laboratory of Clinical Research on STD/AIDS, National Institute of Infectology Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Maria Pia Diniz Ribeiro
- Laboratory of Clinical Research on STD/AIDS, National Institute of Infectology Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Sandra Wagner Cardoso
- Laboratory of Clinical Research on STD/AIDS, National Institute of Infectology Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Beatriz Grinsztejn
- Laboratory of Clinical Research on STD/AIDS, National Institute of Infectology Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Valdiléa G Veloso
- Laboratory of Clinical Research on STD/AIDS, National Institute of Infectology Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Larissa Rodrigues Gomes
- Center of Technological Development in Health (CDTS)/National Institute of Science and Technological for Innovation on Neglected Population Diseases (INCT-IDPN), FIOCRUZ, Rio de Janeiro, Brazil.
| | - Andressa da Silva Cazote
- Laboratory of AIDS & Molecular Immunology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
| | | | | | - Fernanda Heloise Côrtes
- Laboratory of AIDS & Molecular Immunology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Mariza Gonçalves Morgado
- Laboratory of AIDS & Molecular Immunology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
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6
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Gibbs KD, Wang L, Yang Z, Anderson CE, Bourgeois JS, Cao Y, Gaggioli MR, Biel M, Puertollano R, Chen CC, Ko DC. Human variation impacting MCOLN2 restricts Salmonella Typhi replication by magnesium deprivation. CELL GENOMICS 2023; 3:100290. [PMID: 37228749 PMCID: PMC10203047 DOI: 10.1016/j.xgen.2023.100290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/24/2023] [Accepted: 02/27/2023] [Indexed: 05/27/2023]
Abstract
Human genetic diversity can reveal critical factors in host-pathogen interactions. This is especially useful for human-restricted pathogens like Salmonella enterica serovar Typhi (S. Typhi), the cause of typhoid fever. One key defense during bacterial infection is nutritional immunity: host cells attempt to restrict bacterial replication by denying bacteria access to key nutrients or supplying toxic metabolites. Here, a cellular genome-wide association study of intracellular replication by S. Typhi in nearly a thousand cell lines from around the world-and extensive follow-up using intracellular S. Typhi transcriptomics and manipulation of magnesium availability-demonstrates that the divalent cation channel mucolipin-2 (MCOLN2 or TRPML2) restricts S. Typhi intracellular replication through magnesium deprivation. Mg2+ currents, conducted through MCOLN2 and out of endolysosomes, were measured directly using patch-clamping of the endolysosomal membrane. Our results reveal Mg2+ limitation as a key component of nutritional immunity against S. Typhi and as a source of variable host resistance.
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Affiliation(s)
- Kyle D. Gibbs
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Zhuo Yang
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Caroline E. Anderson
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Jeffrey S. Bourgeois
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Yanlu Cao
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Margaret R. Gaggioli
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Martin Biel
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Rosa Puertollano
- Cell and Developmental Biology Center, National Heart, Lung, & Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Cheng-Chang Chen
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Dennis C. Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
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7
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Frantz SI, Small CM, Cresko WA, Singh ND. Ovarian transcriptional response to Wolbachia infection in D. melanogaster in the context of between-genotype variation in gene expression. G3 (BETHESDA, MD.) 2023; 13:jkad047. [PMID: 36857313 PMCID: PMC10151400 DOI: 10.1093/g3journal/jkad047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 08/22/2022] [Accepted: 01/07/2023] [Indexed: 03/02/2023]
Abstract
Wolbachia is a maternally transmitted endosymbiotic bacteria that infects a wide variety of arthropod and nematode hosts. The effects of Wolbachia on host biology are far-reaching and include changes in host gene expression. However, previous work on the host transcriptional response has generally been investigated in the context of a single host genotype. Thus, the relative effect of Wolbachia infection versus vs. host genotype on gene expression is unknown. Here, we explicitly test the relative roles of Wolbachia infection and host genotype on host gene expression by comparing the ovarian transcriptomes of 4 strains of Drosophila melanogaster (D. melanogaster) infected and uninfected with Wolbachia. Our data suggest that infection explains a small amount of transcriptional variation, particularly in comparison to variation in gene expression among strains. However, infection specifically affects genes related to cell cycle, translation, and metabolism. We also find enrichment of cell division and recombination processes among genes with infection-associated differential expression. Broadly, the transcriptomic changes identified in this study provide novel understanding of the relative magnitude of the effect of Wolbachia infection on gene expression in the context of host genetic variation and also point to genes that are consistently differentially expressed in response to infection among multiple genotypes.
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Affiliation(s)
- Sophia I Frantz
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403USA
| | - Clayton M Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR, 97403USA
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR, 97403USA
| | - Nadia D Singh
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403USA
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8
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Badia-Bringué G, Canive M, Alonso-Hearn M. Control of Mycobacterium avium subsp. paratuberculosis load within infected bovine monocyte-derived macrophages is associated with host genetics. Front Immunol 2023; 14:1042638. [PMID: 36911672 PMCID: PMC9992791 DOI: 10.3389/fimmu.2023.1042638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/09/2023] [Indexed: 02/24/2023] Open
Abstract
The genetic loci influencing individual resistance to Mycobacterium avium subsp. paratuberculosis (MAP) infection are still largely unknown. In the current study, we searched for genetic loci associated with resistance to MAP infection by evaluating the performance of monocyte-derived macrophages (MDMs) isolated from the peripheral blood of 75 healthy Holsteins cows and infected ex vivo with MAP. Bacterial load (log colony-forming units, log CFUs) within MDMs was quantified at 2 h and 7 days p. i. using a BACTEC MGIT 960 instrument. In addition, the expression levels of some genes with important roles in the innate immune response including epiregulin (EREG), complement component C3 (C3), galectin-9 (Gal9), and nitric oxide (NO-) were measured in the supernatant of the infected cells. DNA from peripheral blood samples of the animals included in the study was isolated and genotyped with the EuroG MD bead Chip (44,779 single nucleotide-polymorphisms, SNPs). Linear mixed models were used to calculate the heritability (h2 ) estimates for each indicator of MDM performance, MAP load within MDMs and EREG, C3, Gal9, and NO-expression. After performing a genome-wide association study, the only phenotypes that showed SNPs with a significant association were the bacterial load within MDMs at 2 h (h2 = 0. 87) and 7 days (h2 = 0.83) p.i. A total of 6 SNPs, 5 candidate genes, and one microRNA on the Bos taurus chromosomes BTA2, BTA17, BTA18, and BTA21 were associated with MAP load at 2 h p.i. Overlap was seen in two SNPs associated with the log CFUs at 2 h and 7 d p.i. The identified SNPs had negative regression coefficients, and were, therefore, associated with a low bacterial load within MDMs. Some of the identified SNPs were located within QTLs previously associated with longevity, reproductive, and udder health traits. Some of the identified candidate genes; Oxysterol Binding Protein Like 6, Cysteine and Serine Rich Nuclear Protein 3, and the Coiled-Coil Domain Containing 92 regulate cellular cholesterol trafficking and efflux, apoptosis, and interferon production, respectively. Taken together, our results define a heritable and distinct immunogenetic profile in MAP-infected macrophages designed to limit bacterial load early after infection.
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Affiliation(s)
- Gerard Badia-Bringué
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain.,Doctoral Program in Molecular Biology and Biomedicine, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Bizkaia, Spain
| | - María Canive
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Marta Alonso-Hearn
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
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9
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Abstract
Since the identification of sickle cell trait as a heritable form of resistance to malaria, candidate gene studies, linkage analysis paired with sequencing, and genome-wide association (GWA) studies have revealed many examples of genetic resistance and susceptibility to infectious diseases. GWA studies enabled the identification of many common variants associated with small shifts in susceptibility to infectious diseases. This is exemplified by multiple loci associated with leprosy, malaria, HIV, tuberculosis, and coronavirus disease 2019 (COVID-19), which illuminate genetic architecture and implicate pathways underlying pathophysiology. Despite these successes, most of the heritability of infectious diseases remains to be explained. As the field advances, current limitations may be overcome by applying methodological innovations such as cellular GWA studies and phenome-wide association (PheWA) studies as well as by improving methodological rigor with more precise case definitions, deeper phenotyping, increased cohort diversity, and functional validation of candidate loci in the laboratory or human challenge studies.
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Affiliation(s)
- Kyle D Gibbs
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, USA;
| | - Benjamin H Schott
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, USA; .,Duke University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, USA; .,Duke University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA.,Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, North Carolina, USA
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Schott BH, Wang L, Zhu X, Harding AT, Ko ER, Bourgeois JS, Washington EJ, Burke TW, Anderson J, Bergstrom E, Gardener Z, Paterson S, Brennan RG, Chiu C, McClain MT, Woods CW, Gregory SG, Heaton NS, Ko DC. Single-cell genome-wide association reveals that a nonsynonymous variant in ERAP1 confers increased susceptibility to influenza virus. CELL GENOMICS 2022; 2:100207. [PMID: 36465279 PMCID: PMC9718543 DOI: 10.1016/j.xgen.2022.100207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/26/2022] [Accepted: 10/07/2022] [Indexed: 06/17/2023]
Abstract
During pandemics, individuals exhibit differences in risk and clinical outcomes. Here, we developed single-cell high-throughput human in vitro susceptibility testing (scHi-HOST), a method for rapidly identifying genetic variants that confer resistance and susceptibility. We applied this method to influenza A virus (IAV), the cause of four pandemics since the start of the 20th century. scHi-HOST leverages single-cell RNA sequencing (scRNA-seq) to simultaneously assign genetic identity to cells in mixed infections of cell lines of European, African, and Asian origin, reveal associated genetic variants for viral burden, and identify expression quantitative trait loci. Integration of scHi-HOST with human challenge and experimental validation demonstrated that a missense variant in endoplasmic reticulum aminopeptidase 1 (ERAP1; rs27895) increased IAV burden in cells and human volunteers. rs27895 exhibits population differentiation, likely contributing to greater permissivity of cells from African populations to IAV. scHi-HOST is a broadly applicable method and resource for decoding infectious-disease genetics.
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Affiliation(s)
- Benjamin H Schott
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
- These authors contributed equally
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- These authors contributed equally
| | - Xinyu Zhu
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Alfred T Harding
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Emily R Ko
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Hospital Medicine, Division of General Internal Medicine, Department of Medicine, Duke Regional Hospital, Durham, NC 27705, USA
| | - Jeffrey S Bourgeois
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Erica J Washington
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Jack Anderson
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Emma Bergstrom
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Zoe Gardener
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Suzanna Paterson
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Richard G Brennan
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Christopher Chiu
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Micah T McClain
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Nicholas S Heaton
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
- Lead contact
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de Sá NBR, de Souza NCS, Neira-Goulart M, Ribeiro-Alves M, Da Silva TP, Pilotto JH, Rolla VC, Giacoia-Gripp CBW, de Oliveira Pinto LM, Scott-Algara D, Morgado MG, Teixeira SLM. Inflammasome genetic variants are associated with tuberculosis, HIV-1 infection, and TB/HIV-immune reconstitution inflammatory syndrome outcomes. Front Cell Infect Microbiol 2022; 12:962059. [PMID: 36204643 PMCID: PMC9531132 DOI: 10.3389/fcimb.2022.962059] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundTuberculosis (TB) and AIDS are the leading causes of infectious diseases death worldwide. Here, we investigated the relationship between from single nucleotide polymorphisms (SNPs) of the NLRP3, CARD8, AIM2, CASP-1, IFI16, and IL-1β inflammasome genes, as well as the profiles of secreted proinflammatory cytokines (e.g., IL-1β, IL-18, IL-33, and IL-6) with the TB clinical profiles, TB-HIV coinfection, and IRIS onset.MethodsThe individuals were divided into four groups: TB-HIV group (n=88; 11 of them with IRIS), HIV-1 group (n=20), TB group (n=24) and healthy volunteers (HC) group (n=10), and were followed up at INI/FIOCRUZ and HGNI (Rio de Janeiro/Brazil) from 2006 to 2016. Real-time PCR was used to determine the genotypes of the Single Nucleotide Polymorphism (SNPs), and ELISA was used to measure the plasma cytokine levels. Unconditional logistic regression models were used to perform risk estimations.ResultsA higher risk for extrapulmonary TB was associated with the TT genotype (aOR=6.76; P=0.026) in the NLRP3 rs4612666 Single Nucleotide Polymorphism (SNP) and the C-C-T-G-C haplotype (aOR=4.99; P= 0.017) in the NLRP3 variants. This same Single Nucleotide Polymorphism (SNP) was associated with lower risk against extrapulmonary TB when the carrier allele C (aOR=0.15; P=0.021) was present. Among those with HIV-1 infections, a higher risk for TB onset was associated with the GA genotype (aOR=5.5; P=0.044) in the IL1-β rs1143634 Single Nucleotide Polymorphism (SNP). In contrast, lower risk against TB onset was associated with the A-G haplotype (aOR=0.17; P= 0.026) in the CARD8 variants. Higher IL-6 and IL-33 levels were observed in individuals with TB. A higher risk for IRIS onset was associated with CD8 counts ≤ 500 cells/mm3 (aOR=12.32; P=0.010), the presence of extrapulmonary TB (aOR=6.6; P=0.038), and the CT genotype (aOR=61.06; P=0.026) or carrier allele T (aOR=61.06; P=0.026) in the AIM2 rs2276405 Single Nucleotide Polymorphism (SNP), whereas lower risk against IRIS onset was associated with the AT genotype (aOR=0.02; P=0.033) or carrier allele T (aOR=0.02; P=0.029) in the CARD8 rs2043211 Single Nucleotide Polymorphism (SNP) and the T-G haplotype (aOR=0.07; P= 0.033) in the CARD8 variants. No other significant associations were observed.ConclusionsOur results depict the involvement of genetic polymorphisms of crucial innate immunity genes and proinflammatory cytokines in the clinical outcomes related to TB-HIV coinfection.
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Affiliation(s)
- Nathalia Beatriz Ramos de Sá
- 1Laboratory of AIDS & Molecular Immunology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
- *Correspondence: Mariza Gonçalves Morgado, ; Nathalia Beatriz Ramos de Sá,
| | | | - Milena Neira-Goulart
- 1Laboratory of AIDS & Molecular Immunology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Marcelo Ribeiro-Alves
- Laboratory of Clinical Research on STD/AIDS, National Institute of Infectious Diseases Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | - Tatiana Pereira Da Silva
- 1Laboratory of AIDS & Molecular Immunology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Jose Henrique Pilotto
- 1Laboratory of AIDS & Molecular Immunology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
- Nova Iguaçu General Hospital, Nova Iguaçu, Rio de Janeiro, Brazil
| | - Valeria Cavalcanti Rolla
- Clinical Research Laboratory on Mycobacteria, National Institute of Infectious Diseases Evandro Chagas, FIOCRUZ, Rio de Janeiro, Brazil
| | | | | | - Daniel Scott-Algara
- Unité de Biologie Cellulaire des Lymphocytes, Institut Pasteur, Paris, France
| | - Mariza Gonçalves Morgado
- 1Laboratory of AIDS & Molecular Immunology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
- *Correspondence: Mariza Gonçalves Morgado, ; Nathalia Beatriz Ramos de Sá,
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Inflammasome Genetic Variants Are Associated with Protection to Clinical Severity of COVID-19 among Patients from Rio de Janeiro, Brazil. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9082455. [PMID: 36105941 PMCID: PMC9467712 DOI: 10.1155/2022/9082455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/18/2022] [Accepted: 08/24/2022] [Indexed: 11/18/2022]
Abstract
COVID-19 has a broad spectrum of clinical manifestations, from asymptomatic or mild/moderate symptoms to severe symptoms and death. The mechanisms underlying its clinical evolution are still unclear. Upon SARS-CoV-2 infection, host factors, such as the inflammasome system, are activated by the presence of the virus inside host cells. The search for COVID-19 risk factors is of relevance for clinical management. In this study, we investigated the impact of inflammasome single-nucleotide polymorphisms (SNPs) in SARS-CoV-2-infected individuals with distinct severity profiles at clinical presentation. Patients were divided into two groups according to disease severity at clinical presentation based on the WHO Clinical Progression Scale. Group 1 included patients with mild/moderate disease (WHO < 6; n = 76), and group 2 included patients with severe/critical COVID-19 (WHO ≥ 6; n = 357). Inpatients with moderate to severe/critical profiles were recruited and followed-up at Hospital Center for COVID-19 Pandemic – National Institute of Infectology (INI)/FIOCRUZ, RJ, Brazil, from June 2020 to March 2021. Patients with mild disease were recruited at Oswaldo Cruz Institute (IOC)/FIOCRUZ, RJ, Brazil, in August 2020. Genotyping of 11 inflammasome SNPs was determined by real-time PCR. Protection and risk estimation were performed using unconditional logistic regression models. Significant differences in NLRP3 rs1539019 and CARD8 rs2043211 were observed between the two groups. Protection against disease severity was associated with the A/A genotype (ORadj = 0.36; P = 0.032), allele A (ORadj = 0.93; P = 0.010), or carrier-A (ORadj = 0.45; P = 0.027) in the NLRP3 rs1539019 polymorphism; A/T genotype (ORadj = 0.5; P = 0.045), allele T (ORadj = 0.93; P = 0.018), or carrier-T (ORadj = 0.48; P = 0.029) in the CARD8 rs2043211 polymorphism; and the A-C-G-C-C (ORadj = 0.11; P = 0.018), A-C-G-C-G (ORadj = 0.23; P = 0.003), C-C-G-C-C (ORadj = 0.37; P = 0.021), and C-T-G-A-C (ORadj = 0.04; P = 0.0473) in NLRP3 genetic haplotype variants. No significant associations were observed for the other polymorphisms. To the best of our knowledge, this is the first study demonstrating an association between CARD8 and NLRP3 inflammasome genetic variants and protection against COVID-19 severity, contributing to the discussion of the impact of inflammasomes on COVID-19 outcomes.
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Mikacenic C, Bhatraju P, Robinson-Cohen C, Kosamo S, Fohner AE, Dmyterko V, Long SA, Cerosaletti K, Calfee CS, Matthay MA, Walley KR, Russell JA, Christie JD, Meyer NJ, Christiani DC, Wurfel MM. Single Nucleotide Variant in FAS Associates With Organ Failure and Soluble Fas Cell Surface Death Receptor in Critical Illness. Crit Care Med 2022; 50:e284-e293. [PMID: 34593707 PMCID: PMC8863632 DOI: 10.1097/ccm.0000000000005333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Multiple organ failure in critically ill patients is associated with poor prognosis, but biomarkers contributory to pathogenesis are unknown. Previous studies support a role for Fas cell surface death receptor (Fas)-mediated apoptosis in organ dysfunction. Our objectives were to test for associations between soluble Fas and multiple organ failure, identify protein quantitative trait loci, and determine associations between genetic variants and multiple organ failure. DESIGN Retrospective observational cohort study. SETTING Four academic ICUs at U.S. hospitals. PATIENTS Genetic analyses were completed in a discovery (n = 1,589) and validation set (n = 863). Fas gene expression and flow cytometry studies were completed in outpatient research participants (n = 250). INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS In discovery and validation sets of critically ill patients, we tested for associations between enrollment plasma soluble Fas concentrations and Sequential Organ Failure Assessment score on day 3. We conducted a genome-wide association study of plasma soluble Fas (discovery n = 1,042) and carried forward a single nucleotide variant in the FAS gene, rs982764, for validation (n = 863). We further tested whether the single nucleotide variant in FAS (rs982764) was associated with Sequential Organ Failure Assessment score, FAS transcriptional isoforms, and Fas cell surface expression. Higher plasma soluble Fas was associated with higher day 3 Sequential Organ Failure Assessment scores in both the discovery (β = 4.07; p < 0.001) and validation (β = 6.96; p < 0.001) sets. A single nucleotide variant in FAS (rs982764G) was associated with lower plasma soluble Fas concentrations and lower day 3 Sequential Organ Failure Assessment score in meta-analysis (-0.21; p = 0.02). Single nucleotide variant rs982764G was also associated with a lower relative expression of the transcript for soluble as opposed to transmembrane Fas and higher cell surface expression of Fas on CD4+ T cells. CONCLUSIONS We found that single nucleotide variant rs982764G was associated with lower plasma soluble Fas concentrations in a discovery and validation population, and single nucleotide variant rs982764G was also associated with lower organ dysfunction on day 3. These findings support further study of the Fas pathway as a potential mediator of organ dysfunction in critically ill patients.
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Affiliation(s)
| | - Pavan Bhatraju
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA
| | | | - Susanna Kosamo
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Alison E. Fohner
- Department of Epidemiology, Institute of Public Health Genetics, University of Washington, Seattle, WA
| | - Victoria Dmyterko
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA
| | | | | | - Carolyn S. Calfee
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California San Francisco, CA
| | - Michael A. Matthay
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California San Francisco, CA
| | - Keith R. Walley
- St. Paul’s Hospital, University of British Columbia, Vancouver, BC
| | - James A. Russell
- St. Paul’s Hospital, University of British Columbia, Vancouver, BC
| | - Jason D. Christie
- Division of Pulmonary, Allergy, and Critical Care Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Nuala J. Meyer
- Division of Pulmonary, Allergy, and Critical Care Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - David C. Christiani
- Harvard University School of Public Health and Division of Pulmonary and Critical Care, Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Mark M. Wurfel
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA
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Barnes AB, Keener RM, Schott BH, Wang L, Valdivia RH, Ko DC. Human genetic diversity regulating the TLR10/TLR1/TLR6 locus confers increased cytokines in response to Chlamydia trachomatis. HGG ADVANCES 2022; 3:100071. [PMID: 35047856 PMCID: PMC8756536 DOI: 10.1016/j.xhgg.2021.100071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/15/2021] [Indexed: 12/25/2022] Open
Abstract
Human genetic diversity can have profound effects on health outcomes upon exposure to infectious agents. For infections with Chlamydia trachomatis (C. trachomatis), the wide range of genital and ocular disease manifestations are likely influenced by human genetic differences that regulate interactions between C. trachomatis and host cells. We leveraged this diversity in cellular responses to demonstrate the importance of variation at the Toll-like receptor 1 (TLR1), TLR6, and TLR10 locus to cytokine production in response to C. trachomatis. We determined that a single-nucleotide polymorphism (SNP) (rs1057807), located in a region that forms a loop with the TLR6 promoter, is associated with increased expression of TLR1, TLR6, and TLR10 and secreted levels of ten C. trachomatis-induced cytokines. Production of these C. trachomatis-induced cytokines is primarily dependent on MyD88 and TLR6 based on experiments using inhibitors, blocking antibodies, RNAi, and protein overexpression. Population genetic analyses further demonstrated that the mean IL-6 response of cells from two European populations were higher than the mean response of cells from three African populations and that this difference was partially attributable to variation in rs1057807 allele frequency. In contrast, a SNP associated with a different pro-inflammatory cytokine (rs2869462 associated with the chemokine CXCL10) exhibited an opposite response, underscoring the complexity of how different genetic variants contribute to an individual's immune response. This multidisciplinary study has identified a long-range chromatin interaction and genetic variation that regulates TLR6 to broaden our understanding of how human genetic variation affects the C. trachomatis-induced immune response.
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Affiliation(s)
- Alyson B. Barnes
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Rachel M. Keener
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Benjamin H. Schott
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Raphael H. Valdivia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Dennis C. Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
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Darbeheshti F. The Immunogenetics of Melanoma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:383-396. [DOI: 10.1007/978-3-030-92616-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Beck EA, Healey HM, Small CM, Currey MC, Desvignes T, Cresko WA, Postlethwait JH. Advancing human disease research with fish evolutionary mutant models. Trends Genet 2022; 38:22-44. [PMID: 34334238 PMCID: PMC8678158 DOI: 10.1016/j.tig.2021.07.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 01/03/2023]
Abstract
Model organism research is essential to understand disease mechanisms. However, laboratory-induced genetic models can lack genetic variation and often fail to mimic the spectrum of disease severity. Evolutionary mutant models (EMMs) are species with evolved phenotypes that mimic human disease. EMMs complement traditional laboratory models by providing unique avenues to study gene-by-environment interactions, modular mutations in noncoding regions, and their evolved compensations. EMMs have improved our understanding of complex diseases, including cancer, diabetes, and aging, and illuminated mechanisms in many organs. Rapid advancements of sequencing and genome-editing technologies have catapulted the utility of EMMs, particularly in fish. Fish are the most diverse group of vertebrates, exhibiting a kaleidoscope of specialized phenotypes, many that would be pathogenic in humans but are adaptive in the species' specialized habitat. Importantly, evolved compensations can suggest avenues for novel disease therapies. This review summarizes current research using fish EMMs to advance our understanding of human disease.
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Affiliation(s)
- Emily A Beck
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA.
| | - Hope M Healey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Clayton M Small
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Mark C Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - William A Cresko
- Data Science, University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
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Associations of NLRP3 and CARD8 gene polymorphisms with alcohol dependence and commonly related psychiatric disorders: a preliminary study. Arh Hig Rada Toksikol 2021; 72:191-197. [PMID: 34587665 PMCID: PMC8576752 DOI: 10.2478/aiht-2021-72-3432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/01/2021] [Indexed: 12/11/2022] Open
Abstract
We investigated two functional polymorphisms in NLRP3 inflammasome genes (NLRP3 rs35829419 and CARD8 rs2043211) and their association with alcohol dependence and related anxiety, depression, obsession-compulsion, or aggression in 88 hospitalised alcohol-dependent patients, 99 abstinent alcohol-dependent participants, and 94 controls, all male Caucasian. Alcohol dependence-related psychiatric disorders were assessed with the Zung Depression and Anxiety scale, Buss-Durkee Hostility Inventory, Alcohol Use Disorders Identification Test, Brief Social Phobia Scale, Obsessive Compulsive Drinking Scale, and Yale-Brown Obsessive-Compulsive Scale. For genotyping we used the allele-specific quantitative polymerase chain reaction-based methods. The three groups differed significantly in CARD8 rs2043211 distribution (P=0.049; chi-squared=9.557; df=4). The NLPR3 rs35829419 polymorphism was not significantly associated with alcohol dependence. In hospitalised alcohol-dependent patients the investigated polymorphisms were not associated with scores indicating alcohol consumption or comorbid symptoms. In abstinent alcohol-dependent subjects homozygotes for the polymorphic CARD8 allele presented with the highest scores on the Zung Anxiety Scale (p=0.048; df=2; F=3.140). Among controls, CARD8 genotype was associated with high scores on the Obsessive Compulsive Drinking Scale (P=0.027; df=2; F=3.744). In conclusion, our results reveal that CARD8 rs2043211 may play some role in susceptibility to alcohol dependence, expression of anxiety symptoms in abstinent alcohol-dependent subjects, and in obsessive compulsive drinking in healthy controls. However, further studies with larger cohorts are required to confirm these preliminary findings.
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18
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Pang H, Sun X, Luo S, Lin J, Shi X, Xiao Y, Huang G, Li X, Xie Z, Zhou Z. The polymorphism of the CARD8 inflammasome-related gene is associated with glutamic-acid-decarboxylase-antibody positivity in patients with type 1 diabetes mellitus. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1131. [PMID: 34430572 PMCID: PMC8350628 DOI: 10.21037/atm-21-1126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/17/2021] [Indexed: 11/20/2022]
Abstract
Background This study sought to examine the correlation between 2 single-nucleotide polymorphisms (SNPs; rs10403848 and rs2043211) in the caspase recruitment domain-containing protein 8 (CARD8) gene and the risks and clinical features of patients with type 1 diabetes mellitus (T1DM) in the Han Chinese population. Methods A case-control study involving the Han Chinese population was designed, and individuals diagnosed with classical T1DM and healthy controls were enrolled in this study. MassARRAY genotyped the SNPs of rs10403848 and rs2043211. Logistic regression and chi-square analyses were conducted to compare the allele distributions and genotypes of the T1DM and healthy control participants. A Kruskal-Wallis 1-way analysis of variance was used to perform the genotype-phenotype analysis for the T1DM patients. Results In total, 510 participants with classical T1DM and 531 sex-matched healthy control participants participated in this study. The CARD8 SNP of rs2043211 was significantly associated with the rate of glutamic-acid-decarboxylase-antibody (GADA) positivity among T1DM patients (P=0.021). However, no significant differences in the distributions of alleles or the genotypes of rs10403848 and rs2043211 were observed between the case and control groups, and these 2 SNPs were not associated with T1DM under various inheritance models. Conclusions The rs10403848 and rs2043211 polymorphisms of CARD8 were not associated with susceptibility to T1DM. However, rs2043211 was found to be correlated with GADA positivity in participants with T1DM.
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Affiliation(s)
- Haipeng Pang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xiaoxiao Sun
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Shuoming Luo
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Jian Lin
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xiajie Shi
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yang Xiao
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
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ARHGEF26 enhances Salmonella invasion and inflammation in cells and mice. PLoS Pathog 2021; 17:e1009713. [PMID: 34242364 PMCID: PMC8294491 DOI: 10.1371/journal.ppat.1009713] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 07/21/2021] [Accepted: 06/14/2021] [Indexed: 11/25/2022] Open
Abstract
Salmonella hijack host machinery in order to invade cells and establish infection. While considerable work has described the role of host proteins in invasion, much less is known regarding how natural variation in these invasion-associated host proteins affects Salmonella pathogenesis. Here we leveraged a candidate cellular GWAS screen to identify natural genetic variation in the ARHGEF26 (Rho Guanine Nucleotide Exchange Factor 26) gene that renders lymphoblastoid cells susceptible to Salmonella Typhi and Typhimurium invasion. Experimental follow-up redefined ARHGEF26’s role in Salmonella epithelial cell infection. Specifically, we identified complex serovar-by-host interactions whereby ARHGEF26 stimulation of S. Typhi and S. Typhimurium invasion into host cells varied in magnitude and effector-dependence based on host cell type. While ARHGEF26 regulated SopB- and SopE-mediated S. Typhi (but not S. Typhimurium) infection of HeLa cells, the largest effect of ARHGEF26 was observed with S. Typhimurium in polarized MDCK cells through a SopB- and SopE2-independent mechanism. In both cell types, knockdown of the ARHGEF26-associated protein DLG1 resulted in a similar phenotype and serovar specificity. Importantly, we show that ARHGEF26 plays a critical role in S. Typhimurium pathogenesis by contributing to bacterial burden in the enteric fever murine model, as well as inflammation in the colitis infection model. In the enteric fever model, SopB and SopE2 are required for the effects of Arhgef26 deletion on bacterial burden, and the impact of sopB and sopE2 deletion in turn required ARHGEF26. In contrast, SopB and SopE2 were not required for the impacts of Arhgef26 deletion on colitis. A role for ARHGEF26 on inflammation was also seen in cells, as knockdown reduced IL-8 production in HeLa cells. Together, these data reveal pleiotropic roles for ARHGEF26 during infection and highlight that many of the interactions that occur during infection that are thought to be well understood likely have underappreciated complexity. During infection, Salmonella manipulates host cells into engulfing the bacteria and establishing an intracellular niche. While many studies have identified genes involved in different stages of this Salmonella invasion process, few studies have examined how differences between human hosts contribute to infection susceptibility. Here we leveraged a candidate genetic screen to identify natural genetic variation in the human ARHGEF26 gene that correlates with Salmonella invasion. Springboarding from this result, we experimentally tested and redefined ARHGEF26’s role in Salmonella invasion, discovered a new role for ARHGEF26 in regulating inflammation during Salmonella disease, and demonstrated the relevance of these findings in mouse models. Building on how ARHGEF26 functions in other contexts, we implicated two ARHGEF26-interacting host proteins as contributors to Salmonella pathobiology. Collectively, these results identify a potential source of inter-person diversity in susceptibility to Salmonella disease and expand our molecular understanding of Salmonella infection to include a multifaceted role for ARHGEF26. They further identify important future directions in understanding how Salmonella recruit and manipulate ARHGEF26 as well as how ARHGEF26 is able to drive Salmonella-beneficial processes.
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Bourgeois JS, Smith CM, Ko DC. These Are the Genes You're Looking For: Finding Host Resistance Genes. Trends Microbiol 2021; 29:346-362. [PMID: 33004258 PMCID: PMC7969353 DOI: 10.1016/j.tim.2020.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/05/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
Humanity's ongoing struggle with new, re-emerging and endemic infectious diseases serves as a frequent reminder of the need to understand host-pathogen interactions. Recent advances in genomics have dramatically advanced our understanding of how genetics contributes to host resistance or susceptibility to bacterial infection. Here we discuss current trends in defining host-bacterial interactions at the genome-wide level, including screens that harness CRISPR/Cas9 genome editing, natural genetic variation, proteomics, and transcriptomics. We report on the merits, limitations, and findings of these innovative screens and discuss their complementary nature. Finally, we speculate on future innovation as we continue to progress through the postgenomic era and towards deeper mechanistic insight and clinical applications.
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Affiliation(s)
- Jeffrey S Bourgeois
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Clare M Smith
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA; Duke Human Vaccine Institute, School of Medicine, Duke University Durham, NC, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC, USA.
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21
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Schott BH, Antonia AL, Wang L, Pittman KJ, Sixt BS, Barnes AB, Valdivia RH, Ko DC. Modeling of variables in cellular infection reveals CXCL10 levels are regulated by human genetic variation and the Chlamydia-encoded CPAF protease. Sci Rep 2020; 10:18269. [PMID: 33106516 PMCID: PMC7588472 DOI: 10.1038/s41598-020-75129-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/12/2020] [Indexed: 01/01/2023] Open
Abstract
Susceptibility to infectious diseases is determined by a complex interaction between host and pathogen. For infections with the obligate intracellular bacterium Chlamydia trachomatis, variation in immune activation and disease presentation are regulated by both host genetic diversity and pathogen immune evasion. Previously, we discovered a single nucleotide polymorphism (rs2869462) associated with absolute abundance of CXCL10, a pro-inflammatory T-cell chemokine. Here, we report that levels of CXCL10 change during C. trachomatis infection of cultured cells in a manner dependent on both host and pathogen. Linear modeling of cellular traits associated with CXCL10 levels identified a strong, negative correlation with bacterial burden, suggesting that C. trachomatis actively suppresses CXCL10. We identified the pathogen-encoded factor responsible for this suppression as the chlamydial protease- or proteasome-like activity factor, CPAF. Further, we applied our modeling approach to other host cytokines in response to C. trachomatis and found evidence that RANTES, another T-cell chemoattractant, is actively suppressed by Chlamydia. However, this observed suppression of RANTES is not mediated by CPAF. Overall, our results demonstrate that CPAF suppresses CXCL10 to evade the host cytokine response and that modeling of cellular infection parameters can reveal previously unrecognized facets of host-pathogen interactions.
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Affiliation(s)
- Benjamin H Schott
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC, 27710, USA
| | - Alejandro L Antonia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
| | - Kelly J Pittman
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
| | - Barbara S Sixt
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research, Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Alyson B Barnes
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
| | - Raphael H Valdivia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA.
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC, 27710, USA.
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC, 27710, USA.
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Ravimohan S, Maenetje P, Auld SC, Ncube I, Mlotshwa M, Chase W, Tiemessen CT, Vangu MDT, Wallis RS, Churchyard G, Weissman D, Kornfeld H, Bisson GP. A Common NLRC4 Gene Variant Associates With Inflammation and Pulmonary Function in Human Immunodeficiency Virus and Tuberculosis. Clin Infect Dis 2020; 71:924-932. [PMID: 31751447 PMCID: PMC7428399 DOI: 10.1093/cid/ciz898] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 09/27/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Inflammasomes mediate inflammation in adults living with both human immunodeficiency virus (HIV) and tuberculosis (TB), but the relevance of inflammasome gene polymorphisms in TB-associated pulmonary damage is unknown. We hypothesized that functional single-nucleotide polymorphisms (SNPs) in inflammasome pathway genes modify systemic and pulmonary inflammation, contributing to respiratory impairment in adults living with HIV/pulmonary TB. METHODS This was a prospective cohort study set in South Africa following individuals living with HIV/TB up to 48 weeks post-antiretroviral therapy (ART) initiation. Ten functional SNPs in 5 inflammasome pathway genes were related to circulating inflammatory biomarkers and lung function assessed by spirometry pre- and post-ART initiation. Analyses used 2-sided t tests, Wilcoxon rank sum tests, Spearman correlation coefficients, linear regression, and generalized estimating equation models. RESULTS Among 102 patients with baseline samples, the minor allele (T) in NLRC4 rs385076 was independently associated with lower levels of interleukin (IL)-18 and IL-6 before and up to 12 weeks post-ART initiation (Benjamini-Hochberg corrected P values < .02). Patients with the CT/TT genotypes also had improved lung function vs CC patients up to 48 weeks post-ART initiation (forced vital capacity, 206 mL higher; 95% confidence interval [CI], 67-345 mL; P = .004 and forced expiratory volume in 1 second, 143 mL higher; 95% CI, 11-274 mL; P = .034). CONCLUSIONS A common SNP in the NLRC4 inflammasome may modify TB-associated inflammation in clinically relevant ways. This SNP may identify high-risk groups for lung damage in TB. Inhibition of NLRC4 activity may be an important approach for TB host-directed therapy.
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Affiliation(s)
- Shruthi Ravimohan
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Sara C Auld
- Department of Medicine, Emory University Rollins School of Public Health and School of Medicine, Atlanta, Georgia, USA, Johannesburg, South Africa
| | - Itai Ncube
- The Aurum Institute, Johannesburg, South Africa
| | | | - William Chase
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Caroline T Tiemessen
- Centre for HIV-1 and STIs, National Institute for Communicable Diseases, and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mboyo-Di-Tamba Vangu
- Nuclear Medicine, CM Johannesburg Academic Hospital, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Gavin Churchyard
- The Aurum Institute, Johannesburg, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Drew Weissman
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hardy Kornfeld
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Gregory P Bisson
- Department of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biostatistics, Epidemiology, and Informatics, Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Lv J, Jiang X, Zhang J, Peng X, Lin H. Combined polymorphisms in genes encoding the inflammasome components NLRP3 and CARD8 confer risk of ischemic stroke in men. J Stroke Cerebrovasc Dis 2020; 29:104874. [PMID: 32689633 DOI: 10.1016/j.jstrokecerebrovasdis.2020.104874] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 03/23/2020] [Accepted: 04/05/2020] [Indexed: 11/30/2022] Open
Abstract
INTRODUCTION Previous studies have reported the involvement of nucleotide-binding domain (NOD)-like receptor protein 3 (NLRP3) inflammasome in the inflammatory activation and pathophysiology of Ischemic Stroke (IS). Variations in genes encoding the constituent proteins of NLRP3 inflammasome can alter the risk of IS. OBJECTIVE We investigated the role of the NLRP3 inflammasome in the pathogenesis of IS by establishing associations between combined polymorphisms of caspase recruitment domain-containing protein 8 (CARD8) rs2043211 and NLRP3 rs10754558 and the susceptibility to IS in a Chinese population. METHODS Single nucleotide polymorphisms (SNPs) in CARD8 rs2043211 and NLRP3 rs10754558 were analyzed using TaqMan SNP genotyping assays in patients with IS (n=234) and healthy controls (n=115). Logistic regression analysis was carried out to evaluate potential interactions between CARD8 and NLRP3. RESULTS Compared with healthy controls, there were no significant differences in the minor allele frequency (MAF) and the genotype frequency of NLRP3 rs10754558 or CARD8 rs2043211 in patients with IS(P>0.05). After stratification by gender, there was an increased risk for IS in men carrying heterozygous CARD8 rs2043211 when a co-dominant genetic model was applied (P=0.021, OR=3.83[1.22-12.03]). Logistic regression analysis indicated that men carrying both CARD8 rs2043211 AT and NLRP3 rs10754558 CG had a significantly higher risk of IS (P=0.046, OR=7.116[1.033-49.044]). CONCLUSIONS Nucleotide variations in the genes encoding NLRP3 inflammasome proteins may be important to IS, and men carrying CARD8 rs2043211 and NLRP3 rs10754558, both heterozygous, confer a higher risk of IS.
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Affiliation(s)
- Jie Lv
- Department of Neurology, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, Guangxi, China.
| | - Xiaoshan Jiang
- Cell Signaling Laboratory, Guilin Medical University, Guilin, Guangxi, China.
| | - Jing Zhang
- Medical laboratory center, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, Guangxi, China.
| | - Xianghui Peng
- Medical imaging department, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, Guangxi, China.
| | - Hongmei Lin
- Department of Neurology, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, Guangxi, China.
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Xu H, Li B. Relationship of CARD8 Gene Polymorphisms with Susceptibility to Ankylosing Spondylitis: A Case-Control Study. MEDICAL SCIENCE MONITOR : INTERNATIONAL MEDICAL JOURNAL OF EXPERIMENTAL AND CLINICAL RESEARCH 2020; 26:e916935. [PMID: 32080163 PMCID: PMC7055193 DOI: 10.12659/msm.916935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND The aim of this case-control study was to evaluate the correlation of caspase recruitment domain-containing protein 8 (CARD8) gene rs2043211 (exon) and rs7253718 (intron) polymorphisms with the susceptibility of ankylosing spondylitis (AS) in the Chinese Han population. MATERIAL AND METHODS CARD8 polymorphisms were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in 118 AS patients and 122 healthy persons. Linkage disequilibrium (LD) and haplotype analysis were carried out using Haploview software. Distribution differences of genotypes, alleles and haplotypes between the case and control groups were tested by chi-square test. Relative risk of AS was expressed by odds ratios (ORs) and 95% confidence intervals (CIs). Logistic regression analysis was used to adjust the results of association by clinical parameters. RESULTS For rs2043211, distribution of variant allele T was obviously different between AS patients and healthy controls (P=0.046). It indicated that T allele might increase the susceptibility of AS (OR=1.441, 95%CI=1.006-2.065). Adjusted by clinical characteristics, the significance of difference was slightly decreased (P=0.050, OR=1.439, 95%CI=0.999-2.072). Strong LD existed between rs2043211 and rs7253718 polymorphisms, and rs2043211T-rs7253718G haplotype was significantly associated with increased AS susceptibility (OR=1.787, 95%CI=1.165-2.740). In subgroup analysis, we found that the TT genotype and T allele of rs2043211 significantly increased the risk of AS in males (TT versus AA: OR=2.554, 95%CI=1.079-6.049; T versus A: OR=1.661, 95%CI=1.067-2.586), but not females. CONCLUSIONS CARD8 polymorphisms are likely to be associated with the elevated susceptibility of AS. Present results should be confirmed in the future studies.
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Affiliation(s)
- Haitao Xu
- Department of Orthopaedic, The Yongchuan Hospital of Chongqing Medical University, Chongqing, China (mainland)
| | - Bo Li
- Department of Orthopaedic, The Yongchuan Hospital of Chongqing Medical University, Chongqing, China (mainland)
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QTL Mapping of Intestinal Neutrophil Variation in Threespine Stickleback Reveals Possible Gene Targets Connecting Intestinal Inflammation and Systemic Health. G3-GENES GENOMES GENETICS 2020; 10:613-622. [PMID: 31843804 PMCID: PMC7003091 DOI: 10.1534/g3.119.400685] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Selection, via host immunity, is often required to foster beneficial microbial symbionts and suppress deleterious pathogens. In animals, the host immune system is at the center of this relationship. Failed host immune system-microbial interactions can result in a persistent inflammatory response in which the immune system indiscriminately attacks resident microbes, and at times the host cells themselves, leading to diseases such as Ulcerative Colitis, Crohn’s Disease, and Psoriasis. Host genetic variation has been linked to both microbiome diversity and to severity of such inflammatory disease states in humans. However, the microbiome and inflammatory states manifest as quantitative traits, which encompass many genes interacting with one another and the environment. The mechanistic relationships among all of these interacting components are still not clear. Developing natural genetic models of host-microbe interactions is therefore fundamental to understanding the complex genetics of these and other diseases. Threespine stickleback (Gasterosteus aculeatus) fish are a tractable model for attacking this problem because of abundant population-level genetic and phenotypic variation in the gut inflammatory response. Previous work in our laboratory identified genetically divergent stickleback populations exhibiting differences in intestinal neutrophil activity. We took advantage of this diversity to genetically map variation in an emblematic element of gut inflammation - intestinal neutrophil recruitment - using an F2-intercross mapping framework. We identified two regions of the genome associated with increased intestinal inflammation containing several promising candidate genes. Within these regions we found candidates in the Coagulation/Complement System, NFkB and MAPK pathways along with several genes associated with intestinal diseases and neurological diseases commonly accompanying intestinal inflammation as a secondary symptom. These findings highlight the utility of using naturally genetically diverse ‘evolutionary mutant models’ such as threespine stickleback to better understand interactions among host genetic diversity and microbiome variation in health and disease states.
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26
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Gibbs KD, Washington EJ, Jaslow SL, Bourgeois JS, Foster MW, Guo R, Brennan RG, Ko DC. The Salmonella Secreted Effector SarA/SteE Mimics Cytokine Receptor Signaling to Activate STAT3. Cell Host Microbe 2019; 27:129-139.e4. [PMID: 31901521 DOI: 10.1016/j.chom.2019.11.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/05/2019] [Accepted: 11/21/2019] [Indexed: 01/18/2023]
Abstract
Bacteria masterfully co-opt and subvert host signal transduction. As a paradigmatic example, Salmonella uses two type-3 secretion systems to inject effector proteins that facilitate Salmonella entry, establishment of an intracellular niche, and modulation of immune responses. We previously demonstrated that the Salmonella anti-inflammatory response activator SarA (Stm2585, GogC, PagJ, SteE) activates the host transcription factor STAT3 to drive expression of immunomodulatory STAT3-targets. Here, we demonstrate-by sequence, function, and biochemical measurement-that SarA mimics the cytoplasmic domain of glycoprotein 130 (gp130, IL6ST). SarA is phosphorylated at a YxxQ motif, facilitating binding to STAT3 with greater affinity than gp130. Departing from canonical gp130 signaling, SarA function is JAK-independent but requires GSK-3, a key regulator of metabolism and development. Our results reveal that SarA undergoes host phosphorylation to recruit a STAT3-activating complex, circumventing cytokine receptor activation. Effector mimicry of gp130 suggests GSK-3 can regulate normal cytokine signaling, potentially enabling metabolic and immune crosstalk.
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Affiliation(s)
- Kyle D Gibbs
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Erica J Washington
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Sarah L Jaslow
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Jeffrey S Bourgeois
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA; Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Matthew W Foster
- Duke Proteomics and Metabolomics Shared Resource, Duke University Medical Center, Durham, NC 27710, USA
| | - Robyn Guo
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Richard G Brennan
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA; Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA.
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27
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Genetic and Epigenetic Regulation of Immune Response and Resistance to Infectious Diseases in Domestic Ruminants. Vet Clin North Am Food Anim Pract 2019; 35:405-429. [PMID: 31590895 DOI: 10.1016/j.cvfa.2019.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Infectious diseases are the outcome of complex interactions between the host, pathogen, and environment. After exposure to a pathogen, the host immune system uses various mechanisms to remove the pathogen. However, environmental factors and characteristics of pathogens can compromise the host immune responses and subsequently alter the outcome of infection. In this article, genetic and epigenetic factors that shape the individual variation in mounting protective responses are reviewed. Different approaches that have been used by researchers to investigate the genetic regulation of immunity in ruminants and various sources of genetic information are discussed.
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Abstract
ABSTRACT
The rapid development of genomics and other “-omics” approaches has significantly impacted how we have investigated host-pathogen interactions since the turn of the millennium. Technologies such as next-generation sequencing, stem cell biology, and high-throughput proteomics have transformed the scale and sensitivity with which we interrogate biological samples. These approaches are impacting experimental design in the laboratory and transforming clinical management in health care systems. Here, we review this area from the perspective of research on bacterial pathogens.
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Inflammasome Genes' Polymorphisms in Egyptian Chronic Hepatitis C Patients: Influence on Vulnerability to Infection and Response to Treatment. Mediators Inflamm 2019; 2019:3273645. [PMID: 30728751 PMCID: PMC6343134 DOI: 10.1155/2019/3273645] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 12/09/2018] [Indexed: 12/12/2022] Open
Abstract
Chronic inflammation is a pivotal contributor to the liver damage mediated by hepatitis C virus (HCV). The NOD-like receptor, pyrin domain-containing 3 (NLRP3) inflammasome is activated by HCV in both hepatocytes and Kupffer cells. The aim of our study was to investigate the association of nine single-nucleotide polymorphisms in four inflammasome genes (NLRP3, CARD8, IL-1β, and IL-18) with the susceptibility to HCV infection and outcome of interferon treatment in 201 Egyptian chronic hepatitis C patients and 95 healthy controls. The genotyping was conducted using TaqMan predesigned SNP assay. In the comparative analysis, the CC genotype of the NLRP3 rs1539019 was found to be associated with the lower risk to chronic HCV infection (OR: 0.33, 95% CI: 0.17-0.62). This association was also found for the CA genotype and the A allele of the NLRP3 rs35829419 (OR: 0.18 and 0.22, respectively), in addition to the GG genotype and G allele of IL-18 rs1946518 (OR: 0.55 and 0.61, respectively). In contrast, the AA genotype of the IL-1β rs1143629 was significantly more frequent in HCV patients (OR: 1.7, 95% CI: 1-2.86). Notably, the frequency of the AA genotype of NLRP3 rs1539019 was significantly higher in patients with lack of response (NR) to the interferon treatment (OR: 1.95, 95% CI: 1-3.7). A similar association was found for both the CC genotype and C allele of the NLRP3 rs35829419 (OR: 2.78 and 2.73, respectively) and for the TT genotype and T allele of CARD8 rs2043211 (OR: 2.64 and 1.54, respectively). Yet, the IL-1β (rs1143629, rs1143634) and IL-18 (rs187238, rs1946518) polymorphisms did not show any significant association with response to interferon treatment. In conclusion, this study reports, for the first time, the association of genetic variations in NLRP3 with hepatitis C susceptibility and response to treatment in Egyptian patients. However, further large-scale studies are recommended to confirm our findings.
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30
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Wang L, Pittman KJ, Barker JR, Salinas RE, Stanaway IB, Williams GD, Carroll RJ, Balmat T, Ingham A, Gopalakrishnan AM, Gibbs KD, Antonia AL, Heitman J, Lee SC, Jarvik GP, Denny JC, Horner SM, DeLong MR, Valdivia RH, Crosslin DR, Ko DC. An Atlas of Genetic Variation Linking Pathogen-Induced Cellular Traits to Human Disease. Cell Host Microbe 2018; 24:308-323.e6. [PMID: 30092202 PMCID: PMC6093297 DOI: 10.1016/j.chom.2018.07.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/28/2018] [Accepted: 07/05/2018] [Indexed: 12/18/2022]
Abstract
Pathogens have been a strong driving force for natural selection. Therefore, understanding how human genetic differences impact infection-related cellular traits can mechanistically link genetic variation to disease susceptibility. Here we report the Hi-HOST Phenome Project (H2P2): a catalog of cellular genome-wide association studies (GWAS) comprising 79 infection-related phenotypes in response to 8 pathogens in 528 lymphoblastoid cell lines. Seventeen loci surpass genome-wide significance for infection-associated phenotypes ranging from pathogen replication to cytokine production. We combined H2P2 with clinical association data from patients to identify a SNP near CXCL10 as a risk factor for inflammatory bowel disease. A SNP in the transcriptional repressor ZBTB20 demonstrated pleiotropy, likely through suppression of multiple target genes, and was associated with viral hepatitis. These data are available on a web portal to facilitate interpreting human genome variation through the lens of cell biology and should serve as a rich resource for the research community.
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Affiliation(s)
- Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Kelly J Pittman
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Jeffrey R Barker
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Raul E Salinas
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Ian B Stanaway
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Graham D Williams
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Robert J Carroll
- Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN 37212, USA
| | - Tom Balmat
- Social Science Research Institute, Duke University, Durham, NC 27710, USA
| | - Andy Ingham
- Duke Research Computing, Duke University, Durham, NC 27710, USA
| | - Anusha M Gopalakrishnan
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Kyle D Gibbs
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Alejandro L Antonia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Soo Chan Lee
- South Texas Center for Emerging Infectious Diseases (STCEID), Department of Biology, College of Sciences, the University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Gail P Jarvik
- Department of Medicine, Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN 37212, USA
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Mark R DeLong
- Duke Research Computing, Duke University, Durham, NC 27710, USA
| | - Raphael H Valdivia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA.
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Jaslow SL, Gibbs KD, Fricke WF, Wang L, Pittman KJ, Mammel MK, Thaden JT, Fowler VG, Hammer GE, Elfenbein JR, Ko DC. Salmonella Activation of STAT3 Signaling by SarA Effector Promotes Intracellular Replication and Production of IL-10. Cell Rep 2018; 23:3525-3536. [PMID: 29924996 PMCID: PMC6314477 DOI: 10.1016/j.celrep.2018.05.072] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 03/24/2018] [Accepted: 05/21/2018] [Indexed: 12/23/2022] Open
Abstract
Salmonella enterica is an important foodborne pathogen that uses secreted effector proteins to manipulate host pathways to facilitate survival and dissemination. Different S. enterica serovars cause disease syndromes ranging from gastroenteritis to typhoid fever and vary in their effector repertoire. We leveraged this natural diversity to identify stm2585, here designated sarA (Salmonella anti-inflammatory response activator), as a Salmonella effector that induces production of the anti-inflammatory cytokine IL-10. RNA-seq of cells infected with either ΔsarA or wild-type S. Typhimurium revealed that SarA activates STAT3 transcriptional targets. Consistent with this, SarA is necessary and sufficient for STAT3 phosphorylation, STAT3 inhibition blocks IL-10 production, and SarA and STAT3 interact by co-immunoprecipitation. These effects of SarA contribute to intracellular replication in vitro and bacterial load at systemic sites in mice. Our results demonstrate the power of using comparative genomics for identifying effectors and that Salmonella has evolved mechanisms for activating an important anti-inflammatory pathway.
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Affiliation(s)
- Sarah L Jaslow
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Kyle D Gibbs
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - W Florian Fricke
- Department of Nutrigenomics, University of Hohenheim, Stuttgart, Germany
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Kelly J Pittman
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Mark K Mammel
- Division of Molecular Biology, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Joshua T Thaden
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Vance G Fowler
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Gianna E Hammer
- Department of Immunology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Johanna R Elfenbein
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA.
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Ravimohan S, Nfanyana K, Tamuhla N, Tiemessen CT, Weissman D, Bisson GP. Common Variation in NLRP3 Is Associated With Early Death and Elevated Inflammasome Biomarkers Among Advanced HIV/TB Co-infected Patients in Botswana. Open Forum Infect Dis 2018; 5:ofy075. [PMID: 29732382 PMCID: PMC5928406 DOI: 10.1093/ofid/ofy075] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/06/2018] [Indexed: 12/20/2022] Open
Abstract
Background Elevated inflammation is associated with early mortality among HIV/tuberculosis (TB) patients starting antiretroviral therapy (ART); however, the sources of immune activation are unclear. We hypothesized that common variation in innate immune genes contributes to excessive inflammation linked to death. As single nucleotide polymorphisms (SNPs) in inflammasome pathway genes can increase risk for inflammatory diseases, we investigated their association with early mortality among a previously described cohort of HIV/TB patients initiating ART in Botswana. Methods We genotyped 8 SNPs within 5 inflammasome pathway genes and determined their association with death. For adjusted analyses, we used a logistic regression model. For SNPs associated with mortality, we explored their relationship with levels of systemic inflammatory markers using a linear regression model. Results Ninety-four patients in the parent study had samples for genetic analysis. Of these, 82 (87%) were survivors and 12 (13%) died within 6 months of starting ART. In a logistic regression model, NLRP3 rs10754558 was independently associated with a 4.1-fold increased odds of death (95% confidence interval, 1.04–16.5). In adjusted linear regression models, the NLRP3 rs10754558-G allele was linked to elevated IL-18 at baseline (Beta, 0.23; SE, 0.10; P = .033) and week 4 post-ART (Beta, 0.24; SE, 0.11; P = .026). This allele was associated with increased MCP-1 at baseline (Beta, 0.24; SE, 0.10; P = .02) and IL-10 (Beta, 0.27; SE, 0.11; P = .013) at week 4 post-ART. Conclusion The NLRP3 rs10754558-G SNP is associated with an increased risk for early mortality in HIV/TB patients initiating ART. These patients may benefit from therapies that decrease inflammasome-mediated inflammation.
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Affiliation(s)
- Shruthi Ravimohan
- Division of Infectious Diseases, Department of Medicine, Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Botswana-UPenn Partnership, Gaborone, Botswana
| | | | - Neo Tamuhla
- Botswana-UPenn Partnership, Gaborone, Botswana
| | - Caroline T Tiemessen
- Centre for HIV-1 and STIs, National Institute for Communicable Diseases, and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Drew Weissman
- Division of Infectious Diseases, Department of Medicine, Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Botswana-UPenn Partnership, Gaborone, Botswana
| | - Gregory P Bisson
- Division of Infectious Diseases, Department of Medicine, Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Botswana-UPenn Partnership, Gaborone, Botswana.,Department of Biostatistics, Epidemiology, and Informatics, Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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Small CM, Milligan-Myhre K, Bassham S, Guillemin K, Cresko WA. Host Genotype and Microbiota Contribute Asymmetrically to Transcriptional Variation in the Threespine Stickleback Gut. Genome Biol Evol 2017; 9:504-520. [PMID: 28391321 PMCID: PMC5381569 DOI: 10.1093/gbe/evx014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2017] [Indexed: 02/07/2023] Open
Abstract
Recent studies of interactions between hosts and their resident microbes have revealed important ecological and evolutionary consequences that emerge from these complex interspecies relationships, including diseases that occur when the interactions go awry. Given the preponderance of these interactions, we hypothesized that effects of the microbiota on gene expression in the developing gut—an important aspect of host biology—would be pervasive, and that these effects would be both comparable in magnitude to and contingent on effects of the host genetic background. To evaluate the effects of the microbiota, host genotype, and their interaction on gene expression in the gut of a genetically diverse, gnotobiotic host model, the threespine stickleback (Gasterosteus aculeatus), we compared RNA-seq data among 84 larval fish. Surprisingly, we found that stickleback population and family differences explained substantially more gene expression variation than the presence of microbes. Expression levels of 72 genes, however, were affected by our microbiota treatment. These genes, including many associated with innate immunity, comprise a tractable subset of host genetic factors for precise, systems-level study of host–microbe interactions in the future. Importantly, our data also suggest subtle signatures of a statistical interaction between host genotype and the microbiota on expression patterns of genetic pathways associated with innate immunity, coagulation and complement cascades, focal adhesion, cancer, and peroxisomes. These genotype-by-environment interactions may prove to be important leads to the understanding of host genetic mechanisms commonly at the root of sometimes complex molecular relationships between hosts and their resident microbes.
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Affiliation(s)
- Clayton M Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR
| | | | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR
| | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, OR
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR
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Mikacenic C, Price BL, Harju-Baker S, O'Mahony DS, Robinson-Cohen C, Radella F, Hahn WO, Katz R, Christiani DC, Himmelfarb J, Liles WC, Wurfel MM. A Two-Biomarker Model Predicts Mortality in the Critically Ill with Sepsis. Am J Respir Crit Care Med 2017; 196:1004-1011. [PMID: 28418697 DOI: 10.1164/rccm.201611-2307oc] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
RATIONALE Improving the prospective identification of patients with systemic inflammatory response syndrome (SIRS) and sepsis at low risk for organ dysfunction and death is a major clinical challenge. OBJECTIVES To develop and validate a multibiomarker-based prediction model for 28-day mortality in critically ill patients with SIRS and sepsis. METHODS A derivation cohort (n = 888) and internal test cohort (n = 278) were taken from a prospective study of critically ill intensive care unit (ICU) patients meeting two of four SIRS criteria at an academic medical center for whom plasma was obtained within 24 hours. The validation cohort (n = 759) was taken from a prospective cohort enrolled at another academic medical center ICU for whom plasma was obtained within 48 hours. We measured concentrations of angiopoietin-1, angiopoietin-2, IL-6, IL-8, soluble tumor necrosis factor receptor-1, soluble vascular cell adhesion molecule-1, granulocyte colony-stimulating factor, and soluble Fas. MEASUREMENTS AND MAIN RESULTS We identified a two-biomarker model in the derivation cohort that predicted mortality (area under the receiver operator characteristic curve [AUC], 0.79; 95% confidence interval [CI], 0.74-0.83). It performed well in the internal test cohort (AUC, 0.75; 95% CI, 0.65-0.85) and the external validation cohort (AUC, 0.77; 95% CI, 0.72-0.83). We determined a model score threshold demonstrating high negative predictive value (0.95) for death. In addition to a low risk of death, patients below this threshold had shorter ICU length of stay, lower incidence of acute kidney injury, acute respiratory distress syndrome, and need for vasopressors. CONCLUSIONS We have developed a simple, robust biomarker-based model that identifies patients with SIRS/sepsis at low risk for death and organ dysfunction.
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Affiliation(s)
- Carmen Mikacenic
- 1 Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | | | | | - D Shane O'Mahony
- 3 Department of Pulmonary and Critical Care Medicine, Swedish Medical Center, Seattle, Washington
| | | | - Frank Radella
- 1 Division of Pulmonary and Critical Care Medicine, Department of Medicine
| | - William O Hahn
- 5 Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington
| | | | - David C Christiani
- 6 Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; and.,7 Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts
| | | | - W Conrad Liles
- 5 Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington
| | - Mark M Wurfel
- 1 Division of Pulmonary and Critical Care Medicine, Department of Medicine
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Human genetic variation in VAC14 regulates Salmonella invasion and typhoid fever through modulation of cholesterol. Proc Natl Acad Sci U S A 2017; 114:E7746-E7755. [PMID: 28827342 DOI: 10.1073/pnas.1706070114] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Risk, severity, and outcome of infection depend on the interplay of pathogen virulence and host susceptibility. Systematic identification of genetic susceptibility to infection is being undertaken through genome-wide association studies, but how to expeditiously move from genetic differences to functional mechanisms is unclear. Here, we use genetic association of molecular, cellular, and human disease traits and experimental validation to demonstrate that genetic variation affects expression of VAC14, a phosphoinositide-regulating protein, to influence susceptibility to Salmonella enterica serovar Typhi (S Typhi) infection. Decreased VAC14 expression increased plasma membrane cholesterol, facilitating Salmonella docking and invasion. This increased susceptibility at the cellular level manifests as increased susceptibility to typhoid fever in a Vietnamese population. Furthermore, treating zebrafish with a cholesterol-lowering agent, ezetimibe, reduced susceptibility to S Typhi. Thus, coupling multiple genetic association studies with mechanistic dissection revealed how VAC14 regulates Salmonella invasion and typhoid fever susceptibility and may open doors to new prophylactic/therapeutic approaches.
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36
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Bhatraju PK, Robinson-Cohen C, Mikacenic C, Harju-Baker S, Dmyterko V, Slivinski NSJ, Liles WC, Himmelfarb J, Heckbert SR, Wurfel MM. Circulating levels of soluble Fas (sCD95) are associated with risk for development of a nonresolving acute kidney injury subphenotype. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2017; 21:217. [PMID: 28814331 PMCID: PMC5559814 DOI: 10.1186/s13054-017-1807-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/01/2017] [Indexed: 12/16/2022]
Abstract
Background Critically ill patients with acute kidney injury (AKI) can be divided into two subphenotypes, resolving or nonresolving, on the basis of the trajectory of serum creatinine. It is unknown if the biology underlying these two AKI recovery patterns is different. Methods We measured eight circulating biomarkers in plasma obtained from a cohort of patients admitted to an intensive care unit (ICU) (n = 1241) with systemic inflammatory response syndrome. The biomarkers were representative of several biologic processes: apoptosis (soluble Fas), inflammation (soluble tumor necrosis factor receptor 1, interleukin 6, interleukin 8) and endothelial dysfunction, (angiopoietin 1, angiopoietin 2, and soluble vascular cell adhesion molecule 1). We tested for associations between biomarker levels and AKI subphenotypes using relative risk regression accounting for multiple hypotheses with the Bonferroni correction. Results During the first 3 days of ICU admission, 868 (70%) subjects developed AKI; 502 (40%) had a resolving subphenotype, and 366 (29%) had a nonresolving subphenotype. Hospital mortality was 12% in the resolving subphenotype and 21% in the nonresolving subphenotype. Soluble Fas was the only biomarker associated with a nonresolving subphenotype after adjustment for age, body mass index, diabetes, and Acute Physiology and Chronic Health Evaluation III score (p = 0.005). Conclusions Identifying modifiable targets in the Fas-mediated pathway may lead to strategies for prevention and treatment of a clinically important form of AKI. Electronic supplementary material The online version of this article (doi:10.1186/s13054-017-1807-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pavan K Bhatraju
- Pulmonary and Critical Care Medicine, University of Washington, Harborview Medical Center, 325 9th Avenue, Seattle, WA, 98104, USA.
| | | | - Carmen Mikacenic
- Pulmonary and Critical Care Medicine, University of Washington, Harborview Medical Center, 325 9th Avenue, Seattle, WA, 98104, USA
| | - Susanna Harju-Baker
- Pulmonary and Critical Care Medicine, University of Washington, Harborview Medical Center, 325 9th Avenue, Seattle, WA, 98104, USA
| | - Victoria Dmyterko
- Pulmonary and Critical Care Medicine, University of Washington, Harborview Medical Center, 325 9th Avenue, Seattle, WA, 98104, USA
| | | | - W Conrad Liles
- Department of Medicine, University of Washington, Harborview Medical Center, Seattle, WA, USA
| | - Jonathan Himmelfarb
- Kidney Research Institute, Division of Nephrology, University of Washington, Seattle, WA, USA
| | - Susan R Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Mark M Wurfel
- Pulmonary and Critical Care Medicine, University of Washington, Harborview Medical Center, 325 9th Avenue, Seattle, WA, 98104, USA
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Wang L, Ko ER, Gilchrist JJ, Pittman KJ, Rautanen A, Pirinen M, Thompson JW, Dubois LG, Langley RJ, Jaslow SL, Salinas RE, Rouse DC, Moseley MA, Mwarumba S, Njuguna P, Mturi N, Williams TN, Scott JAG, Hill AVS, Woods CW, Ginsburg GS, Tsalik EL, Ko DC. Human genetic and metabolite variation reveals that methylthioadenosine is a prognostic biomarker and an inflammatory regulator in sepsis. SCIENCE ADVANCES 2017; 3:e1602096. [PMID: 28345042 PMCID: PMC5342653 DOI: 10.1126/sciadv.1602096] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/03/2017] [Indexed: 06/06/2023]
Abstract
Sepsis is a deleterious inflammatory response to infection with high mortality. Reliable sepsis biomarkers could improve diagnosis, prognosis, and treatment. Integration of human genetics, patient metabolite and cytokine measurements, and testing in a mouse model demonstrate that the methionine salvage pathway is a regulator of sepsis that can accurately predict prognosis in patients. Pathway-based genome-wide association analysis of nontyphoidal Salmonella bacteremia showed a strong enrichment for single-nucleotide polymorphisms near the components of the methionine salvage pathway. Measurement of the pathway's substrate, methylthioadenosine (MTA), in two cohorts of sepsis patients demonstrated increased plasma MTA in nonsurvivors. Plasma MTA was correlated with levels of inflammatory cytokines, indicating that elevated MTA marks a subset of patients with excessive inflammation. A machine-learning model combining MTA and other variables yielded approximately 80% accuracy (area under the curve) in predicting death. Furthermore, mice infected with Salmonella had prolonged survival when MTA was administered before infection, suggesting that manipulating MTA levels could regulate the severity of the inflammatory response. Our results demonstrate how combining genetic data, biomolecule measurements, and animal models can shape our understanding of disease and lead to new biomarkers for patient stratification and potential therapeutic targeting.
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Affiliation(s)
- Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Emily R. Ko
- Duke Regional Hospital, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, School of Medicine, Duke University, Durham, NC 27708, USA
| | - James J. Gilchrist
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, U.K
- Department of Paediatrics, University of Oxford, Oxford OX3 9DU, U.K
| | - Kelly J. Pittman
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Anna Rautanen
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, U.K
| | - Matti Pirinen
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, U.K
| | - J. Will Thompson
- Proteomics and Metabolomics Core Facility, Duke University Medical Center, Durham, NC 27710, USA
| | - Laura G. Dubois
- Proteomics and Metabolomics Core Facility, Duke University Medical Center, Durham, NC 27710, USA
| | - Raymond J. Langley
- Department of Pharmacology and Center for Lung Biology, University of South Alabama College of Medicine, Mobile, AL 36688, USA
| | - Sarah L. Jaslow
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Raul E. Salinas
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - D. Clayburn Rouse
- Division of Laboratory Animal Resources, Duke University Medical Center, Durham, NC 27710, USA
| | - M. Arthur Moseley
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, School of Medicine, Duke University, Durham, NC 27708, USA
- Proteomics and Metabolomics Core Facility, Duke University Medical Center, Durham, NC 27710, USA
| | - Salim Mwarumba
- Kenya Medical Research Institute–Wellcome Trust Clinical Research Programme, Kilifi 80108, Kenya
| | - Patricia Njuguna
- Kenya Medical Research Institute–Wellcome Trust Clinical Research Programme, Kilifi 80108, Kenya
| | - Neema Mturi
- Kenya Medical Research Institute–Wellcome Trust Clinical Research Programme, Kilifi 80108, Kenya
| | | | | | - Thomas N. Williams
- Kenya Medical Research Institute–Wellcome Trust Clinical Research Programme, Kilifi 80108, Kenya
- Department of Medicine, Imperial College, Norfolk Place, London W2 1PG, U.K
| | - J. Anthony G. Scott
- Kenya Medical Research Institute–Wellcome Trust Clinical Research Programme, Kilifi 80108, Kenya
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, U.K
| | - Adrian V. S. Hill
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford OX3 7BN, U.K
- Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, U.K
| | - Christopher W. Woods
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, School of Medicine, Duke University, Durham, NC 27708, USA
- Division of Infectious Diseases and International Health, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
- Medical Service, Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
| | - Geoffrey S. Ginsburg
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, School of Medicine, Duke University, Durham, NC 27708, USA
| | - Ephraim L. Tsalik
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, School of Medicine, Duke University, Durham, NC 27708, USA
- Division of Infectious Diseases and International Health, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
- Emergency Medicine Service, Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
| | - Dennis C. Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
- Division of Infectious Diseases and International Health, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
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Wang H, Hua M, Wang S, Yu J, Chen C, Zhao X, Zhang C, Zhong C, Wang R, He N, Hou M, Ma D. Genetic polymorphisms of IL-18 rs1946518 and IL-1β rs16944 are associated with prognosis and survival of acute myeloid leukemia. Inflamm Res 2016; 66:249-258. [PMID: 27928589 DOI: 10.1007/s00011-016-1012-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 11/16/2016] [Accepted: 11/22/2016] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Though the pathogenesis of AML is still unknown, accumulating evidence revealed that immune response plays a vital part in it. NLRP3 inflammasome as a component of immune system has been found related to several cancers. The single nucleotide polymorphisms (SNPs) of NLRP3 inflammasome genes may be related to pathogenesis and prognosis of AML. METHODS AND RESULTS We determined polymorphisms of NLRP3 (rs35829419), CARD8 (rs2043211), IL-1β (rs16944), IL-18 (rs1946518) and NF-κB -94 ins/del ATTG in de novo AML patients to find out whether they play roles in the susceptibility and severity of AML. In our study, 383 AML cases and 300 randomly selected healthy individuals were examined for the polymorphisms and expression of NLRP3 genes. IL-1β (rs16944) polymorphism in different risk AML subgroups was found statistically different, with more GA genotype in favorable-risk cytogenetics group. We also demonstrated that the bone marrow blasts of patients carrying IL-18 (rs1946518) GG or GT genotype were higher than patients of TT genotype. IL-18 plasma level of patients with IL-18 (rs1946518) GT or TT genotype was higher than GG genotype. Moreover, the GT genotype of IL-18 (rs1946518) led to statistically poorer AML-specific survival. CONCLUSION IL-1β (rs16944) and IL-18 (rs1946518) may be served as potential predictors for AML.
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Affiliation(s)
- Hong Wang
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China.,Department of Hematology, Zibo Central Hospital, Zibo, Shandong, People's Republic of China
| | - Mingqiang Hua
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China
| | - Shukang Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Shandong University, Jinan, People's Republic of China
| | - Jie Yu
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China
| | - Chen Chen
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China
| | - Xueyun Zhao
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China
| | - Chen Zhang
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China
| | - Chaoqin Zhong
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China
| | - Ruiqing Wang
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China
| | - Na He
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China
| | - Ming Hou
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China
| | - Daoxin Ma
- Department of Hematology, Qilu Hospital, Shandong University, 107 West Wenhua Rd, Jinan, 250012, People's Republic of China.
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da Silva WC, Oshiro TM, de Sá DC, Franco DDGS, Festa Neto C, Pontillo A. Genotyping and differential expression analysis of inflammasome genes in sporadic malignant melanoma reveal novel contribution of CARD8, IL1B and IL18 in melanoma susceptibility and progression. Cancer Genet 2016; 209:474-480. [PMID: 27810076 DOI: 10.1016/j.cancergen.2016.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/30/2016] [Accepted: 09/08/2016] [Indexed: 10/21/2022]
Abstract
Sporadic melanoma malignancy is correlated with constitutive secretion of IL-1β in transformed melanocytes suggesting the involvement of inflammasome in melanoma. Common variants in inflammasome genes are known to affect IL-1β expression. To investigate the contribution of inflammasome genetics in melanoma development and progression and to identify a potential prognostic marker, the distribution of selected inflammasome SNPs was analysed in a Brazilian case/control cohort of sporadic malignant melanoma (SMM) and then the expression of inflammasome components was evaluated in melanoma biopsies. Allele and gene-specific Taqman assays were implied for genotyping of case/control DNA samples and for relative expression analysis in skin biopsies respectively. CARD8 rs6509365 was found to be significantly more common in healthy volunteers than in SMM patients suggesting a protection effect of this variant towards melanoma development. Accordingly, CARD8 expression was found to be reduced in nevus compared to melanoma biopsies. Upon stratification, NLRP1 rs11651270 and CARD8 rs2043211 were found associated with nodular melanoma; IL1B rs1143643 to a lower value of Breslow index; IL18 rs5744256 to melanoma development in sun sensitive individuals. As expected, IL1B expression was up-regulated in tumour biopsies especially in metastatic samples, whereas IL18 was down-regulated compared to nevus. Our results demonstrated for the first time the contribution of inflammasome genes CARD8, IL1B and IL18 in SMM.
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Affiliation(s)
- Wanessa Cardoso da Silva
- Laboratory of Medical Investigation in Dermatology and Immunodeficiences-LIM 56, Department of Dermatology, Faculty of Medicine, University of Sao Paulo, Avenida Dr Eneas de Carvalho Aguiar, 470 - Prédio 2-3° andar, 05403-000 Cerqueira César, Sao Paulo, Brazil.
| | - Telma Miyuki Oshiro
- Laboratory of Medical Investigation in Dermatology and Immunodeficiences-LIM 56, Department of Dermatology, Faculty of Medicine, University of Sao Paulo, Avenida Dr Eneas de Carvalho Aguiar, 470 - Prédio 2-3° andar, 05403-000 Cerqueira César, Sao Paulo, Brazil
| | - Daniel Coelho de Sá
- Department of Dermatology, Faculty of Medicine, University of Sao Paulo, Avenida Dr. Eneas de Carvalho Aguiar 500, 05403-000 Cerqueira Cesar, Sao Paulo, Brazil
| | - Dilcilea D G S Franco
- Department of Dermatology, Faculty of Medicine, University of Sao Paulo, Avenida Dr. Eneas de Carvalho Aguiar 500, 05403-000 Cerqueira Cesar, Sao Paulo, Brazil
| | - Cyro Festa Neto
- Department of Dermatology, Faculty of Medicine, University of Sao Paulo, Avenida Dr. Eneas de Carvalho Aguiar 500, 05403-000 Cerqueira Cesar, Sao Paulo, Brazil
| | - Alessandra Pontillo
- Laboratory of Immunogenetics, Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo, Avenida Prof. Lineu Prestes 1730, 05508-000 Cidade Universitaria, Sao Paulo, Brazil
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Pittman KJ, Glover LC, Wang L, Ko DC. The Legacy of Past Pandemics: Common Human Mutations That Protect against Infectious Disease. PLoS Pathog 2016; 12:e1005680. [PMID: 27442518 PMCID: PMC4956310 DOI: 10.1371/journal.ppat.1005680] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Kelly J. Pittman
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Luke C. Glover
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Dennis C. Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, United States of America
- Department of Medicine, School of Medicine, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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Ferwerda B, Valls Serón M, Jongejan A, Zwinderman AH, Geldhoff M, van der Ende A, Baas F, Brouwer MC, van de Beek D. Variation of 46 Innate Immune Genes Evaluated for their Contribution in Pneumococcal Meningitis Susceptibility and Outcome. EBioMedicine 2016; 10:77-84. [PMID: 27432718 PMCID: PMC5006661 DOI: 10.1016/j.ebiom.2016.07.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/08/2016] [Accepted: 07/11/2016] [Indexed: 01/06/2023] Open
Abstract
Pneumococcal meningitis is the most common and severe form of bacterial meningitis. Early recognition of the pathogen and subsequent innate immune response play a vital role in disease susceptibility and outcome. Genetic variations in innate immune genes can alter the immune response and influence susceptibility and outcome of meningitis disease. Here we conducted a sequencing study of coding regions from 46 innate immune genes in 435 pneumococcal meningitis patients and 416 controls, to determine the role of genetic variation on pneumococcal meningitis susceptibility and disease outcome. Strongest signals for susceptibility were rs56078309 CXCL1 (p=4.8e-04) and rs2008521 in CARD8 (p=6.1e-04). For meningitis outcome the rs2067085 in NOD2 (p=5.1e-04) and rs4251552 of IRAK4 were the strongest associations with unfavorable outcome (p=6.7e-04). Haplotype analysis showed a haplotype block, determined by IRAK4 rs4251552, significantly associated with unfavorable outcome (p=0.004). Cytokine measurements from cerebrospinal fluid showed that with the IRAK4 rs4251552 G risk allele had higher levels of IL-6 compared to individuals with A/A genotype (p=0.04). We show that genetic variation within exons and flanking regions of 46 innate immunity genes does not yield significant association with pneumococcal meningitis. The strongest identified signal IRAK4 does imply a potential role of genetic variation in pneumococcal meningitis.
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Affiliation(s)
- Bart Ferwerda
- Department of Neurology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, P.O. Box 22660, Amsterdam, The Netherlands
| | - Mercedes Valls Serón
- Department of Neurology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, P.O. Box 22660, Amsterdam, The Netherlands
| | - Aldo Jongejan
- Bioinformatics Laboratory, Academic Medical Center, P.O. Box 22660, Amsterdam, The Netherlands
| | - Aeilko H Zwinderman
- Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Academic Medical Center, University of Amsterdam, P.O. Box 22660, Amsterdam, The Netherlands
| | - Madelijn Geldhoff
- Department of Neurology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, P.O. Box 22660, Amsterdam, The Netherlands
| | - Arie van der Ende
- Department of Medical Microbiology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, P.O. Box 22660, Amsterdam, The Netherlands; The Netherlands Reference Laboratory for Bacterial Meningitis, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, P.O. Box 22660, Amsterdam, The Netherlands
| | - Frank Baas
- Department of Clinical Genetics, Academic Medical Center, P.O. Box 22660, Amsterdam, The Netherlands
| | - Matthijs C Brouwer
- Department of Neurology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, P.O. Box 22660, Amsterdam, The Netherlands
| | - Diederik van de Beek
- Department of Neurology, Center of Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, P.O. Box 22660, Amsterdam, The Netherlands.
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Inflammasome genetics contributes to the development and control of active pulmonary tuberculosis. INFECTION GENETICS AND EVOLUTION 2016; 41:240-244. [DOI: 10.1016/j.meegid.2016.04.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 04/12/2016] [Accepted: 04/13/2016] [Indexed: 12/16/2022]
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Chaudhary A, Leite M, Kulasekara BR, Altura MA, Ogahara C, Weiss E, Fu W, Blanc MP, O'Keeffe M, Terhorst C, Akey JM, Miller SI. Human Diversity in a Cell Surface Receptor that Inhibits Autophagy. Curr Biol 2016; 26:1791-801. [PMID: 27345162 DOI: 10.1016/j.cub.2016.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 04/27/2016] [Accepted: 05/03/2016] [Indexed: 02/01/2023]
Abstract
Mutations in genes encoding autophagy proteins have been associated with human autoimmune diseases, suggesting that diversity in autophagy responses could be associated with disease susceptibility or severity. A cellular genome-wide association study (GWAS) screen was performed to explore normal human diversity in responses to rapamycin, a microbial product that induces autophagy. Cells from several human populations demonstrated variability in expression of a cell surface receptor, CD244 (SlamF4, 2B4), that correlated with changes in rapamycin-induced autophagy. High expression of CD244 and receptor activation with its endogenous ligand CD48 inhibited starvation- and rapamycin-induced autophagy by promoting association of CD244 with the autophagy complex proteins Vps34 and Beclin-1. The association of CD244 with this complex reduced Vps34 lipid kinase activity. Lack of CD244 is associated with auto-antibody production in mice, and lower expression of human CD244 has previously been implicated in severity of human rheumatoid arthritis and systemic lupus erythematosus, indicating that increased autophagy as a result of low levels of CD244 may alter disease outcomes.
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Affiliation(s)
- Anu Chaudhary
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Mara Leite
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | | | - Melissa A Altura
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Cassandra Ogahara
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Eli Weiss
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Wenqing Fu
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Marie-Pierre Blanc
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Michael O'Keeffe
- Division of Immunology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Cox Terhorst
- Division of Immunology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Joshua M Akey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Samuel I Miller
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA; Department of Immunology, University of Washington, Seattle, WA 98195, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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Miller SI, Chaudhary A. A Cellular GWAS Approach to Define Human Variation in Cellular Pathways Important to Inflammation. Pathogens 2016; 5:pathogens5020039. [PMID: 27128945 PMCID: PMC4931390 DOI: 10.3390/pathogens5020039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 04/07/2016] [Accepted: 04/21/2016] [Indexed: 12/17/2022] Open
Abstract
An understanding of common human diversity in innate immune pathways should be beneficial in understanding autoimmune diseases, susceptibility to infection, and choices of anti-inflammatory treatment. Such understanding could also result in definition of currently unknown components of human inflammation pathways. A cellular genome-wide association studies (GWAS) platform, termed Hi-HOST (High-throughput human in vitro susceptibility testing), was developed to assay in vitro cellular phenotypes of infection in genotyped lymphoblastoid cells from genetically diverse human populations. Hi-HOST allows for measurement of multiple host and pathogen parameters of infection/inflammation including: bacterial invasion and intracellular replication, host cell death, and cytokine production. Hi-HOST has been used to successfully define a significant portion of the heritable human diversity in inflammatory cell death in response to Salmonella typhimurium. It also led to the discovery of genetic variants important to protection against systemic inflammatory response syndrome (SIRS) and protection against death and bacteremia in individuals with SIRS. Our laboratory is currently using this platform to define human diversity in autophagy and the NLPR3 inflammasome pathways, and to define new components that can impact the expression of phenotypes related to these pathways.
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Affiliation(s)
- Samuel I Miller
- Department of Microbiology, Department of Immunology, Department of Medicine, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
| | - Anu Chaudhary
- Department of Microbiology, University of Washington, Seattle, WA 98195, USA.
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Mikacenic C, Hahn WO, Price BL, Harju-Baker S, Katz R, Kain KC, Himmelfarb J, Liles WC, Wurfel MM. Biomarkers of Endothelial Activation Are Associated with Poor Outcome in Critical Illness. PLoS One 2015; 10:e0141251. [PMID: 26492036 PMCID: PMC4619633 DOI: 10.1371/journal.pone.0141251] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 10/06/2015] [Indexed: 12/23/2022] Open
Abstract
Background Endothelial activation plays a role in organ dysfunction in the systemic inflammatory response syndrome (SIRS). Angiopoietin-1 (Ang-1) promotes vascular quiescence while angiopoietin-2 (Ang-2) mediates microvascular leak. Circulating levels of Ang-1 and Ang-2 in patients with SIRS could provide insight on risks for organ dysfunction and death distinct from inflammatory proteins. In this study, we determined if biomarkers of endothelial activation and inflammation exhibit independent associations with poor outcomes in SIRS. Methods We studied 943 critically ill patients with SIRS admitted to an Intensive Care Unit (ICU) of an academic medical center. We measured plasma levels of endothelial markers (Ang-1, Ang-2, soluble vascular cell adhesion molecule-1 (sVCAM-1)) and inflammatory markers (interleukin-6 (IL-6), interleukin-8 (IL-8), granulocyte-colony stimulating factor (G-CSF), soluble tumor necrosis factor receptor-1 (sTNFR-1)) within 24 hours of enrollment. We tested for associations between each marker and 28 day mortality, shock, and day 3 sequential organ failure assessment (SOFA) score. For 28 day mortality, we performed sensitivity analysis for those subjects with sepsis and those with sterile inflammation. We used multivariate models to adjust for clinical covariates and determine if associations identified with endothelial activation markers were independent of those observed with inflammatory markers. Results Higher levels of all biomarkers were associated with increased 28 day mortality except levels of Ang-1 which were associated with lower mortality. After adjustment for comorbidities and sTNFR-1 concentration, a doubling of Ang-1 concentration was associated with lower 28 day mortality (Odds ratio (OR) = 0.81; p<0.01), shock (OR = 0.82; p<0.001), and SOFA score (β = -0.50; p<0.001), while Ang-2 concentration was associated with increased mortality (OR = 1.55; p<0.001), shock (OR = 1.51; p<0.001), and SOFA score (β = +0.63; p<0.001). sVCAM-1 was not independently associated with SIRS outcomes. Conclusions In critically ill patients with SIRS, early measurements of Ang-1 and Ang-2 are associated with death and organ dysfunction independently of simultaneously-measured markers of inflammation.
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Affiliation(s)
- Carmen Mikacenic
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - William O. Hahn
- Department of Medicine, Division of Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Brenda L. Price
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Susanna Harju-Baker
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington, United States of America
| | - Ronit Katz
- Kidney Research Institute, University of Washington, Seattle, Washington, United States of America
| | - Kevin C. Kain
- Department of Medicine, Sandra Rotman Centre for Global Health, University Health Network-Toronto General Hospital and the Tropical Disease Unit, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan Himmelfarb
- Kidney Research Institute, University of Washington, Seattle, Washington, United States of America
| | - W. Conrad Liles
- Department of Medicine, Division of Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Mark M. Wurfel
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Washington, Seattle, Washington, United States of America
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Wang L, Oehlers SH, Espenschied ST, Rawls JF, Tobin DM, Ko DC. CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation. Genome Biol 2015; 16:190. [PMID: 26374098 PMCID: PMC4570686 DOI: 10.1186/s13059-015-0722-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/09/2015] [Indexed: 12/31/2022] Open
Abstract
Meta-analyses of genome-wide association studies (GWAS) have demonstrated that the same genetic variants can be associated with multiple diseases and other complex traits. We present software called CPAG (Cross-Phenotype Analysis of GWAS) to look for similarities between 700 traits, build trees with informative clusters, and highlight underlying pathways. Clusters are consistent with pre-defined groups and literature-based validation but also reveal novel connections. We report similarity between plasma palmitoleic acid and Crohn's disease and find that specific fatty acids exacerbate enterocolitis in zebrafish. CPAG will become increasingly powerful as more genetic variants are uncovered, leading to a deeper understanding of complex traits. CPAG is freely available at www.sourceforge.net/projects/CPAG/.
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Affiliation(s)
- Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, 27710, USA.
| | - Stefan H Oehlers
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, 27710, USA.
| | - Scott T Espenschied
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, 27710, USA.
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, 27710, USA.
| | - David M Tobin
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, 27710, USA.
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, 27710, USA. .,Department of Medicine and the Center for Human Genome Variation, School of Medicine, Duke University, Durham, NC, 27710, USA.
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Derrick T, Roberts CH, Last AR, Burr SE, Holland MJ. Trachoma and Ocular Chlamydial Infection in the Era of Genomics. Mediators Inflamm 2015; 2015:791847. [PMID: 26424969 PMCID: PMC4573990 DOI: 10.1155/2015/791847] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/05/2015] [Indexed: 12/19/2022] Open
Abstract
Trachoma is a blinding disease usually caused by infection with Chlamydia trachomatis (Ct) serovars A, B, and C in the upper tarsal conjunctiva. Individuals in endemic regions are repeatedly infected with Ct throughout childhood. A proportion of individuals experience prolonged or severe inflammatory episodes that are known to be significant risk factors for ocular scarring in later life. Continued scarring often leads to trichiasis and in-turning of the eyelashes, which causes pain and can eventually cause blindness. The mechanisms driving the chronic immunopathology in the conjunctiva, which largely progresses in the absence of detectable Ct infection in adults, are likely to be multifactorial. Socioeconomic status, education, and behavior have been identified as contributing to the risk of scarring and inflammation. We focus on the contribution of host and pathogen genetic variation, bacterial ecology of the conjunctiva, and host epigenetic imprinting including small RNA regulation by both host and pathogen in the development of ocular pathology. Each of these factors or processes contributes to pathogenic outcomes in other inflammatory diseases and we outline their potential role in trachoma.
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Affiliation(s)
- Tamsyn Derrick
- Department of Clinical Research, Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Chrissy h. Roberts
- Department of Clinical Research, Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Anna R. Last
- Department of Clinical Research, Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Sarah E. Burr
- Department of Clinical Research, Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Martin J. Holland
- Department of Clinical Research, Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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Role of genetic alterations in the NLRP3 and CARD8 genes in health and disease. Mediators Inflamm 2015; 2015:846782. [PMID: 25788762 PMCID: PMC4348606 DOI: 10.1155/2015/846782] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/05/2015] [Indexed: 12/30/2022] Open
Abstract
The complexity of a common inflammatory disease is influenced by multiple genetic and environmental factors contributing to the susceptibility of disease. Studies have reported that these exogenous and endogenous components may perturb the balance of innate immune response by activating the NLRP3 inflammasome. The multimeric NLRP3 complex results in the caspase-1 activation and the release of potent inflammatory cytokines, like IL-1β. Several studies have been performed on the association of the genetic alterations in genes encoding NLRP3 and CARD8 with the complex diseases with inflammatory background, like inflammatory bowel disease, cardiovascular diseases, rheumatoid arthritis, and type 1 diabetes. The aim of the present review is therefore to summarize the literature regarding genetic alterations in these genes and their association with health and disease.
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Liu J, Liu YY, Liu J, Li BZ, Cen H, Xu WD, Leng RX, Pan HF, Ye DQ. Association between CARD8 rs2043211 polymorphism and inflammatory bowel disease: a meta-analysis. Immunol Invest 2015; 44:253-64. [PMID: 25564880 DOI: 10.3109/08820139.2014.988721] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVE The aim of this study was to determine whether caspase recruitment domain-containing protein 8 (CARD8) rs2043211 polymorphism was associated with susceptibility to inflammatory bowel disease (IBD). METHODS Relevant studies were searched using PubMed and Embase up to February 2014. A meta-analysis was conducted on the association between rs2043211 polymorphism and IBD using: (1) allele contrast, (2) the dominant model, (3) the recessive model, and (4) homozygote contrast. The pooled estimated of risk was obtained by random-effects model or fixed-effects model. Publication bias was assessed by Egger's test. RESULTS Eight relevant articles with a total of 10 534 IBD patients [6785 Crohn's disease (CD), 3713 ulcerative colitis (UC) and 36 indeterminate colitis (IC)] and 6755 healthy controls were included in the meta-analysis, which consisted of 12 studies, 12 for CD, 10 for UC, 2 for IC. There was no significant association between rs2043211 polymorphism and IBD, CD, and IC in overall population. However, stratified meta-analysis by ethnicity showed significant association between rs2043211 polymorphism and CD in the European population under the dominant model [odds ratio (OR) = 1.210, 95% confidence interval (CI) = 1.013-1.445, p = 0.036] and homozygote contrast (OR = 1.212, 95% CI = 1.005-1.461, p = 0.044). CONCLUSIONS Our meta-analysis results indicated significant association between rs2043211 polymorphism and the susceptibility to CD under the dominant model and homozygote contrast in the European population.
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Affiliation(s)
- Juan Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University , Hefei, Anhui , PR China and
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Ko DC, Jaslow SL. The marriage of quantitative genetics and cell biology: a novel screening approach reveals people have genetically encoded variation in microtubule stability. BIOARCHITECTURE 2014; 4:58-61. [PMID: 24618686 DOI: 10.4161/bioa.28481] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Microtubules play a central role in many essential cellular processes, including chromosome segregation, intracellular transport, and cell polarity. As these dynamic polymers are crucial components of eukaryotic cellular architecture, we were surprised by our recent discovery that a common human genetic difference leads to variation in microtubule stability in cells from different people. A single nucleotide polymorphism (SNP) near the TUBB6 gene, encoding class V β-tubulin, is associated with the expression level of this protein, which reduces microtubule stability at higher levels of expression. We discuss the novel cellular GWAS (genome-wide association study) platform that led to this discovery of natural, common variation in microtubule stability and the implications this finding may have for human health and disease, including cancer and neurological disorders. Furthermore, our generalizable approach provides a gateway for cell biologists to help interpret the functional consequences of human genetic variation.
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Affiliation(s)
- Dennis C Ko
- Department of Molecular Genetics and Microbiology; School of Medicine; Duke University; Durham, NC USA; Department of Medicine and the Center for Human Genome Variation; School of Medicine; Duke University; Durham, NC USA
| | - Sarah L Jaslow
- Department of Molecular Genetics and Microbiology; School of Medicine; Duke University; Durham, NC USA
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